@article {pmid36990698,
year = {2023},
author = {Lu, BH},
title = {[Basic competence for etiological diagnosis of lower respiratory tract infection after application of metagenomic next-generation sequencing].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {46},
number = {4},
pages = {315-318},
doi = {10.3760/cma.j.cn112147-20221121-00915},
pmid = {36990698},
issn = {1001-0939},
abstract = {In addition to clinical manifestations, medical history, and imaging, the diagnosis of low respiratory tract infection (LRTI) depends mainly on the ability of the clinical microbiology laboratory to detect the pathogens. However, conventional culture may be time-consuming, the sensitivity of microscopy is low, and nucleic acid-based targeted tests (e.g., PCR) could only cover limited range of pathogens. The use of mNGS technology has improved the diagnostic rate of LRTI, but the conventional microbiology detection has been neglected to some extent. This review addressed the appropriate use of these methods with the aim of strengthening the ability of traditional microbiology methods in LRTI diagnosis after mNGS application.},
}

@article {pmid36990697,
year = {2023},
author = {Shi, Y and Li, P},
title = {[Diagnostic value and consideration of low sequence pathogens detected by metagenomic next-generation sequencing in lower respiratory tract infection].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {46},
number = {4},
pages = {311-314},
doi = {10.3760/cma.j.cn112147-20221129-00939},
pmid = {36990697},
issn = {1001-0939},
abstract = {Pathogenic diagnosis of lower respiratory tract infection has always been a clinical problem. The widespread application of metagenomic next-generation sequencing(mNGS)provides a rapid and accurate method for pathogenic diagnosis. However, how to interpret the results of mNGS detection, especially whether it has diagnostic value in detecting pathogens with low sequence number, has always puzzled clinicians. This paper discusses the definition of low sequence number (lower reads)detected by mNGS in lower respiratory tract infection, the cause of occurrence, the method to determine the reliability of the results, and how to correctly interpret the low sequence number report in combination with clinical practice. It is hoped that by comprehensively mastering the detection knowledge, the proper clinical analysis thinking can be established to improve the diagnostic ability of pathogens with low sequence number detected by mNGS in lower respiratory tract infection.},
}

@article {pmid36990340,
year = {2023},
author = {Qin, G and Zhang, Q and Zhang, Z and Chen, Y and Zhu, J and Yang, Y and Peijnenburg, WJGM and Qian, H},
title = {Understanding the ecological effects of the fungicide difenoconazole on soil and Enchytraeus crypticus gut microbiome.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {121518},
doi = {10.1016/j.envpol.2023.121518},
pmid = {36990340},
issn = {1873-6424},
abstract = {Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress.},
}

@article {pmid36990333,
year = {2023},
author = {Su, X and Zhu, XR and Li, J and Wu, L and Li, X and Zhang, Q and Peng, Y},
title = {Determination of partial denitrification kinetic model parameters based on batch tests and metagenomic sequencing.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {128977},
doi = {10.1016/j.biortech.2023.128977},
pmid = {36990333},
issn = {1873-2976},
abstract = {In this study, a model was developed to investigate the partial denitrification(PD) process. The heterotrophic biomass (XH) proportion in the sludge was determined to be 66.4% based on metagenomic sequencing. The kinetic parameters were first calibrated, then validated using the batch tests results . The results showed rapid decreases in the chemical oxygen demand (COD) and nitrate concentrations and gradual increases in the nitrite concentrations in the first four hours, then remained constant from 4 to 8 h. Anoxic reduction factor (ηNO3 and ηNO2) and half saturation constant (KS1 and KS2) were calibrated at 0.097, 0.13, 89.28 mg COD/L, and 102.29 mg COD/L, respectively. Whereas the simulation results demonstrated that the increase in carbon-to-nitrogen (C/N) ratios and the reduction in XH contributed to the increase in the nitrite transformation rate. This model provides potential strategies for optimizing the PD/A process.},
}

@article {pmid36990280,
year = {2023},
author = {Pyden, A and Rugwizangoga, B and Solomon, IH and Laga, AC},
title = {`Teaching Infectious Disease Pathology and Taking it To Africa.},
journal = {Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc},
volume = {},
number = {},
pages = {100168},
doi = {10.1016/j.modpat.2023.100168},
pmid = {36990280},
issn = {1530-0285},
abstract = {With the advent of increasing emerging infectious diseases, rising antibiotic resistance, and the growing number of immunocompromised patients, there is increasing demand for infectious disease (ID) pathology expertise and microbiology testing. At present, infectious disease pathology training and emerging molecular microbiology techniques (e.g. metagenomic next-generation sequencing and whole genome sequencing) are not included in most American Council of Graduate Medical Education (ACGME) medical microbiology fellowship curricula, and, not surprisingly, many institutions lack anatomic pathologists with expertise in ID pathology and advanced molecular diagnostics. In this article, we describe the curriculum and structure of the Franz von Lichtenberg Fellowship in Infectious Disease and Molecular Microbiology at Brigham and Women's Hospital in Boston, MA. We emphasize the value of a training model that strives to integrate anatomic pathology, clinical pathology, and molecular pathology by providing examples in a case-based format and presenting selected metrics of the potential impact of such integrative infectious disease pathology service, and briefly describing opportunities and challenges of our global health efforts in Rwanda.},
}

@article {pmid36990236,
year = {2023},
author = {Xiang, R and Tian, Z and Zhang, C and Zheng, B and Jia, H},
title = {Characterization of dissolved organic matter content, composition, and source during spring algal bloom in tributaries of the Three Gorges Reservoir.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {163139},
doi = {10.1016/j.scitotenv.2023.163139},
pmid = {36990236},
issn = {1879-1026},
abstract = {Dissolved organic matter (DOM) is a key component of aquatic ecosystem function and biogeochemical processes. The characteristics of DOM in tributaries of the Three Gorges Reservoir (TGR) during the severe spring algal bloom period and their relationship with algal growth are unclear. In this study, the content, composition, and source of DOM in the Pengxi River (PXR) and Ruxi River (RXR) exhibiting typical TGR bloom problems were analyzed using various physicochemical indexes, carbon isotopes, fatty acids, and metagenomics. The results showed that chlorophyll a content increased with rising DOM concentration in the PXR and RXR. The dissolved organic carbon (DOC) and chromophoric dissolved organic matter (CDOM) contents in the two rivers were 4.656-16.560 mg/L and 14.373-50.848 μg/L, respectively, and increased during the bloom period. Four fluorescent components were identified, namely, two humic-like substances, and two protein-like substances. Proteobacteria, bacteroidetes, and actinobacteria were the greatest contributors to DOM content. The carbon fixation pathway of microorganisms increased the DOC concentration in both rivers during the bloom period. Physicochemical parameters (WT, pH, DO, and PAR) affected the DOM concentration by influencing microbial activity and DOM degradation. DOM in both rivers was derived from allochthonous and autogenous sources. Meanwhile, the DOC content was more strongly correlated with allochthonous sources. These findings might provide essential information for improving water environment management and algal bloom control in the TGR.},
}

@article {pmid36990166,
year = {2023},
author = {Yang, H and Wu, C and Chen, L and Chang, X and Luo, G and Wu, K and Tian, W},
title = {A. macrocephala polysaccharide induces alterations to gut microbiome and serum metabolome in constipated mice.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {106084},
doi = {10.1016/j.micpath.2023.106084},
pmid = {36990166},
issn = {1096-1208},
abstract = {Atractylodes macrocephala polysaccharide (AC1) is extracted from the root of the Chinese herb Atractylodes Macrocephala and is used in the treatment of constipation due to its effects on strengthening cellular immunity and regulating intestinal function. In this study, Metagenomics and Metabolomic are used to analyze the effects of AC1 on the gut microbiota and host metabolites in mice models of constipation. The results show that the abundance of Lachnospiraceae_bacterium_A4, Bact-oides_vulgatus and Prevotella_sp_CAG:891 increased significantly, indicating that AC1-targeted strain modulation effectively alleviated the dysbiosis of the gut microbiota. Besides, the microbial alterations also influenced the metabolic pathways of the mice, including tryptophan metabolism, unsaturated fatty acid synthesis and bile acid metabolism. The physiological parameters of the mice treated with AC1 are improved, such as tryptophan in the colon, 5-hydroxytryptamine (5-HT) and short-chain fatty acids (SCFAs). In conclusion, AC1 as a probiotic can regulate intestinal flora to normal levels and achieve the effect of treating constipation.},
}

@article {pmid36989806,
year = {2023},
author = {Yan, Y and Zhang, J and Tian, L and Yan, X and Du, L and Leininger, A and Zhang, M and Li, N and Ren, ZJ and Wang, X},
title = {DIET-like mutualism of Geobacter and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate.},
journal = {Water research},
volume = {235},
number = {},
pages = {119911},
doi = {10.1016/j.watres.2023.119911},
pmid = {36989806},
issn = {1879-2448},
abstract = {Direct interspecies electron transfer (DIET) has been demonstrated to be an efficient type of mutualism in methanogenesis. However, few studies have reported its presence in mixed microbial communities and its trigger mechanism in the natural environment and engineered systems. Here, we reported DIET-like mutualism of Geobacter and methanogens in the planktonic microbiome for the first time in anaerobic electrochemical digestion (AED) fed with propionate, potentially triggered by excessive cathodic hydrogen (56 times higher than the lowest) under the electrochemical condition. In contrast with model prediction without DIET, the highest current density and hydrogen and methane production were concurrently observed at -0.2 V where an abundance of Geobacter (49%) and extracellular electron transfer genes were identified in the planktonic microbiome via metagenomic analysis. Metagenomic assembly genomes annotated to Geobacter anodireducens were identified alongside two methanogens, Methanothrix harundinacea and Methanosarcina mazei, which were previously identified to participate in DIET. This discovery revealed that DIET-like mutualism could be triggered without external conductive materials, highlighting its potentially ubiquitous presence. Such mutualism simultaneously boosted methane and hydrogen production, thereby demonstrating the potential of AED in engineering applications.},
}

@article {pmid36989799,
year = {2023},
author = {Calderón-Franco, D and Corbera-Rubio, F and Cuesta-Sanz, M and Pieterse, B and de Ridder, D and van Loosdrecht, MCM and van Halem, D and Laureni, M and Weissbrodt, DG},
title = {Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems.},
journal = {Water research},
volume = {235},
number = {},
pages = {119905},
doi = {10.1016/j.watres.2023.119905},
pmid = {36989799},
issn = {1879-2448},
abstract = {Drinking water treatment plants (DWTPs) are designed to remove physical, chemical, and biological contaminants. However, until recently, the role of DWTPs in minimizing the cycling of antibiotic resistance determinants has got limited attention. In particular, the risk of selecting antibiotic-resistant bacteria (ARB) is largely overlooked in chlorine-free DWTPs where biological processes are applied. Here, we combined high-throughput quantitative PCR and metagenomics to analyze the abundance and dynamics of microbial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) across the treatment trains of two chlorine-free DWTPs involving dune-based and reservoir-based systems. The microbial diversity of the water increased after all biological unit operations, namely rapid and slow sand filtration (SSF), and granular activated carbon filtration. Both DWTPs reduced the concentration of ARGs and MGEs in the water by circa 2.5 log gene copies mL[-1], despite their relative increase in the disinfection sub-units (SSF in dune-based and UV treatment in reservoir-based DWTPs). The total microbial concentration was also reduced (2.5 log units), and none of the DWTPs enriched for bacteria containing genes linked to antibiotic resistance. Our findings highlight the effectiveness of chlorine-free DWTPs in supplying safe drinking water while reducing the concentration of antibiotic resistance determinants. To the best of our knowledge, this is the first study that monitors the presence and dynamics of antibiotic resistance determinants in chlorine-free DWTPs.},
}

@article {pmid36989208,
year = {2023},
author = {Rajamanikam, A and Isa, MNM and Samudi, C and Devaraj, S and Govind, SK},
title = {Gut bacteria influence Blastocystis sp. phenotypes and may trigger pathogenicity.},
journal = {PLoS neglected tropical diseases},
volume = {17},
number = {3},
pages = {e0011170},
doi = {10.1371/journal.pntd.0011170},
pmid = {36989208},
issn = {1935-2735},
abstract = {Whilst the influence of intestinal microbiota has been shown in many diseases such as irritable bowel syndrome, colorectal cancer, and aging, investigations are still scarce on its role in altering the nature of other infective organisms. Here we studied the association and interaction of Blastocystis sp. and human intestinal microbiota. In this study, we investigated the gut microbiome of Blastocystis sp.-free and Blastocystis sp. ST3-infected individuals who are symptomatic and asymptomatic. We tested if the expression of phenotype and pathogenic characteristics of Blastocystis sp. ST3 was influenced by the alteration of its accompanying microbiota. Blastocystis sp. ST3 infection alters bacterial composition. Its presence in asymptomatic individuals showed a significant effect on microbial richness compared to symptomatic ones. Inferred metagenomic findings suggest that colonization of Blastocystis sp. ST3 could contribute to the alteration of microbial functions. For the first time, we demonstrate the influence of bacteria on Blastocystis sp. pathogenicity. When Blastocystis sp. isolated from a symptomatic individual was co-cultured with bacterial suspension of Blastocystis sp. from an asymptomatic individual, the parasite demonstrated increased growth and reduced potential pathogenic expressions. This study also reveals that Blastocystis sp. infection could influence microbial functions without much effect on the microbiota diversity itself. Our results also demonstrate evidence on the influential role of gut microbiota in altering the characteristics of the parasite, which becomes the basis for the contradictory findings on the parasite's pathogenic role seen across different studies. Our study provides evidence that asymptomatic Blastocystis sp. in a human gut can be triggered to show pathogenic characteristics when influenced by the intestinal microbiota.},
}

@article {pmid36988865,
year = {2023},
author = {Xu, J and Zhou, P and Liu, J and Zhao, L and Fu, H and Han, Q and Wang, L and Wu, W and Ou, Q and Ma, Y and He, J},
title = {Utilizing Metagenomic Next-Generation Sequencing (mNGS) for Rapid Pathogen Identification and to Inform Clinical Decision-Making: Results from a Large Real-World Cohort.},
journal = {Infectious diseases and therapy},
volume = {},
number = {},
pages = {},
pmid = {36988865},
issn = {2193-8229},
abstract = {INTRODUCTION: Clinical metagenomic next-generation sequencing (mNGS) has proven to be a powerful diagnostic tool in pathogen detection. However, its clinical utility has not been thoroughly evaluated.

METHODS: In this single-center prospective study at the First Affiliated Hospital of Soochow University, a total of 228 samples from 215 patients suspected of having acute or chronic infections between June 2018 and December 2018 were studied. Samples that met the mNGS quality control (QC) criteria (N = 201) were simultaneously analyzed using conventional tests (CTs), including multiple clinical microbiological tests and real-time PCR (if applicable).

RESULTS: Pathogen detection results of mNGS in the 201 QC-passed samples were compared to CTs and exhibited a sensitivity of 98.8%, specificity of 38.5%, and accuracy of 87.1%. Specifically, 109 out of 160 (68.1%) CT+/mNGS+ samples exhibited concordant results at the species/genus level, 25 samples (15.6%) showed overlapping results, while the remaining 26 samples (16.3%) had discordant results between the CT and mNGS assays. In addition, mNGS could identify pathogens at the species level, whereas only the genera of some pathogens could be identified by CT. In this cohort, mNGS results were used to guide treatment plans in 24 out of 41 cases that had available follow-up information, and the symptoms were improved in over 70% (17/24) of them.

CONCLUSION: Our data demonstrated the analytic performance of our mNGS pipeline for pathogen detection using a large clinical cohort and strongly supports the notion that in clinical practice, mNGS represents a valuable supplementary tool to CTs to rapidly determine etiological factors of various types of infection and to guide treatment decision-making.},
}

@article {pmid36987093,
year = {2023},
author = {Ventimiglia, M and Castellacci, M and Usai, G and Vangelisti, A and Simoni, S and Natali, L and Cavallini, A and Mascagni, F and Giordani, T},
title = {Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study.},
journal = {Plants (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/plants12061405},
pmid = {36987093},
issn = {2223-7747},
abstract = {Genome divergence by repeat proliferation and/or loss is a process that plays a crucial role in species evolution. Nevertheless, knowledge of the variability related to repeat proliferation among species of the same family is still limited. Considering the importance of the Asteraceae family, here we present a first contribution towards the metarepeatome of five Asteraceae species. A comprehensive picture of the repetitive components of all genomes was obtained by genome skimming with Illumina sequence reads and by analyzing a pool of full-length long terminal repeat retrotransposons (LTR-REs). Genome skimming allowed us to estimate the abundance and variability of repetitive components. The structure of the metagenome of the selected species was composed of 67% repetitive sequences, of which LTR-REs represented the bulk of annotated clusters. The species essentially shared ribosomal DNA sequences, whereas the other classes of repetitive DNA were highly variable among species. The pool of full-length LTR-REs was retrieved from all the species and their age of insertion was established, showing several lineage-specific proliferation peaks over the last 15-million years. Overall, a large variability of repeat abundance at superfamily, lineage, and sublineage levels was observed, indicating that repeats within individual genomes followed different evolutionary and temporal dynamics, and that different events of amplification or loss of these sequences may have occurred after species differentiation.},
}

@article {pmid36985385,
year = {2023},
author = {García-Maldonado, JQ and Latisnere-Barragán, H and Escobar-Zepeda, A and Cadena, S and Ramírez-Arenas, PJ and Vázquez-Juárez, R and Rojas-Contreras, M and López-Cortés, A},
title = {Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030812},
pmid = {36985385},
issn = {2076-2607},
abstract = {Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments.},
}

@article {pmid36985376,
year = {2023},
author = {Baev, V and Apostolova, E and Gotcheva, V and Koprinarova, M and Papageorgiou, M and Rocha, JM and Yahubyan, G and Angelov, A},
title = {16S-rRNA-Based Metagenomic Profiling of the Bacterial Communities in Traditional Bulgarian Sourdoughs.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030803},
pmid = {36985376},
issn = {2076-2607},
abstract = {Sourdoughs (SDs) are spontaneously formed microbial ecosystems composed of various species of lactic acid bacteria (LAB) and acid-tolerant yeasts in food matrices of cereal flours mixed with water. To date, more than 90 LAB species have been isolated, significantly impacting the organoleptic characteristics, shelf life, and health properties of bakery products. To learn more about the unique bacterial communities involved in creating regional Bulgarian sourdoughs, we examined the metacommunities of five sourdoughs produced by spontaneous fermentation and maintained by backslopping in bakeries from three geographic locations. The 16S rRNA gene amplicon sequencing showed that the former genus Lactobacillus was predominant in the studied sourdoughs (51.0-78.9%). Weissella (0.9-42.8%), Herbaspirillum (1.6-3.8%), Serratia (0.1-11.7%), Pediococcus (0.2-7.5%), Bacteroides (0.1-1.3%), and Sphingomonas (0.1-0.5%) were also found in all 5 samples. Genera Leuconostoc, Enterococcus, Bacillus, and Asaia were sample-specific. It is interesting to note that the genus Weissella was more abundant in wholegrain samples. The greatest diversity at the species level was found in the former genus Lactobacillus, presented in the sourdough samples with 13 species. The UPGMA cluster analysis clearly demonstrated similarity in species' relative abundance between samples from the same location. In addition, we can conclude that the presence of two main clusters-one including samples from mountainous places (the cities of Smolyan and Bansko) and the other including samples from the city of Ruse (the banks of the Danube River)-may indicate the impact of climate and geographic location (e.g., terrain, elevation, land use, and nearby water bodies and their streams) on the abundance of microbiome taxa. As the bacterial population is crucial for bread standardization, we expect the local bakery sector to be interested in the relationship between process variables and their effect on bacterial dynamics described in this research study.},
}

@article {pmid36985338,
year = {2023},
author = {Xiao, Y and Zhang, P and Zhang, H and Wang, H and Min, G and Wang, H and Wang, Y and Xu, J},
title = {Effects of Resource Availability and Antibiotic Residues on Intestinal Antibiotic Resistance in Bellamya aeruginosa.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030765},
pmid = {36985338},
issn = {2076-2607},
abstract = {Widespread and inappropriate use of antibiotics has been shown to increase the spread of antibiotics and antimicrobial resistance genes (ARGs) in aquatic environments and organisms. Antibiotic use for the treatment of human and animal diseases is increasing continuously globally. However, the effects of legal antibiotic concentrations on benthic consumers in freshwater environments remain unclear. In the present study, we tested the growth response of Bellamya aeruginosa to florfenicol (FF) for 84 days under high and low concentrations of sediment organic matter (carbon [C] and nitrogen [N]). We characterized FF and sediment organic matter impact on the bacterial community, ARGs, and metabolic pathways in the intestine using metagenomic sequencing and analysis. The high concentrations of organic matter in the sediment impacted the growth, intestinal bacterial community, intestinal ARGs, and microbiome metabolic pathways of B. aeruginosa. B. aeruginosa growth increased significantly following exposure to high organic matter content sediment. Proteobacteria, at the phylum level, and Aeromonas at the genus level, were enriched in the intestines. In particular, fragments of four opportunistic pathogens enriched in the intestine of high organic matter content sediment groups, Aeromonas hydrophila, Aeromonas caviae, Aeromonas veronii, and Aeromonas salmonicida, carried 14 ARGs. The metabolic pathways of the B. aeruginosa intestine microbiome were activated and showed a significant positive correlation with sediment organic matter concentrations. In addition, genetic information processing and metabolic functions may be inhibited by the combined exposure to sediment C, N, and FF. The findings of the present study suggest that antibiotic resistance dissemination from benthic animals to the upper trophic levels in freshwater lakes should be studied further.},
}

@article {pmid36985314,
year = {2023},
author = {Lozano, FM and Lledó, B and Morales, R and Cascales, A and Hortal, M and Bernabeu, A and Bernabeu, R},
title = {Characterization of the Endometrial Microbiome in Patients with Recurrent Implantation Failure.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030741},
pmid = {36985314},
issn = {2076-2607},
abstract = {An abnormal endometrial microbiota has been associated with implantation failure; therefore, it may be important to evaluate it in order to improve reproductive outcomes in infertile patients. The main objective of our study was to compare the endometrial microbiome of patients with recurrent implantation failure (RIF) and control patients undergoing assisted reproduction treatment (ART). A prospective cohort study including forty-five patients with their own or donated gametes. The endometrial microbiome was analysed by massive sequencing of the bacterial 16S rRNA gene. Different bacterial communities were detected in RIF and control patients. Lactobacillus stands out as the most frequent genus, with 92.27% in RIF patients and 97.96% in control patients, and significant differences were reported between the two groups (p = 0.002). No significant differences were found regarding alpha diversity index. In beta diversity analysis, a significant trend was observed in the separation of the bacterial community between established groups (p < 0.07). Relative abundance analysis identified genera Prevotella (p < 0.001), Streptococcus (p < 0.001), Bifidobacterium (p = 0.002), Lactobacillus (p = 0.002) and Dialister (p = 0.003). Our results demonstrated the existence of an endometrial microbiota characteristic of RIF patients and showed that there might be a relationship between population of the endometrial microbiome and embryo implantation failure, providing us the possibility to improve clinical results in this patients.},
}

@article {pmid36985295,
year = {2023},
author = {Goma-Tchimbakala, EJCD and Pietrini, I and Goma-Tchimbakala, J and Corgnati, SP},
title = {Use of Shotgun Metagenomics to Assess the Microbial Diversity and Hydrocarbons Degrading Functions of Auto-Mechanic Workshops Soils Polluted with Gasoline and Diesel Fuel.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030722},
pmid = {36985295},
issn = {2076-2607},
abstract = {Bioaugmentation is a valuable technique for oil recovery. This study investigates the composition and functions of microbial communities in gasoline- and diesel-contaminated soils of garages Matoko (SGM) and Guy et Paul (SGP) originating from auto mechanic workshops as well as the concentration of soil enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase. The work aimed to evaluate the presence of petroleum-hydrocarbon-degrading bacteria for the development of foreseen bioremediation of oil-contaminated soils. Microbial diversity, as given by shotgun metagenomics, indicated the presence of 16 classes, among which Actinobacteria and Gammaproteobacteria dominated, as well as more than 50 families, including the dominant Gordoniaceae (26.63%) in SGM and Pseudomonadaceae (57.89%) in SGP. The dominant bacterial genera in the two soils were, respectively, Gordonia (26.7%) and Pseudomonas (57.9%). The exploration of the bacterial metabolic abilities using HUMANn2 allowed to detect genes and pathways involved in alkanes and aromatic hydrocarbons in the two contaminated soils. Furthermore, enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase were found in high concentrations ranging between 90.27 ± 5.3 and 804.17 ± 20.5 µg pN/g soil/h, which indicated active microbial metabolism. The high diversity of microorganisms with a hydrocarbon degradation genetic package revealed that the bacteria inhabiting the two soils are likely good candidates for the bioaugmentation of oil-contaminated soils.},
}

@article {pmid36985280,
year = {2023},
author = {Jamwal, VL and Rather, IA and Ahmed, S and Kumar, A and Gandhi, SG},
title = {Changing Rhizosphere Microbial Community and Metabolites with Developmental Stages of Coleus barbatus.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030705},
pmid = {36985280},
issn = {2076-2607},
abstract = {Coleus barbatus is a medicinal herb belonging to Lamiaceae. It is the only living organism known to produce forskolin, which is a labdane diterpene and is reported to activate adenylate cyclase. Microbes associated with plants play an important role in maintaining plant health. Recently, the targeted application of beneficial plant-associated microbes and their combinations in abiotic and biotic stress tolerance has gained momentum. In this work, we carried out the rhizosphere metagenome sequencing of C. barbatus at different developmental stages to understand how rhizosphere microflora are affected by and affect the metabolite content in plants. We found that the Kaistobacter genus was abundantly present in the rhizosphere of C. barbatus and its accumulation pattern appears to correlate with the quantities of forskolin in the roots at different developmental stages. Members of the Phoma genus, known for several pathogenic species, were in lower numbers in the C. barbatus rhizosphere in comparison with C. blumei. To our knowledge, this is the first metagenomic study of the rhizospheric microbiome of C. barbatus, which may help to explore and exploit the culturable and non-culturable microbial diversity present in the rhizosphere.},
}

@article {pmid36985245,
year = {2023},
author = {Cruz-Silva, A and Laureano, G and Pereira, M and Dias, R and Silva, JMD and Oliveira, N and Gouveia, C and Cruz, C and Gama-Carvalho, M and Alagna, F and Duarte, B and Figueiredo, A},
title = {A New Perspective for Vineyard Terroir Identity: Looking for Microbial Indicator Species by Long Read Nanopore Sequencing.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030672},
pmid = {36985245},
issn = {2076-2607},
abstract = {Grapevine is one of the most important fruit crops worldwide, being Portugal one of the top wine producers. It is well established that wine sensory characteristics from a particular region are defined by the physiological responses of the grapevine to its environment and thus, the concept of terroir in viticulture was established. Among all the factors that contribute to terroir definition, soil microorganisms play a major role from nutrient recycling to a drastic influence on plant fitness (growth and protection) and of course wine production. Soil microbiome from four different terroirs in Quinta dos Murças vineyard was analysed through long-read Oxford Nanopore sequencing. We have developed an analytical pipeline that allows the identification of function, ecologies, and indicator species based on long read sequencing data. The Douro vineyard was used as a case study, and we were able to establish microbiome signatures of each terroir.},
}

@article {pmid36985231,
year = {2023},
author = {Bandarupalli, VVK and St-Pierre, B},
title = {Metagenomics-Based Analysis of Candidate Lactate Utilizers from the Rumen of Beef Cattle.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030658},
pmid = {36985231},
issn = {2076-2607},
abstract = {In ruminant livestock production, ruminal acidosis is an unintended consequence of the elevated dietary intake of starch-rich feedstuffs. The transition from a state of subacute acidosis (SARA) to acute acidosis is due in large part to the accumulation of lactate in the rumen, which is a consequence of the inability of lactate utilizers to compensate for the increased production of lactate. In this report, we present the 16S rRNA gene-based identification of two bacterial operational taxonomic units (OTUs), Bt-01708_Bf (89.0% identical to Butyrivibrio fibrisolvens) and Bt-01899_Ap (95.3% identical to Anaerococcus prevotii), that were enriched from rumen fluid cultures in which only lactate was provided as an exogenous substrate. Analyses of in-silico-predicted proteomes from metagenomics-assembled contigs assigned to these candidate ruminal bacterial species (Bt-01708_Bf: 1270 annotated coding sequences, 1365 hypothetical coding sequences; Bt-01899_Ap: 871 annotated coding sequences, 1343 hypothetical coding sequences) revealed genes encoding lactate dehydrogenase, a putative lactate transporter, as well as pathways for the production of short chain fatty acids (formate, acetate and butyrate) and for the synthesis of glycogen. In contrast to these shared functions, each OTU also exhibited distinct features, such as the potential for the utilization of a diversified set of small molecules as substrates (Bt-01708_Bf: malate, quinate, taurine and polyamines) or for the utilization of starch (Bt-01899_Ap: alpha-amylase enzymes). Together, these results will contribute to the continued characterization of ruminal bacterial species that can metabolize lactate into distinct subgroups based on other metabolic capabilities.},
}

@article {pmid36985222,
year = {2023},
author = {Yongsawas, R and In-On, A and Inta, A and Kampuansai, J and Pandith, H and Suwannarach, N and Lumyong, S and Chitov, T and Disayathanoowat, T},
title = {Bacterial Communities in Lanna Fermented Soybeans from Three Different Ethnolinguistic Groups in Northern Thailand.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030649},
pmid = {36985222},
issn = {2076-2607},
abstract = {Northern Thailand, the main part of the Lanna region, is home to a diverse range of ethnic groups, each with their own food and cultural heritage. The bacterial compositions in fermented soybean (FSB) products indigenous to three Lanna ethnolinguistic groups, including Karen, Lawa, and Shan, were investigated in this study. Bacterial DNA was extracted from the FSB samples and subjected to 16S rRNA gene sequencing using the Illumina sequencing platform. Metagenomic data showed that the predominant bacteria in all FSBs were members of the genus Bacillus (49.5-86.8%), and the Lawa FSB had the greatest bacterial diversity. The presence of genera Ignatzschineria, Yaniella, Atopostipes in the Karen and Lawa FSBs and Proteus in the Shan FSB might be indicators of food hygiene problems during processing. The network analysis predicted antagonistic effects of Bacillus against some indicator and pathogenic bacteria. The functional prediction revealed some potential functional properties of these FSBs. The presence of Bacillus in all FSBs and Vagococcus in the Shan FSB suggests that these FSBs could potentially be good sources of beneficial bacteria, and they should be conserved and promoted for health and food security reasons. However, food processing hygiene measures should be introduced and monitored to warrant their properties as health foods.},
}

@article {pmid36985129,
year = {2023},
author = {Slobodkin, AI and Ratnikova, NM and Slobodkina, GB and Klyukina, AA and Chernyh, NA and Merkel, AY},
title = {Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030555},
pmid = {36985129},
issn = {2076-2607},
abstract = {The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood-Ljungdahl pathway for autotrophic CO2 fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide.},
}

@article {pmid36985120,
year = {2023},
author = {Guo, Y and Yuan, W and Lyu, N and Pan, Y and Cao, X and Wang, Y and Han, Y and Zhu, B},
title = {Association Studies on Gut and Lung Microbiomes in Patients with Lung Adenocarcinoma.},
journal = {Microorganisms},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/microorganisms11030546},
pmid = {36985120},
issn = {2076-2607},
abstract = {Lung adenocarcinoma (LADC) is a prevalent type of lung cancer that is associated with lung and gut microbiota. However, the interactions between these microbiota and cancer development remain unclear. In this study, a microbiome study was performed on paired fecal and bronchoalveolar lavage fluid (BALF) samples from 42 patients with LADC and 64 healthy controls using 16S rRNA gene amplicon and shotgun metagenome sequencing, aiming to correlate the lung and gut microbiota with LADC. Patients with LADC had reduced α-diversity in the gut microbiome and altered β-diversity compared with healthy controls, and the abundances of Flavonifractor, Eggerthella, and Clostridium were higher in the gut microbiome of LADC patients. The increased abundance of microbial species, such as Flavonifractor plautii, was associated with advanced-stage LADC and a higher metastasis rate. Phylogenetically, Haemophilus parainfluenzae was the most frequently shared taxon in the lung and gut microbiota of LADC patients. Gut microbiome functional pathways involving leucine, propanoate, and fatty acids were associated with LADC progression. In conclusion, the low diversity of the gut microbiota and the presence of H. parainfluenzae in gut and lung microbiota were linked to LADC development, while an increased abundance of F. plautii and the enriched metabolic pathways could be associated with the progression of LADC.},
}

@article {pmid36984841,
year = {2023},
author = {Cohen, CC and Huneault, H and Accardi, CJ and Jones, DP and Liu, K and Maner-Smith, KM and Song, M and Welsh, JA and Ugalde-Nicalo, PA and Schwimmer, JB and Vos, MB},
title = {Metabolome × Microbiome Changes Associated with a Diet-Induced Reduction in Hepatic Fat among Adolescent Boys.},
journal = {Metabolites},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/metabo13030401},
pmid = {36984841},
issn = {2218-1989},
support = {UL1TR001442/TR/NCATS NIH HHS/United States ; UL1TR001442/TR/NCATS NIH HHS/United States ; P30ES019776/ES/NIEHS NIH HHS/United States ; P20GM103436/GM/NIGMS NIH HHS/United States ; P20GM113226/GM/NIGMS NIH HHS/United States ; P20GM106396/GM/NIGMS NIH HHS/United States ; T32DK07658/DK/NIDDK NIH HHS/United States ; F32DK131757/DK/NIDDK NIH HHS/United States ; R01DK125701/DK/NIDDK NIH HHS/United States ; R01NR019083/NR/NINR NIH HHS/United States ; },
abstract = {Dietary sugar reduction is one therapeutic strategy for improving nonalcoholic fatty liver disease (NAFLD), and the underlying mechanisms for this effect warrant further investigation. Here, we employed metabolomics and metagenomics to examine systemic biological adaptations associated with dietary sugar restriction and (subsequent) hepatic fat reductions in youth with NAFLD. Data/samples were from a randomized controlled trial in adolescent boys (11-16 years, mean ± SD: 13.0 ± 1.9 years) with biopsy-proven NAFLD who were either provided a low free-sugar diet (LFSD) (n = 20) or consumed their usual diet (n = 20) for 8 weeks. Plasma metabolomics was performed on samples from all 40 participants by coupling hydrophilic interaction liquid chromatography (HILIC) and C18 chromatography with mass spectrometry. In a sub-sample (n = 8 LFSD group and n = 10 usual diet group), 16S ribosomal RNA (rRNA) sequencing was performed on stool to examine changes in microbial composition/diversity. The diet treatment was associated with differential expression of 419 HILIC and 205 C18 metabolite features (p < 0.05), which were enriched in amino acid pathways, including methionine/cysteine and serine/glycine/alanine metabolism (p < 0.05), and lipid pathways, including omega-3 and linoleate metabolism (p < 0.05). Quantified metabolites that were differentially changed in the LFSD group, compared to usual diet group, and representative of these enriched metabolic pathways included increased serine (p = 0.001), glycine (p = 0.004), 2-aminobutyric acid (p = 0.012), and 3-hydroxybutyric acid (p = 0.005), and decreased linolenic acid (p = 0.006). Microbiome changes included an increase in richness at the phylum level and changes in a few genera within Firmicutes. In conclusion, the LFSD treatment, compared to usual diet, was associated with metabolome and microbiome changes that may reflect biological mechanisms linking dietary sugar restriction to a therapeutic decrease in hepatic fat. Studies are needed to validate our findings and test the utility of these "omics" changes as response biomarkers.},
}

@article {pmid36984783,
year = {2023},
author = {Fu, X and Zhang, M and Yuan, Y and Chen, Y and Ou, Z and Hashim, Z and Hashim, JH and Zhang, X and Zhao, Z and Norbäck, D and Sun, Y},
title = {Microbial Virulence Factors, Antimicrobial Resistance Genes, Metabolites, and Synthetic Chemicals in Cabins of Commercial Aircraft.},
journal = {Metabolites},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/metabo13030343},
pmid = {36984783},
issn = {2218-1989},
abstract = {Passengers are at a higher risk of respiratory infections and chronic diseases due to microbial exposure in airline cabins. However, the presence of virulence factors (VFs), antimicrobial resistance genes (ARGs), metabolites, and chemicals are yet to be studied. To address this gap, we collected dust samples from the cabins of two airlines, one with textile seats (TSC) and one with leather seats (LSC), and analyzed the exposure using shotgun metagenomics and LC/MS. Results showed that the abundances of 17 VFs and 11 risk chemicals were significantly higher in TSC than LSC (p < 0.01). The predominant VFs in TSC were related to adherence, biofilm formation, and immune modulation, mainly derived from facultative pathogens such as Haemophilus parainfluenzae and Streptococcus pneumoniae. The predominant risk chemicals in TSC included pesticides/herbicides (carbofuran, bromacil, and propazine) and detergents (triethanolamine, diethanolamine, and diethyl phthalate). The abundances of these VFs and detergents followed the trend of TSC > LSC > school classrooms (p < 0.01), potentially explaining the higher incidence of infectious and chronic inflammatory diseases in aircraft. The level of ARGs in aircraft was similar to that in school environments. This is the first multi-omic survey in commercial aircraft, highlighting that surface material choice is a potential intervention strategy for improving passenger health.},
}

@article {pmid36983633,
year = {2023},
author = {Kartti, S and Bendani, H and Boumajdi, N and Bouricha, EM and Zarrik, O and El Agouri, H and Fokar, M and Aghlallou, Y and El Jaoudi, R and Belyamani, L and Elkhannoussi, B and Ibrahimi, A},
title = {Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues.},
journal = {Journal of personalized medicine},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/jpm13030450},
pmid = {36983633},
issn = {2075-4426},
abstract = {Breast cancer is one of the main global priorities in terms of public health. It remains the most frequent cancer in women and is the leading cause of their death. The human microbiome plays various roles in maintaining health by ensuring a dynamic balance with the host or in the appearance of various pathologies including breast cancer. In this study, we performed an analysis of bacterial signature differences between tumor and adjacent tissues of breast cancer patients in Morocco. Using 16S rRNA gene sequencing, we observed that adjacent tissue contained a much higher percentage of the Gammaproteobacteria class (35.7%) while tumor tissue was characterized by a higher percentage of Bacilli and Actinobacteria classes, with about 18.8% and 17.2% average abundance, respectively. Analysis of tumor subtype revealed enrichment of genus Sphingomonodas in TNBC while Sphingomonodas was predominant in HER2. The LEfSe and the genus level heatmap analysis revealed a higher abundance of the Rothia genus in tumor tissues. The identified microbial communities can therefore serve as potential biomarkers for prognosis and diagnosis, while also helping to develop new strategies for the treatment of breast cancer patients.},
}

@article {pmid36982690,
year = {2023},
author = {Belalov, IS and Sokolov, AA and Letarov, AV},
title = {Diversity-Generating Retroelements in Prokaryotic Immunity.},
journal = {International journal of molecular sciences},
volume = {24},
number = {6},
pages = {},
doi = {10.3390/ijms24065614},
pmid = {36982690},
issn = {1422-0067},
abstract = {Adaptive immunity systems found in different organisms fall into two major types. Prokaryotes possess CRISPR-Cas systems that recognize former invaders using memorized (captured) pieces of their DNA as pathogen signatures. Mammals possess a vast repertoire of antibodies and T-cell receptor variants generated in advance. In this second type of adaptive immunity, a pathogen presentation to the immune system specifically activates the cells that express matching antibodies or receptors. These cells proliferate to fight the infection and form the immune memory. The principle of preemptive production of diverse defense proteins for future use can hypothetically take place in microbes too. We propose a hypothesis that prokaryotes employ diversity-generating retroelements to prepare defense proteins against yet-unknown invaders. In this study, we test this hypothesis with the methods of bioinformatics and identify several candidate defense systems based on diversity-generating retroelements.},
}

@article {pmid36982303,
year = {2023},
author = {Giuffrè, M and Moretti, R and Tiribelli, C},
title = {Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease.},
journal = {International journal of molecular sciences},
volume = {24},
number = {6},
pages = {},
doi = {10.3390/ijms24065229},
pmid = {36982303},
issn = {1422-0067},
abstract = {The human gut microbiome plays a crucial role in human health and has been a focus of increasing research in recent years. Omics-based methods, such as metagenomics, metatranscriptomics, and metabolomics, are commonly used to study the gut microbiome because they provide high-throughput and high-resolution data. The vast amount of data generated by these methods has led to the development of computational methods for data processing and analysis, with machine learning becoming a powerful and widely used tool in this field. Despite the promising results of machine learning-based approaches for analyzing the association between microbiota and disease, there are several unmet challenges. Small sample sizes, disproportionate label distribution, inconsistent experimental protocols, or a lack of access to relevant metadata can all contribute to a lack of reproducibility and translational application into everyday clinical practice. These pitfalls can lead to false models, resulting in misinterpretation biases for microbe-disease correlations. Recent efforts to address these challenges include the construction of human gut microbiota data repositories, improved data transparency guidelines, and more accessible machine learning frameworks; implementation of these efforts has facilitated a shift in the field from observational association studies to experimental causal inference and clinical intervention.},
}

@article {pmid36981070,
year = {2023},
author = {Zhang, T and Yue, Y and Jeong, SJ and Ryu, MS and Wu, X and Yang, HJ and Li, C and Jeong, DY and Park, S},
title = {Improvement of Estrogen Deficiency Symptoms by the Intake of Long-Term Fermented Soybeans (Doenjang) Rich in Bacillus Species through Modulating Gut Microbiota in Estrogen-Deficient Rats.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/foods12061143},
pmid = {36981070},
issn = {2304-8158},
abstract = {Traditionally made doenjang (TMD) produced by the long-term fermentation of soybeans with salt may improve symptoms of estrogen deficiency. We aimed to evaluate the effects of four TMD types, containing low and high amounts of Bacillus species and biogenic amines (HBHA, HBLA, LBHA, and LBLA), on energy, glucose, and lipid metabolism, by altering the gut microbiota in estrogen-deficient ovariectomized (OVX) rats. Their mechanisms were also examined. The OVX rats were divided into the control, cooked soybean (CSB), HBHA, LBHA, HBLA, and LBLA groups. Sham-operated rats were the normal control group. Serum 17β-estradiol concentrations were similar among all OVX groups. Tail skin temperatures, which are indicative of hot flashes, were higher in the control than the HBHA and HBLA groups and were similar to the normal control group. Weight gain and visceral fat mass were lower in the TMD and CSB intake groups but not as low as in the normal control group. Lean body mass showed a trend opposite to that of visceral fat in the respective groups. The hepatic triglyceride content decreased with the TMD intake compared to the control and CSB groups. mRNA expressions of the peroxisome proliferator-activated receptor-γ (PPAR-γ) and carnitine palmitoyltransferase-1 in the TMD and CSB groups were as high as in the normal control group, and the PPAR-γ mRNA expression was more elevated in the HBLA group than in the normal control group. The morphology of the intestines improved in the TMD groups compared to the control, and the HBHA and HBLA groups showed an enhanced improvement compared to the CSB group. The HBHA, HBLA, and LBHA groups increased the α-diversity of the cecal microbiota compared to the control. Akkermenia and Lactobacillus were higher in the HBLA and LBLA groups compared to the control. The expression of the estrogen, forkhead box proteins of the class-O subgroup, and insulin-signaling pathways were lower in the control group, and HBHA and HBLA prevented their decrement. In conclusion, long-term treatment with TMD containing high amounts of Bacillus potentially improves estrogen deficiency symptoms more than unfermented soybeans.},
}

@article {pmid36980929,
year = {2023},
author = {Baeza, JA and Barata, R and Rajapakse, D and Penaloza, J and Harrison, P and Haberski, A},
title = {Mitochondrial Genomes Assembled from Non-Invasive eDNA Metagenomic Scat Samples in Critically Endangered Mammals.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/genes14030657},
pmid = {36980929},
issn = {2073-4425},
abstract = {The abundance of many large-bodied vertebrates, both in marine and terrestrial environments, has declined substantially due to global and regional climate stressors that define the Anthropocene. The development of genetic tools that can serve to monitor population's health non-intrusively and inform strategies for the recovery of these species is crucial. In this study, we formally evaluate whether whole mitochondrial genomes can be assembled from environmental DNA (eDNA) metagenomics scat samples. Mitogenomes of four different large vertebrates, the panda bear (Ailuropoda melanoleuca), the moon bear (Ursus thibetanus), the Java pangolin (Manis javanica), and the the North Atlantic right whale (Eubalaena glacialis) were assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 12x to 480x in 14 out of 18 different eDNA samples. Partial mitochondrial genomes were retrieved from three other eDNA samples. The complete mitochondrial genomes of the studied species were AT-rich and comprised 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative D-loop/control region. Synteny observed in all assembled mitogenomes was identical to that reported for specimens of the same and other closely related species. This study demonstrates that it is possible to assemble accurate whole mitochondrial chromosomes from eDNA samples (scats) using forthright bench and bioinformatics workflows. The retrieval of mitochondrial genomes from eDNA samples represents a tool to support bioprospecting, bio-monitoring, and other non-intrusive conservation strategies in species considered 'vulnerable', 'endangered', and/or 'critically endangered' by the IUCN Red List of Threatened Species.},
}

@article {pmid36980906,
year = {2023},
author = {Das, R and Rai, A and Mishra, DC},
title = {CNN_FunBar: Advanced Learning Technique for Fungi ITS Region Classification.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/genes14030634},
pmid = {36980906},
issn = {2073-4425},
abstract = {Fungal species identification from metagenomic data is a highly challenging task. Internal Transcribed Spacer (ITS) region is a potential DNA marker for fungi taxonomy prediction. Computational approaches, especially deep learning algorithms, are highly efficient for better pattern recognition and classification of large datasets compared to in silico techniques such as BLAST and machine learning methods. Here in this study, we present CNN_FunBar, a convolutional neural network-based approach for the classification of fungi ITS sequences from UNITE+INSDC reference datasets. Effects of convolution kernel size, filter numbers, k-mer size, degree of diversity and category-wise frequency of ITS sequences on classification performances of CNN models have been assessed at all taxonomic levels (species, genus, family, order, class and phylum). It is observed that CNN models can produce >93% average accuracy for classifying ITS sequences from balanced datasets with 500 sequences per category and 6-mer frequency features at all levels. The comparative study has revealed that CNN_FunBar can outperform machine learning-based algorithms (SVM, KNN, Naïve-Bayes and Random Forest) as well as existing fungal taxonomy prediction software (funbarRF, Mothur, RDP Classifier and SINTAX). The present study will be helpful for fungal taxonomy classification using large metagenomic datasets.},
}

@article {pmid36979819,
year = {2023},
author = {Leitao Filho, FS and Monica Peters, C and Sheel, AW and Yang, J and Nislow, C and Lam, S and Leung, JM and Sin, DD},
title = {Characterization of the Lower Airways and Oral Microbiota in Healthy Young Persons in the Community.},
journal = {Biomedicines},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/biomedicines11030841},
pmid = {36979819},
issn = {2227-9059},
abstract = {Lower airway dysbiosis contributes to disease pathogenesis in respiratory diseases. However, little is known regarding the microbiota of lower airways or the oral cavity of healthy young persons. To address this gap, 25 healthy persons (24.3 ± 3.3 years; 52% females; no current smokers) underwent bronchoscopy during which bronchial brushing (BB) and bronchoalveolar lavage (BAL) fluid were collected. Prior to the procedure, an oral wash (OW) sample was also obtained. Microbiome analyses (16S rRNA locus) were performed (alpha- and beta-diversity, taxa annotations, and predicted functional metagenomic profiles) according to the airway compartment (BB, BAL, and OW). The greatest microbial richness was observed in OW and the lowest in BB (p < 0.001). Microbial communities differed significantly across compartments (p < 0.001), especially between BB and OW. Taxa analyses showed a significantly higher abundance of Firmicutes (BB: 32.7%; BAL: 31.4%) compared to OW (20.9%) (p < 0.001). Conversely, Proteobacteria predominated in OW (27.9%) as opposed to BB (7.0%) and BAL (12.5%) (p < 0.001), mostly due to a greater abundance of the bacteria in the Haemophilus genus in the OW (p < 0.001). The lower airway microbiota (BB and BAL) is significantly different from the OW microbiota in healthy young persons with respect to microbial diversity, taxa profiles, and predicted function.},
}

@article {pmid36979806,
year = {2023},
author = {Athanasopoulou, K and Adamopoulos, PG and Scorilas, A},
title = {Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics.},
journal = {Biomedicines},
volume = {11},
number = {3},
pages = {},
doi = {10.3390/biomedicines11030827},
pmid = {36979806},
issn = {2227-9059},
abstract = {Over 10[14] symbiotic microorganisms are present in a healthy human body and are responsible for the synthesis of vital vitamins and amino acids, mediating cellular pathways and supporting immunity. However, the deregulation of microbial dynamics can provoke diverse human diseases such as diabetes, human cancers, cardiovascular diseases, and neurological disorders. The human gastrointestinal tract constitutes a hospitable environment in which a plethora of microbes, including diverse species of archaea, bacteria, fungi, and microeukaryotes as well as viruses, inhabit. In particular, the gut microbiome is the largest microbiome community in the human body and has drawn for decades the attention of scientists for its significance in medical microbiology. Revolutions in sequencing techniques, including 16S rRNA and ITS amplicon sequencing and whole genome sequencing, facilitate the detection of microbiomes and have opened new vistas in the study of human microbiota. Especially, the flourishing fields of metagenomics and metatranscriptomics aim to detect all genomes and transcriptomes that are retrieved from environmental and human samples. The present review highlights the complexity of the gastrointestinal tract microbiome and deciphers its implication not only in cellular homeostasis but also in human diseases. Finally, a thorough description of the widely used microbiome detection methods is discussed.},
}

@article {pmid36979367,
year = {2023},
author = {Saxena, A and Mathur, N and Pathak, P and Tiwari, P and Mathur, SK},
title = {Machine Learning Model Based on Insulin Resistance Metagenes Underpins Genetic Basis of Type 2 Diabetes.},
journal = {Biomolecules},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/biom13030432},
pmid = {36979367},
issn = {2218-273X},
abstract = {Insulin resistance (IR) is considered the precursor and the key pathophysiological mechanism of type 2 diabetes (T2D) and metabolic syndrome (MetS). However, the pathways that IR shares with T2D are not clearly understood. Meta-analysis of multiple DNA microarray datasets could provide a robust set of metagenes identified across multiple studies. These metagenes would likely include a subset of genes (key metagenes) shared by both IR and T2D, and possibly responsible for the transition between them. In this study, we attempted to find these key metagenes using a feature selection method, LASSO, and then used the expression profiles of these genes to train five machine learning models: LASSO, SVM, XGBoost, Random Forest, and ANN. Among them, ANN performed well, with an area under the curve (AUC) > 95%. It also demonstrated fairly good performance in differentiating diabetics from normal glucose tolerant (NGT) persons in the test dataset, with 73% accuracy across 64 human adipose tissue samples. Furthermore, these core metagenes were also enriched in diabetes-associated terms and were found in previous genome-wide association studies of T2D and its associated glycemic traits HOMA-IR and HOMA-B. Therefore, this metagenome deserves further investigation with regard to the cardinal molecular pathological defects/pathways underlying both IR and T2D.},
}

@article {pmid36978958,
year = {2023},
author = {Lauritano, C and Montuori, E and De Falco, G and Carrella, S},
title = {In Silico Methodologies to Improve Antioxidants' Characterization from Marine Organisms.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/antiox12030710},
pmid = {36978958},
issn = {2076-3921},
abstract = {Marine organisms have been reported to be valuable sources of bioactive molecules that have found applications in different industrial fields. From organism sampling to the identification and bioactivity characterization of a specific compound, different steps are necessary, which are time- and cost-consuming. Thanks to the advent of the -omic era, numerous genome, metagenome, transcriptome, metatranscriptome, proteome and microbiome data have been reported and deposited in public databases. These advancements have been fundamental for the development of in silico strategies for basic and applied research. In silico studies represent a convenient and efficient approach to the bioactivity prediction of known and newly identified marine molecules, reducing the time and costs of "wet-lab" experiments. This review focuses on in silico approaches applied to bioactive molecule discoveries from marine organisms. When available, validation studies reporting a bioactivity assay to confirm the presence of an antioxidant molecule or enzyme are reported, as well. Overall, this review suggests that in silico approaches can offer a valuable alternative to most expensive approaches and proposes them as a little explored field in which to invest.},
}

@article {pmid36978337,
year = {2023},
author = {Rovira, P},
title = {Short-Term Impact of Oxytetracycline Administration on the Fecal Microbiome, Resistome and Virulome of Grazing Cattle.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/antibiotics12030470},
pmid = {36978337},
issn = {2079-6382},
abstract = {Antimicrobial resistance (AMR) is an important public health concern around the world. Limited information exists about AMR in grasslands-based systems where antibiotics are seldom used in beef cattle. The present study investigated the impacts of oxytetracycline (OTC) on the microbiome, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in grazing steers with no previous exposure to antibiotic treatments. Four steers were injected with a single dose of OTC (TREAT), and four steers were kept as control (CONT). The effects of OTC on fecal microbiome, ARGs, and VFGs were assessed for 14 days using 16S rRNA sequencing and shotgun metagenomics. Alpha and beta microbiome diversities were significantly affected by OTC. Following treatment, less than 8% of bacterial genera had differential abundance between CONT and TREAT samples. Seven ARGs conferring resistance to tetracycline (tet32, tet40, tet44, tetO, tetQ, tetW, and tetW/N/W) increased their abundance in the post-TREAT samples compared to CONT samples. In addition, OTC use was associated with the enrichment of macrolide and lincosamide ARGs (mel and lnuC, respectively). The use of OTC had no significant effect on VFGs. In conclusion, OTC induced short-term alterations of the fecal microbiome and enrichment of ARGs in the feces of grazing beef cattle.},
}

@article {pmid36977970,
year = {2023},
author = {Amin, DH and Nageeb, WM and Elkelish, A and Makharita, RR},
title = {Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {36977970},
issn = {1678-4405},
abstract = {Pathogens resistant to antimicrobials form a significant threat to public health worldwide. Tackling multidrug-resistant pathogens via screening metagenomic libraries has become a common approach for the discovery of new antibiotics from uncultured microorganisms. This study focuses on capturing nonribosomal peptide synthase (NRPS) gene clusters implicated in the synthesis of many natural compounds of industrial relevance. A NRPS PCR assay was used to screen 2976 Escherichia coli clones in a soil metagenomic library to target NRPS genes. DNA extracts from 4 clones were sequenced and subjected to bioinformatic analysis to identify NRPS domains, their phylogeny, and substrate specificity.Successfully, 17 NRPS-positive hits with a biosynthetic potential were identified. DNA sequencing and BLAST analysis confirmed that NRPS protein sequences shared similarities with members of the genus Delftia in the Proteobacteria taxonomic position. Multiple alignment and phylogenetic analysis demonstrated that clones no. 15cd35 and 15cd37 shared low bootstrap values (54%) and were distantly far from close phylogenetic neighbors. Additionally, NRPS domain substrate specificity has no hits with the known ones; hence, they are more likely to use different substrates to produce new diverse antimicrobials. Further analysis confirmed that the NRPS hits resemble several transposon elements from other bacterial taxa, confirming its diversity. We confirmed that the analyses of the soil metagenomic library revealed a diverse set of NRPS related to the genus Delftia. An in-depth understanding of those positive NRPS hits is a crucial step for genetic manipulation of NRPS, shedding light on alternative novel antimicrobial compounds that can be used in drug discovery and hence supports the pharmaceutical sector.},
}

@article {pmid36977954,
year = {2023},
author = {Mahiddine, FY and You, I and Park, H and Kim, MJ},
title = {Management of dog sperm parameters and gut microbiota composition with Lactobacillus rhamnosus supplementation.},
journal = {Veterinary research communications},
volume = {},
number = {},
pages = {},
pmid = {36977954},
issn = {1573-7446},
abstract = {The effects of probiotics supplementation on the reproductive function have been evaluated in many species, but no study has evaluated the changes in the gut microbiome along with the sperm quality changes simultaneously. This study evaluated the effects of dietary supplementation with probiotics on the gut microbiome, sperm quality and gene expression, along with possible correlations between these parameters in dogs. The dogs were supplemented with Lactobacillus rhamnosus for six weeks, and fecal and semen samples were collected at 0, 3, and 6 weeks. Fecal samples were assessed using 16S Metagenomic Sequencing for gut microbiome analysis; and semen samples were analyzed using computer-assisted sperm analysis, DNA and acrosome integrity assessment, viability and morphology assessment, and real-time PCR. The analyses suggested that probiotic supplementation improved kinematic parameters, viability, DNA and acrosome integrity, and morphology of sperms. The mRNA levels of genes associated with fertility, DNA repair and integrity, and antioxidation were also upregulated. The sperm parameters were positively correlated with the relative abundance of Actinobacteria, Allobaculum, Phascolarctobacterium and Catenibacterium, and negatively correlated with Faecalibacterium and Streptococcus. Taken together, the sperm quality enhancement through the gut-testis axis may be due to a change in the gut microorganisms populations.},
}

@article {pmid36977254,
year = {2023},
author = {Becker, AAMJ and Munden, S and McCabe, E and Hurley, D and Fanning, S and Chapwanya, A and Butaye, P},
title = {The Endometrial Microbiota-16S rRNA Gene Sequence Signatures in Healthy, Pregnant and Endometritis Dairy Cows.},
journal = {Veterinary sciences},
volume = {10},
number = {3},
pages = {},
doi = {10.3390/vetsci10030215},
pmid = {36977254},
issn = {2306-7381},
abstract = {Endometritis is one of the most important causes of infertility in dairy cows, resulting in high economic losses in the dairy industry. Though the presence of a commensal uterine microbiota is now well established, the complex role of these bacteria in genital health, fertility, and susceptibility to uterine diseases remains unclear. In this study, we explore the endometrial microbiota through 16S rRNA gene profiling from cytobrush samples taken ex vivo from healthy, pregnant, and endometritis cows. There were no significant differences between healthy and pregnant cows, whose uterine microbiota were dominated by Streptococcus, Pseudomonas, Fusobacterium, Lactococcus and Bacteroides. Compared to pregnant and clinically healthy cows, the uterine bacterial community of endometritis cows was significantly decreased in species diversity (p < 0.05), reflecting uneven community composition in different patterns with either dominance of Escherichia-Shigella, Histophilus, Bacteroides and Porphyromonas or Actinobacteria.},
}

@article {pmid36976417,
year = {2023},
author = {Zhou, Q and Yu, J and Song, X and Zhang, J and Zhang, B},
title = {The discovery of novel papillomaviruses in cats in Southwest China.},
journal = {Virus genes},
volume = {},
number = {},
pages = {1-5},
pmid = {36976417},
issn = {1572-994X},
abstract = {Feline viral diarrhea is a significant cause of death in kittens. In this study, 12 mammalian viruses were identified by metagenomic sequencing in diarrheal feces in 2019, 2020, and 2021, respectively. Interestingly, a novel of felis catus papillomavirus (FcaPV) was identified for the first time in China. Subsequently, we investigated the prevalence of FcaPV in 252 feline samples, including 168 diarrheal feces and 84 oral swabs, with a total of 57 (22.62%, 57/252) samples detected positive. Of the 57 positive samples, FcaPV genotype 3 (FcaPV-3) was detected at high prevalence rate (68.42%, 39/57), followed by FcaPV-4 (22.8%, 13/57), FcaPV-2 (17.54%, 10/57), and FcaPV-1 (1.75%, 1/55), while no FcaPV-5 and FcaPV-6. In addition, two novel putative FcaPVs were identified, which were the highest similarity to Lambdapillomavirus from Leopardus wiedii or canis familiaris, respectively. Therefore, this study was the first characterization of the viral diversity in feline diarrheal feces and the prevalence of FcaPV in Southwest China.},
}

@article {pmid36976214,
year = {2023},
author = {Elvheim, AI and Li, C and Landfald, B},
title = {Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates.},
journal = {Marine drugs},
volume = {21},
number = {3},
pages = {},
doi = {10.3390/md21030165},
pmid = {36976214},
issn = {1660-3397},
abstract = {Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2-850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources.},
}

@article {pmid36975940,
year = {2023},
author = {Manee, MM and Alqahtani, FH and Al-Shomrani, BM and El-Shafie, HAF and Dias, GB},
title = {Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest.},
journal = {Insects},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/insects14030255},
pmid = {36975940},
issn = {2075-4450},
abstract = {The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of palm trees worldwide. Mitigation of the economic and biodiversity impact it causes is an international priority that could be greatly aided by a better understanding of its biology and genetics. Despite its relevance, the biology of the RPW remains poorly understood, and research on management strategies often focuses on outdated empirical methods that produce sub-optimal results. With the development of omics approaches in genetic research, new avenues for pest control are becoming increasingly feasible. For example, genetic engineering approaches become available once a species's target genes are well characterized in terms of their sequence, but also population variability, epistatic interactions, and more. In the last few years alone, there have been major advances in omics studies of the RPW. Multiple draft genomes are currently available, along with short and long-read transcriptomes, and metagenomes, which have facilitated the identification of genes of interest to the RPW scientific community. This review describes omics approaches previously applied to RPW research, highlights findings that could be impactful for pest management, and emphasizes future opportunities and challenges in this area of research.},
}

@article {pmid36975833,
year = {2023},
author = {Xiao, X and Luo, M and Zhang, C and Zhang, T and Yin, X and Wu, X and Zhao, J and Tao, J and Chen, Z and Liang, Q and Dong, X},
title = {Metal-Driven Anaerobic Oxidation of Methane as an Important Methane Sink in Methanic Cold Seep Sediments.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0533722},
doi = {10.1128/spectrum.05337-22},
pmid = {36975833},
issn = {2165-0497},
abstract = {Anaerobic oxidation of methane (AOM) coupled with reduction of metal oxides is supposed to be a globally important bioprocess in marine sediments. However, the responsible microorganisms and their contributions to methane budget are not clear in deep sea cold seep sediments. Here, we combined geochemistry, muti-omics, and numerical modeling to study metal-dependent AOM in methanic cold seep sediments in the northern continental slope of the South China Sea. Geochemical data based on methane concentrations, carbon stable isotope, solid-phase sediment analysis, and pore water measurements indicate the occurrence of anaerobic methane oxidation coupled to metal oxides reduction in the methanic zone. The 16S rRNA gene and transcript amplicons, along with metagenomic and metatranscriptomic data suggest that diverse anaerobic methanotrophic archaea (ANME) groups actively mediated methane oxidation in the methanic zone either independently or in syntrophy with, e.g., ETH-SRB1, as potential metal reducers. Modeling results suggest that the estimated rates of methane consumption via Fe-AOM and Mn-AOM were both 0.3 μmol cm[-2] year[-1], which account for ~3% of total CH4 removal in sediments. Overall, our results highlight metal-driven anaerobic oxidation of methane as an important methane sink in methanic cold seep sediments. IMPORTANCE Anaerobic oxidation of methane (AOM) coupled with reduction of metal oxides is supposed to be a globally important bioprocess in marine sediments. However, the responsible microorganisms and their contributions to methane budget are not clear in deep sea cold seep sediments. Our findings provide a comprehensive view of metal-dependent AOM in the methanic cold seep sediments and uncovered the potential mechanisms for involved microorganisms. High amounts of buried reactive Fe(III)/Mn(IV) minerals could be an important available electron acceptors for AOM. It is estimated that metal-AOM at least contributes 3% of total methane consumption from methanic sediments to the seep. Therefore, this research paper advances our understanding of the role of metal reduction to the global carbon cycle, especially the methane sink.},
}

@article {pmid36975809,
year = {2023},
author = {Falardeau, J and Yildiz, E and Yan, Y and Castellarin, SD and Wang, S},
title = {Microbiome and Physicochemical Features Associated with Differential Listeria monocytogenes Growth in Soft, Surface-Ripened Cheeses.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0200422},
doi = {10.1128/aem.02004-22},
pmid = {36975809},
issn = {1098-5336},
abstract = {Soft-ripened cheeses (SRCs) are at a higher risk for the growth of the foodborne pathogen Listeria monocytogenes due to favorable moisture content and pH compared to other cheeses. L. monocytogenes growth is not consistent across SRCs, however, and may be affected by physicochemical and/or microbiome characteristics of the cheeses. Therefore, the purpose of this study was to investigate how the physicochemical and microbiome profiles of SRCs may affect L. monocytogenes growth. Forty-three SRCs produced from raw (n = 12) or pasteurized (n = 31) milk were inoculated with L. monocytogenes (10[3] CFU/g), and the pathogen growth was monitored over 12 days at 8°C. In parallel, the pH, water activity (aw), microbial plate counts, and organic acid content of cheeses were measured, and the taxonomic profiles of the cheese microbiomes were measured using 16S rRNA gene targeted amplicon sequencing and shotgun metagenomic sequencing. L. monocytogenes growth differed significantly between cheeses (analysis of variance [ANOVA]; P < 0.001), with increases ranging from 0 to 5.4 log CFU (mean of 2.5 ± 1.2 log CFU), and was negatively correlated with aw. Raw milk cheeses showed significantly lower L. monocytogenes growth than pasteurized-milk cheeses (t test; P = 0.008), possibly due to an increase in microbial competition. L. monocytogenes growth in cheeses was positively correlated with the relative abundance of Streptococcus thermophilus (Spearman correlation; P < 0.0001) and negatively correlated with the relative abundances of Brevibacterium aurantiacum (Spearman correlation; P = 0.0002) and two Lactococcus spp. (Spearman correlation; P < 0.01). These results suggest that the cheese microbiome may influence the food safety in SRCs. IMPORTANCE Previous studies have identified differences in L. monocytogenes growth between SRCs, but no clear mechanism has yet been elucidated. To the best of our knowledge, this is the first study to collect a wide range of SRCs from retail sources and attempt to identify key factors associated with pathogen growth. A key finding in this research was the positive correlation between the relative abundance of S. thermophilus and the growth of L. monocytogenes. The inclusion of S. thermophilus as a starter culture is more common in industrialized SRC production, suggesting that industrial production of SRC may increase the risk of L. monocytogenes growth. Overall, the results of this study further our understanding of the impact of aw and the cheese microbiome on the growth of L. monocytogenes in SRCs, hopefully leading toward the development of SRC starter/ripening cultures that can prevent L. monocytogenes growth.},
}

@article {pmid36975807,
year = {2023},
author = {Zhang, W and Liu, Y and Zheng, K and Xing, J and Li, Q and Gu, C and Wang, Z and Shao, H and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Wong, LL and Liang, Y and McMinn, A and Wang, M},
title = {Discovery of an Abundant Viral Genus in Polar Regions through the Isolation and Genomic Characterization of a New Virus against Oceanospirillaceae.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0189622},
doi = {10.1128/aem.01896-22},
pmid = {36975807},
issn = {1098-5336},
abstract = {The marine bacterial family Oceanospirillaceae, is well-known for its ability to degrade hydrocarbons and for its close association with algal blooms. However, only a few Oceanospirillaceae-infecting phages have been reported thus far. Here, we report on a novel Oceanospirillum phage, namely, vB_OsaM_PD0307, which has a 44,421 bp linear dsDNA genome and is the first myovirus infecting Oceanospirillaceae. A genomic analysis demonstrated that vB_OsaM_PD0307 is a variant of current phage isolates from the NCBI data set but that it has similar genomic features to two high-quality, uncultured viral genomes identified from marine metagenomes. Hence, we propose that vB_OsaM_PD0307 can be classified as the type phage of a new genus, designated Oceanospimyovirus. Additionally, metagenomic read mapping results have further shown that Oceanospimyovirus species are widespread in the global ocean, display distinct biogeographic distributions, and are abundant in polar regions. In summary, our findings expand the current understanding of the genomic characteristics, phylogenetic diversity, and distribution of Oceanospimyovirus phages. IMPORTANCE Oceanospirillum phage vB_OsaM_PD0307 is the first myovirus found to infect Oceanospirillaceae, and it represents a novel abundant viral genus in polar regions. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral genus, namely Oceanospimyovirus.},
}

@article {pmid36975801,
year = {2023},
author = {Carter, KA and Fodor, AA and Balkus, JE and Zhang, A and Serrano, MG and Buck, GA and Engel, SM and Wu, MC and Sun, S},
title = {Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0100322},
doi = {10.1128/msystems.01003-22},
pmid = {36975801},
issn = {2379-5077},
abstract = {Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome. Findings from other body sites cannot easily be generalized to the vaginal microbiome due to unique features of vaginal microbial ecology, and investigators seeking to use metagenome inference in vaginal microbiome research are "flying blind" with respect to potential bias these methods may introduce into analyses. We compared the performance of PICRUSt2 and Tax4Fun2 using paired 16S rRNA gene amplicon sequencing and whole-metagenome sequencing data from vaginal samples from 72 pregnant individuals enrolled in the Pregnancy, Infection, and Nutrition (PIN) cohort. Participants were selected from those with known birth outcomes and adequate 16S rRNA gene amplicon sequencing data in a case-control design. Cases experienced early preterm birth (<32 weeks of gestation), and controls experienced term birth (37 to 41 weeks of gestation). PICRUSt2 and Tax4Fun2 performed modestly overall (median Spearman correlation coefficients between observed and predicted KEGG ortholog [KO] relative abundances of 0.20 and 0.22, respectively). Both methods performed best among Lactobacillus crispatus-dominated vaginal microbiotas (median Spearman correlation coefficients of 0.24 and 0.25, respectively) and worst among Lactobacillus iners-dominated microbiotas (median Spearman correlation coefficients of 0.06 and 0.11, respectively). The same pattern was observed when evaluating correlations between univariable hypothesis test P values generated with observed and predicted metagenome data. Differential metagenome inference performance across vaginal microbiota community types can be considered differential measurement error, which often causes differential misclassification. As such, metagenome inference will introduce hard-to-predict bias (toward or away from the null) in vaginal microbiome research. IMPORTANCE Compared to taxonomic composition, the functional potential within a bacterial community is more relevant to establishing mechanistic understandings and causal relationships between the microbiome and health outcomes. Metagenome inference attempts to bridge the gap between 16S rRNA gene amplicon sequencing and whole-metagenome sequencing by predicting a microbiome's gene content based on its taxonomic composition and annotated genome sequences of its members. Metagenome inference methods have been evaluated primarily among gut samples, where they appear to perform fairly well. Here, we show that metagenome inference performance is markedly worse for the vaginal microbiome and that performance varies across common vaginal microbiome community types. Because these community types are associated with sexual and reproductive outcomes, differential metagenome inference performance will bias vaginal microbiome studies, obscuring relationships of interest. Results from such studies should be interpreted with substantial caution and the understanding that they may over- or underestimate associations with metagenome content.},
}

@article {pmid36975791,
year = {2023},
author = {Mejia, ME and Robertson, CM and Patras, KA},
title = {Interspecies Interactions within the Host: the Social Network of Group B Streptococcus.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0044022},
doi = {10.1128/iai.00440-22},
pmid = {36975791},
issn = {1098-5522},
abstract = {Group B Streptococcus (GBS) is a pervasive neonatal pathogen accounting for a combined half a million deaths and stillbirths annually. The most common source of fetal or neonatal GBS exposure is the maternal microbiota. GBS asymptomatically colonizes the gastrointestinal and vaginal mucosa of 1 in 5 individuals globally, although its precise role in these niches is not well understood. To prevent vertical transmission, broad-spectrum antibiotics are administered to GBS-positive mothers during labor in many countries. Although antibiotics have significantly reduced GBS early-onset neonatal disease, there are several unintended consequences, including an altered neonatal microbiota and increased risk for other microbial infections. Additionally, the incidence of late-onset GBS neonatal disease remains unaffected and has sparked an emerging hypothesis that GBS-microbe interactions in developing neonatal gut microbiota may be directly involved in this disease process. This review summarizes our current understanding of GBS interactions with other resident microbes at the mucosal surface from multiple angles, including clinical association studies, agriculture and aquaculture observations, and experimental animal model systems. We also include a comprehensive review of in vitro findings of GBS interactions with other bacterial and fungal microbes, both commensal and pathogenic, along with newly established animal models of GBS vaginal colonization and in utero or neonatal infection. Finally, we provide a perspective on emerging areas of research and current strategies to design microbe-targeting prebiotic or probiotic therapeutic intervention strategies to prevent GBS disease in vulnerable populations.},
}

@article {pmid36974462,
year = {2023},
author = {Zhang, S and Li, S and Huang, J and Ding, X and Qiu, Y and Luo, X and Meng, J and Hu, Y and Zhou, H and Fan, H and Cao, Y and Gao, F and Xue, Y and Zou, M},
title = {Gram-negative bacteria and lipopolysaccharides as risk factors for the occurrence of diabetic foot.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1210/clinem/dgad178},
pmid = {36974462},
issn = {1945-7197},
abstract = {CONTEXT: Imbalance of the skin microbial community could impair skin immune homeostasis and thus trigger skin lesions. Dysbiosis of skin microbiome may be involved in the early pathogenesis of diabetic foot (DF). However, the potential mechanism remains unclear.

OBJECTIVE: To investigate the dynamic composition and function of the foot skin microbiome with risk stratification for DF and assess whether dysbiosis of the skin microbiome induces diabetic skin lesions.

METHODS: We enrolled 90 consecutive subjects who were divided into five groups based on DF risk stratification: very low, low, moderate and high risk for ulcers and a healthy control group. Integrated analysis of 16S rRNA and metagenomic sequencing of cotton swab samples was applied to identify the foot skin microbiome composition and functions in subjects. Then, a mouse model of microbiota transplantation was used to evaluate the effects of the skin microbiome on diabetic skin lesions.

RESULTS: The results demonstrated that, with the progression of diabetic complications, the proportion of gram-negative bacteria in plantar skin increased. At the species level, metagenome sequencing analyses showed Moraxella osloensis to be a representative core strain in the high-risk group. The major microbial metabolites affecting diabetic skin lesions were increased amino acid metabolites, and antibiotic resistance genes in microorganisms were abundant. Skin microbiota from high-risk patients induced more inflammatory cell infiltration, similar to the lipopolysaccharide (LPS)-stimulated response, which was inhibited by Toll-like receptor 4 (TLR4) antagonists.

CONCLUSIONS: The skin microbiome in patients with diabetes undergoes dynamic changes at taxonomic and functional levels with the progression of diabetic complications. The increase in gram-negative bacteria on the skin surface through LPS-TLR4 signal transduction could induce inflammatory response in early diabetic skin lesions.},
}

@article {pmid36973750,
year = {2023},
author = {Rivarez, MPS and Pecman, A and Bačnik, K and Maksimović, O and Vučurović, A and Seljak, G and Mehle, N and Gutiérrez-Aguirre, I and Ravnikar, M and Kutnjak, D},
title = {In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {60},
pmid = {36973750},
issn = {2049-2618},
abstract = {BACKGROUND: In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data.

RESULTS: Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments.

CONCLUSIONS: We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies. Video Abstract.},
}

@article {pmid36973710,
year = {2023},
author = {Li, H and Wang, H and Ju, H and Lv, J and Yang, S and Zhang, W and Lu, H},
title = {Comparison of gut viral communities in children under 5 years old and newborns.},
journal = {Virology journal},
volume = {20},
number = {1},
pages = {52},
pmid = {36973710},
issn = {1743-422X},
abstract = {OBJECTIVES: The gut virome of humans is mainly composed of bacteriophages and their role in shaping the gut microbiome and influencing human health is increasingly recognized. However, little is known about the dynamic changes of the gut virome in children and its role in growth and development. In this study, we collected fecal samples from newborns and children under 5 years old from the same area during the same time period to investigate the gut viral community using viral metagenomic technique.

METHODS: We used viral metagenomics to compare the gut bacteriophage composition between newborns and children under 5 years of age. We collected fecal samples from 45 newborns who were born at the Affiliated Hospital of Jiangsu University and 45 healthy children who were examined at the same hospital. The two groups were classified as the newborn group and the children group.

RESULTS: Our sequencing analysis showed that the number of seqeunce reads of the children group were more than that of the newborn group. The results of alpha diversity and beta diversity both indicated that the diversity of the children group was significantly higher than that of the newborn group and the children group is different from the newborn group. The abundance of gut virome in the children group was also higher than that in the newborn group. The analysis of the genetic characteristics of the viruses showed that the phage genome was scattered and clustered with specificity.

CONCLUSION: Our findings indicate that the gut bacteriophage communities undergo changes over time, presenting diversity and dynamic characteristics. We characterized the composition of gut virome in children and newborns in this region. However, further research is needed to investigate the function of bacteriophages in the ecology of the gastrointestinal tract.},
}

@article {pmid36973336,
year = {2023},
author = {Rodríguez-Gijón, A and Buck, M and Andersson, AF and Izabel-Shen, D and Nascimento, FJA and Garcia, SL},
title = {Linking prokaryotic genome size variation to metabolic potential and environment.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {25},
pmid = {36973336},
issn = {2730-6151},
abstract = {While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.},
}

@article {pmid36972958,
year = {2023},
author = {Muzny, CA and Van Gerwen, OT and Schroeder, JA and Kay-Duncan, ES and Siwakoti, K and Aaron, KJ and Eastlund, IC and Graves, KJ and Elnaggar, JH and Tamhane, A and Long, D and Van Wagoner, N and Toh, E and Taylor, CM},
title = {Impact of testosterone use on the vaginal microbiota of transgender men, including susceptibility to bacterial vaginosis: study protocol for a prospective, observational study.},
journal = {BMJ open},
volume = {13},
number = {3},
pages = {e073068},
doi = {10.1136/bmjopen-2023-073068},
pmid = {36972958},
issn = {2044-6055},
abstract = {INTRODUCTION: The effect of testosterone (T) therapy on the vaginal microbiota of transgender men (TGM) is not well characterised, although one cross-sectional study comparing the vaginal microbiota of cisgender women to TGM on T≥1 year found that, in 71% of the TGM, the vaginal microbiota was less likely to be Lactobacillus-dominated and more likely to be enriched with >30 other bacterial species, many associated with bacterial vaginosis (BV). This prospective study aims to investigate changes in the composition of the vaginal microbiota over time in TGM who retain their natal genitalia (ie, vagina) and initiate T. In addition, we will identify changes in the vaginal microbiota preceding incident BV (iBV) in this cohort while investigating behavioural factors, along with hormonal shifts, which may be associated with iBV.

METHODS AND ANALYSIS: T-naïve TGM who have not undergone gender-affirming genital surgery with normal baseline vaginal microbiota (ie, no Amsel criteria, normal Nugent Score with no Gardnerella vaginalis morphotypes) will self-collect daily vaginal specimens for 7 days prior to initiating T and for 90 days thereafter. These specimens will be used for vaginal Gram stain, 16S rRNA gene sequencing and shotgun metagenomic sequencing to characterise shifts in the vaginal microbiota over time, including development of iBV. Participants will complete daily diaries on douching, menses and behavioural factors including sexual activity during the study.

ETHICS AND DISSEMINATION: This protocol is approved through the single Institutional Review Board mechanism by the University of Alabama at Birmingham. External relying sites are the Louisiana State University Health Sciences Center, New Orleans Human Research Protection Program and the Indiana University Human Research Protection Program. Study findings will be presented at scientific conferences and peer-reviewed journals as well as shared with community advisory boards at participating gender health clinics and community-based organisations servicing transgender people.

REGISTRATION DETAILS: Protocol # IRB-300008073.},
}

@article {pmid36805473,
year = {2023},
author = {Jia, Y and Liu, ML and López-Pujol, J and Jia, RW and Kou, YX and Yue, M and Guan, TX and Li, ZH},
title = {The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis.},
journal = {Molecular phylogenetics and evolution},
volume = {182},
number = {},
pages = {107736},
doi = {10.1016/j.ympev.2023.107736},
pmid = {36805473},
issn = {1095-9513},
mesh = {*Apiaceae/genetics ; Bayes Theorem ; Ecosystem ; Metagenomics ; Phylogeny ; *Hybridization, Genetic ; },
abstract = {Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.},
}

*Apiaceae/genetics
Bayes Theorem
Ecosystem
Metagenomics
Phylogeny
*Hybridization, Genetic

@article {pmid36801373,
year = {2023},
author = {Spaulding, F and McLaughlin, JF and Cheek, RG and McCracken, KG and Glenn, TC and Winker, K},
title = {Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex.},
journal = {Molecular phylogenetics and evolution},
volume = {182},
number = {},
pages = {107733},
doi = {10.1016/j.ympev.2023.107733},
pmid = {36801373},
issn = {1095-9513},
mesh = {Humans ; Animals ; *Ducks/genetics ; *Gene Flow ; Phylogeny ; Metagenomics ; DNA, Mitochondrial/genetics ; },
abstract = {The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspecies (Anas crecca crecca, A. c. nimia, and A. c. carolinensis) with a close relative, the yellow-billed teal (Anas flavirostris) from South America. A. c. crecca and A. c. carolinensis are seasonal migrants, while the other taxa are sedentary. We examined divergence and speciation patterns in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and genome-wide nuclear DNA obtained from 1,393 ultraconserved element (UCE) loci. Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca, A. c. nimia, and A. c. carolinensis clustering together to form one polytomous clade, with A. flavirostris sister to this clade. This relationship can be summarized as (crecca, nimia, carolinensis)(flavirostris). However, whole mitogenomes revealed a different phylogeny: (crecca, nimia)(carolinensis, flavirostris). The best demographic model for key pairwise comparisons supported divergence with gene flow as the probable speciation mechanism in all three contrasts (crecca-nimia, crecca-carolinensis, and carolinensis-flavirostris). Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris (M ∼0.1-0.4 individuals/generation), albeit low, was not expected. Three geographically oriented modes of divergence are likely involved in the diversification of this complex: heteropatric (crecca-nimia), parapatric (crecca-carolinensis), and (mostly) allopatric (carolinensis-flavirostris). Our study shows that ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems with historically uncertain relationships and species limits.},
}

Humans
Animals
*Ducks/genetics
*Gene Flow
Phylogeny
Metagenomics
DNA, Mitochondrial/genetics

@article {pmid36972812,
year = {2023},
author = {Tian, H and Li, Y and Chen, H and Zhang, J and Hui, M and Xu, X and Su, Q and Smets, BF},
title = {Aerobic biodegradation of quinoline under denitrifying conditions in membrane-aerated biofilm reactor.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {121507},
doi = {10.1016/j.envpol.2023.121507},
pmid = {36972812},
issn = {1873-6424},
abstract = {Aerobic denitrification is being investigated as a novel biological nitrogen removal process, yet the knowledge on aerobic denitrification is limited to pure culture isolations and its occurrence in bioreactors remains unclear. This study investigated the feasibility and capacity of applying aerobic denitrification in membrane aerated biofilm reactor (MABR) for biological treatment of quinoline-laden wastewater. Stable and efficient removals of quinoline (91.5 ± 5.2%) and nitrate (NO3[-]) (86.5 ± 9.3%) were obtained under different operational conditions. Enhanced formation and function of extracellular polymeric substances (EPS) were observed at increasing quinoline loadings. MABR biofilm was highly enriched with aerobic quinoline-degrading bacteria, with a predominance of Rhodococcus (26.9 ± 3.7%) and secondary abundance of Pseudomonas (1.7 ± 1.2%) and Comamonas (0.94 ± 0.9%). Metagenomic analysis indicated that Rhodococcus contributed significantly to both aromatic degradation (24.5 ± 21.3%) and NO3[-] reduction (4.5 ± 3.9%), indicating its key role in aerobic denitrifying quinoline biodegradation. At increasing quinoline loadings, abundances of aerobic quinoline degradation gene oxoO and denitrifying genes of napA, nirS and nirK increased; there was a significant positive correlation of oxoO with nirS and nirK (p < 0.05). Aerobic quinoline degradation was likely initiated by hydroxylation, encoded by oxoO, followed by stepwise oxidations through 5,6-dihydroxy-1H-2-oxoquinoline or 8-hydroxycoumarin pathway. The results advance our understanding of quinoline degradation during biological nitrogen removal, and highlight the potential implementation of aerobic denitrification driven quinoline biodegradation in MABR for simultaneous removal of nitrogen and recalcitrant organic carbon from coking, coal gasification and pharmaceutical wastewaters.},
}

@article {pmid36972309,
year = {2023},
author = {Krishnan, S and DeMaere, MZ and Beck, D and Ostrowski, M and Seymour, JR and Darling, AE},
title = {Rhometa: Population recombination rate estimation from metagenomic read datasets.},
journal = {PLoS genetics},
volume = {19},
number = {3},
pages = {e1010683},
doi = {10.1371/journal.pgen.1010683},
pmid = {36972309},
issn = {1553-7404},
abstract = {Prokaryotic evolution is influenced by the exchange of genetic information between species through a process referred to as recombination. The rate of recombination is a useful measure for the adaptive capacity of a prokaryotic population. We introduce Rhometa (https://github.com/sid-krish/Rhometa), a new software package to determine recombination rates from shotgun sequencing reads of metagenomes. It extends the composite likelihood approach for population recombination rate estimation and enables the analysis of modern short-read datasets. We evaluated Rhometa over a broad range of sequencing depths and complexities, using simulated and real experimental short-read data aligned to external reference genomes. Rhometa offers a comprehensive solution for determining population recombination rates from contemporary metagenomic read datasets. Rhometa extends the capabilities of conventional sequence-based composite likelihood population recombination rate estimators to include modern aligned metagenomic read datasets with diverse sequencing depths, thereby enabling the effective application of these techniques and their high accuracy rates to the field of metagenomics. Using simulated datasets, we show that our method performs well, with its accuracy improving with increasing numbers of genomes. Rhometa was validated on a real S. pneumoniae transformation experiment, where we show that it obtains plausible estimates of the rate of recombination. Finally, the program was also run on ocean surface water metagenomic datasets, through which we demonstrate that the program works on uncultured metagenomic datasets.},
}

@article {pmid36971593,
year = {2023},
author = {Liu, F and Lu, H and Dong, B and Huang, X and Cheng, H and Qu, R and Hu, Y and Zhong, L and Guo, Z and You, Y and Xu, ZZ},
title = {Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/- Bacteria.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0073822},
doi = {10.1128/msystems.00738-22},
pmid = {36971593},
issn = {2379-5077},
abstract = {PMA (propidium monoazide) is one of the few methods that are compatible with metagenomic sequencing to characterize the live/intact microbiota. However, its efficiency in complex communities such as saliva and feces is still controversial. An effective method for depleting host and dead bacterial DNA in human microbiome samples is lacking. Here, we systematically evaluate the efficiency of osmotic lysis and PMAxx treatment (lyPMAxx) in characterizing the viable microbiome with four live/dead Gram+/Gram- microbial strains in simple synthetic and spiked-in complex communities. We show that lyPMAxx-quantitative PCR (qPCR)/sequencing eliminated more than 95% of the host and heat-killed microbial DNA and had a much smaller effect on the live microbes in both simple mock and spiked-in complex communities. The overall microbial load and the alpha diversity of the salivary and fecal microbiome were decreased by lyPMAxx, and the relative abundances of the microbes were changed. The relative abundances of Actinobacteria, Fusobacteria, and Firmicutes in saliva were decreased by lyPMAxx, as was that of Firmicutes in feces. We also found that the frequently used sample storage method, freezing with glycerol, killed or injured 65% and 94% of the living microbial cells in saliva and feces, respectively, with the Proteobacteria phylum affected most in saliva and the Bacteroidetes and Firmicutes phyla affected most in feces. By comparing the absolute abundance variation of the shared species among different sample types and individuals, we found that sample habitat and personal differences affected the response of microbial species to lyPMAxx and freezing. IMPORTANCE The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes. PMA-qPCR was used to characterize the viable microbes in previous studies. However, its efficiency in complex communities such as saliva and feces is still controversial. By spiking-in four live/dead Gram+/Gram- bacterial strains, we demonstrate that lyPMAxx can effectively discriminate between live and dead microbes in the simple synthetic community and complex human microbial communities (saliva and feces). In addition, freezing storage was found to kill or injure the microbes in saliva and feces significantly, as measured with lyPMAxx-qPCR/sequencing. This method has a promising prospect in the viable/intact microbiota detection of complex human microbial communities.},
}

@article {pmid36971577,
year = {2023},
author = {Balière, C and Hourdel, V and Kwasiborski, A and Grassin, Q and Feher, M and Hoinard, D and Vanhomwegen, J and Taieb, F and Consigny, PH and Manuguerra, JC and Leclercq, I and Batéjat, C and Caro, V},
title = {Complete Genome Sequences of Monkeypox Virus from a French Clinical Sample and the Corresponding Isolated Strain, Obtained Using Nanopore Sequencing.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0000923},
doi = {10.1128/mra.00009-23},
pmid = {36971577},
issn = {2576-098X},
abstract = {We report the whole-genome sequences of a monkeypox virus from the skin lesion of a French patient and the corresponding isolated viral strain. Both viral genomic sequences were successfully obtained by applying shotgun metagenomics using the Oxford Nanopore Technologies sequencing approach.},
}

@article {pmid36971547,
year = {2023},
author = {Etienne-Mesmin, L and Meslier, V and Uriot, O and Fournier, E and Deschamps, C and Denis, S and David, A and Jegou, S and Morabito, C and Quinquis, B and Thirion, F and Plaza Oñate, F and Le Chatelier, E and Ehrlich, SD and Blanquet-Diot, S and Almeida, M},
title = {In Vitro Modelling of Oral Microbial Invasion in the Human Colon.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0434422},
doi = {10.1128/spectrum.04344-22},
pmid = {36971547},
issn = {2165-0497},
abstract = {Recent advances in the human microbiome characterization have revealed significant oral microbial detection in stools of dysbiotic patients. However, little is known about the potential interactions of these invasive oral microorganisms with commensal intestinal microbiota and the host. In this proof-of-concept study, we proposed a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Oral invasion of the intestinal microbiota was simulated by injection of enriched saliva in the in vitro colon model inoculated with a fecal sample from the same healthy adult donor. The mucosal compartment of M-ARCOL was able to retain the highest species richness levels over time, while species richness levels decreased in the luminal compartment. This study also showed that oral microorganisms preferably colonized the mucosal microenvironment, suggesting potential oral-to-intestinal mucosal competitions. This new model of oral-to-gut invasion can provide useful mechanistic insights into the role of oral microbiome in various disease processes. IMPORTANCE Here, we propose a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Our study revealed the importance of integrating the mucus compartment, which retained higher microbial richness during fermentation, showed the preference of oral microbial invaders for the mucosal resources, and indicated potential oral-to-intestinal mucosal competitions. It also underlined promising opportunities to further understand mechanisms of oral invasion into the human gut microbiome, define microbe-microbe and mucus-microbe interactions in a compartmentalized fashion, and help to better characterize the potential of oral microbial invasion and their persistence in the gut.},
}

@article {pmid36970947,
year = {2023},
author = {Ermolenko, E and Sitkin, S and Vakhitov, T and Solovyeva, O and Karaseva, A and Morozova, A and Kotyleva, M and Shumikhina, I and Lavrenova, N and Demyanova, E and Dmitriev, A and Suvorov, A},
title = {Evaluation of the effectiveness of personalised therapy for the patients with irritable bowel syndrome.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-12},
doi = {10.3920/BM2022.0053},
pmid = {36970947},
issn = {1876-2891},
abstract = {Intestinal microbiota correction in the therapy of irritable bowel syndrome (IBS) is an important medical problem. We conducted a laboratory and pilot clinical trial to investigate the effect of autoprobiotic bacteria, indigenous bifidobacteria and enterococci isolated from faeces and grown on artificial media to use as personified food additives in IBS treatment. Convincing evidence of the clinical efficacy of autoprobiotic was demonstrated by the disappearance of dyspeptic symptoms. The microbiome of patients with IBS was compared to a group of healthy volunteers and changes in the microbiome after autoprobiotic use were detected by quantitative polymerase chain reaction and 16S rRNA metagenome analysis. The possibility of reducing opportunistic microorganisms in the treatment of IBS with autoprobiotics has been convincingly proven. The quantitative content of enterococci in the intestinal microbiota was higher in IBS patients than in healthy volunteers and increased after therapy. An increase in the relative abundance of genera Coprococcus, Blautia and a decrease in the relative abundance of Paraprevotella spp. were found at the end of therapy. A metabolome study which was performed by gas chromatography and mass spectrometry demonstrated an increase in the content of oxalic acid, a decrease of dodecanoate, lauric acid, and other metabolome components after taking autoprobiotics. Some of these parameters correlated with the relative abundances of Paraprevotella spp., Enterococcus spp., and Coprococcus spp. representative of the microbiome. Apparently, they reflected the peculiarities of metabolic compensation and changes in the microbiota. Therefore, the use of autoprobiotics for treatment of IBS may lead to a stable positive clinical effect, associated with compensatory changes in the intestinal microbiota, and accompanied by corresponding changes in metabolic processes in the organism.},
}

@article {pmid36970703,
year = {2023},
author = {Pan, J and Zeng, M and Zhao, M and Huang, L},
title = {Research Progress on the detection methods of porcine reproductive and respiratory syndrome virus.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1097905},
pmid = {36970703},
issn = {1664-302X},
abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) causes clinical syndromes typified as reproductive disorders in sows and respiratory diseases in piglets. PRRSV remains one of the most prevalent pathogens affecting the pig industry, because of its complex infection profile and highly heterogeneous genetic and recombination characteristics. Therefore, a rapid and effective PRRSV detection method is important for the prevention and control of PRRS. With extensive in-depth research on PRRSV detection methods, many detection methods have been improved and promoted. Laboratory methods include techniques based on virus isolation (VI), enzyme-linked immunosorbent assays (ELISA), indirect immunofluorescence assays (IFA), immunoperoxidase monolayer assays (IPMA), polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), digital PCR (dPCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), clustered regularly interspaced short palindromic repeats (CRISPR), metagenomic next-generation sequencing (mNGS), and other methods. This study reviews the latest research on improving the main PRRSV detection methods and discusses their advantages and disadvantages.},
}

@article {pmid36970696,
year = {2023},
author = {Dai, R and Wu, H and Liu, G and Shen, L and Geng, Y and Zhang, S and Zhou, H and Jiang, C and Gong, J and Fan, X and Ji, C},
title = {Investigation of bacterial and fungal population structure on environmental surfaces of three medical institutions during the COVID-19 pandemic.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1089474},
pmid = {36970696},
issn = {1664-302X},
abstract = {OBJECTIVES: To evaluate the population structure of environmental bacteria and fungi in three different types of medical institutions and the potential risks due to antibiotic resistance during the coronavirus disease 2019 (COVID-19) pandemic.

METHODS: One hundred twenty-six environmental surface samples were collected from three medical institutions during the COVID-19 pandemic. A total of 6,093 and 13,514 representative sequences of 16S and ITS ribosomal RNA (rRNA) were obtained by amplicon sequencing analysis. The functional prediction was performed using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States tool based on the Greengenes database and the FAPROTAX database.

RESULTS: On environmental surfaces in three medical institutions during the COVID-19 pandemic, Firmicutes (51.6%) and Bacteroidetes (25%) were the dominant bacteria, while Ascomycota (39.4%) and Basidiomycota (14.2%) were the dominant fungi. A number of potential bacterial and fungal pathogens were successfully identified by the metagenomic approach. Furthermore, compared with the bacterial results, the fungi showed a generally closer Bray Curtis distance between samples. The overall ratio of Gram-negative bacteria to Gram-positive bacteria was about 3:7. The proportion of stress-tolerant bacteria in medical institutions A, B and C reached 88.9, 93.0 and 93.8%, respectively. Anaerobic bacteria accounted for 39.6% in outdoor environments, 77.7% in public areas, 87.9% in inpatient areas and 79.6% in restricted areas. Finally, the β-Lactam resistance pathway and polymyxin resistance pathway were revealed through functional prediction.

CONCLUSION: We described the microbial population structure changes in three different types of medical institutions using the metagenomic approach during the COVID-19 pandemic. We found that the disinfection measures performed by three healthcare facilities may be effective on the "ESKAPE" pathogens, but less effective on fungal pathogens. Moreover, emphasis should be given to the prevention and control of β-lactam and polymyxin antibiotics resistance bacteria during the COVID-19 pandemic.},
}

@article {pmid36970681,
year = {2023},
author = {Guo, K and Li, J and Li, X and Huang, J and Zhou, Z},
title = {Emerging trends and focus on the link between gut microbiota and type 1 diabetes: A bibliometric and visualization analysis.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1137595},
pmid = {36970681},
issn = {1664-302X},
abstract = {OBJECTIVE: To conduct the first thorough bibliometric analysis to evaluate and quantify global research regarding to the gut microbiota and type 1 diabetes (T1D).

METHODS: A literature search for research studies on gut microbiota and T1D was conducted using the Web of Science Core Collection (WoSCC) database on 24 September 2022. VOSviewer software and the packages Bibliometrix R and ggplot used in RStudio were applied to perform the bibliometric and visualization analysis.

RESULTS: A total of 639 publications was extracted using the terms "gut microbiota" and "type 1 diabetes" (and their synonyms in MeSH). Ultimately, 324 articles were included in the bibliometric analysis. The United States and European countries are the main contributors to this field, and the top 10 most influential institutions are all based in the United States, Finland and Denmark. The three most influential researchers in this field are Li Wen, Jorma Ilonen and Mikael Knip. Historical direct citation analysis showed the evolution of the most cited papers in the field of T1D and gut microbiota. Clustering analysis defined seven clusters, covering the current main topics in both basic and clinical research on T1D and gut microbiota. The most commonly found high-frequency keywords in the period from 2018 to 2021 were "metagenomics," "neutrophils" and "machine learning."

CONCLUSION: The application of multi-omics and machine learning approaches will be a necessary future step for better understanding gut microbiota in T1D. Finally, the future outlook for customized therapy toward reshaping gut microbiota of T1D patients remains promising.},
}

@article {pmid36970670,
year = {2023},
author = {Seyler, LM and Kraus, EA and McLean, C and Spear, JR and Templeton, AS and Schrenk, MO},
title = {An untargeted exometabolomics approach to characterize dissolved organic matter in groundwater of the Samail Ophiolite.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1093372},
pmid = {36970670},
issn = {1664-302X},
abstract = {The process of serpentinization supports life on Earth and gives rise to the habitability of other worlds in our Solar System. While numerous studies have provided clues to the survival strategies of microbial communities in serpentinizing environments on the modern Earth, characterizing microbial activity in such environments remains challenging due to low biomass and extreme conditions. Here, we used an untargeted metabolomics approach to characterize dissolved organic matter in groundwater in the Samail Ophiolite, the largest and best characterized example of actively serpentinizing uplifted ocean crust and mantle. We found that dissolved organic matter composition is strongly correlated with both fluid type and microbial community composition, and that the fluids that were most influenced by serpentinization contained the greatest number of unique compounds, none of which could be identified using the current metabolite databases. Using metabolomics in conjunction with metagenomic data, we detected numerous products and intermediates of microbial metabolic processes and identified potential biosignatures of microbial activity, including pigments, porphyrins, quinones, fatty acids, and metabolites involved in methanogenesis. Metabolomics techniques like the ones used in this study may be used to further our understanding of life in serpentinizing environments, and aid in the identification of biosignatures that can be used to search for life in serpentinizing systems on other worlds.},
}

@article {pmid36970663,
year = {2023},
author = {Zhong, X and Zhao, Y and Huang, L and Liu, J and Wang, K and Gao, X and Zhao, X and Wang, X},
title = {Remodeling of the gut microbiome by Lactobacillus johnsonii alleviates the development of acute myocardial infarction.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1140498},
pmid = {36970663},
issn = {1664-302X},
abstract = {INTRODUCTION: The gut microbial community, which can be disturbed or repaired by changes in the internal environment, contributes to the development of acute myocardial infarction (AMI). Gut probiotics play a role in microbiome remodeling and nutritional intervention post-AMI. A newly isolated Lactobacillus johnsonii strain EU03 has shown potential as a probiotic. Here, we investigated the cardioprotective function and mechanism of L. johnsonii through gut microbiome remodeling in AMI rats.

METHODS: A rat model of left anterior descending coronary artery ligation (LAD)-mediated AMI was assessed with echocardiography, histology, and serum cardiac biomarkers to evaluate the beneficial effects of L. johnsonii. The immunofluorescence analysis was utilized to visualize the intestinal barrier changes. Antibiotic administration model was used for assessing the gut commensals' function in the improvement of cardiac function post-AMI. The underlying beneficial mechanism through L. johnsonii enrichment was further investigated by metagenomics and metabolomics analysis.

RESULTS: A 28-day treatment with L. johnsonii protected cardiac function, delayed cardiac pathology, suppressed myocardial injury cytokines, and improved gut barrier integrity. The microbiome composition was reprogrammed by enhancing the abundance of L. johnsonii. Microbiome dysbiosis by antibiotics abrogated the improvement of cardiac function post-AMI by L. johnsonii. L. johnsonii enrichment caused remodeling of gut microbiome by increasing the abundance of Muribaculaceae, Lactobacillus, and decreasing Romboutsia, Clostridia UCG-014, which were correlated with cardiac traits and serum metabolic biomarkers 16,16-dimethyl-PGA2, and Lithocholate 3-O-glucuronide.

CONCLUSION: These findings reveal that gut microbiome remodeling by L. johnsonii ameliorates the cardiac function post-AMI and might advance microbiome-targeted nutritional intervention.Graphical Abstract.},
}

@article {pmid36970502,
year = {2023},
author = {Liu, B and Warnow, T},
title = {WITCH-NG: efficient and accurate alignment of datasets with sequence length heterogeneity.},
journal = {Bioinformatics advances},
volume = {3},
number = {1},
pages = {vbad024},
pmid = {36970502},
issn = {2635-0041},
abstract = {SUMMARY: Multiple sequence alignment is a basic part of many bioinformatics pipelines, including in phylogeny estimation, prediction of structure for both RNAs and proteins, and metagenomic sequence analysis. Yet many sequence datasets exhibit substantial sequence length heterogeneity, both because of large insertions and deletions in the evolutionary history of the sequences and the inclusion of unassembled reads or incompletely assembled sequences in the input. A few methods have been developed that can be highly accurate in aligning datasets with sequence length heterogeneity, with UPP one of the first methods to achieve good accuracy, and WITCH a recent improvement on UPP for accuracy. In this article, we show how we can speed up WITCH. Our improvement includes replacing a critical step in WITCH (currently performed using a heuristic search) by a polynomial time exact algorithm using Smith-Waterman. Our new method, WITCH-NG (i.e. 'next generation WITCH') achieves the same accuracy but is substantially faster. WITCH-NG is available at https://github.com/RuneBlaze/WITCH-NG.

The datasets used in this study are from prior publications and are freely available in public repositories, as indicated in the Supplementary Materials.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.},
}

@article {pmid36970243,
year = {2023},
author = {Wang, L and Lin, C and Qi, Y},
title = {Gestational psittacosis causes severe pneumonia and miscarriage: A case report and literature review.},
journal = {Radiology case reports},
volume = {18},
number = {5},
pages = {1959-1962},
pmid = {36970243},
issn = {1930-0433},
abstract = {Psittacosis is an uncommon zoonotic illness, and gestational psittacosis is even rarer. The clinical signs and symptoms of psittacosis are varied, often overlooked, and swiftly identified by metagenomic next-generation sequencing. We recorded the case of a 41-year-old pregnant woman with psittacosis where the disease was not detected early on, resulting in severe pneumonia and fetal miscarriage. The clinical symptoms, diagnosis, and treatment of psittacosis in pregnancy are the subject of this case study.},
}

@article {pmid36969214,
year = {2023},
author = {Feng, R and Zhu, Q and Li, Q and Zhai, Y and Wang, J and Qin, C and Liang, D and Zhang, R and Tian, H and Liu, H and Chen, Y and Fu, Y and Wang, X and Ding, X},
title = {Microbiota-ear-brain interaction is associated with generalized anxiety disorder through activation of inflammatory cytokine responses.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1117726},
pmid = {36969214},
issn = {1664-3224},
abstract = {INTRODUCTION: Generalized anxiety disorder (GAD) is one of the most enduring anxiety disorders, being associated with increased systemic inflammation. However, the trigger and mechanisms underlying the activation of inflammatory cytokine responses in GAD remain poorly understood.

MATERIALS AND METHODS: We characterized the ear canal microbiome in GAD patients through 16S rRNA gene sequencing and metagenomic sequencing and identified the serum inflammatory markers in GAD patients. Spearman correlations were applied to test the relationship between the microbiota changes and systemic inflammation.

RESULTS: Our findings showed the higher microbial diversity, accompanied with the significantly increased abundance of Proteobacteria, and decreased abundance of Firmicutes in the ear canal of GAD participants compared to that of the age- and sex-matched healthy controls (HC). Metagenomic sequencing showed that Pseudomonas aeruginosa were significantly increased at species-level in GAD patients. Furthermore, we observed the relative abundance of Pseudomonas aeruginosa was positively associated with elevated systemic inflammatory markers and the severity of disease, suggesting that these ear canal microbiota alterations might be correlated with GAD by activating the inflammatory response.

CONCLUSIONS: These findings indicate that microbiota-ear-brain interaction via upregulating inflammatory reaction involve in the development of GAD, as well as suggest that ear canal bacterial communities may be a target for therapeutic intervention.},
}

@article {pmid36968950,
year = {2023},
author = {Brochu, E and Huletsky, A and Boudreau, DK and Raymond, F and Bérubé, È and Ouameur, AA and Frenette, J and Boissinot, M and Corbeil, J and Bergeron, MG},
title = {Characterization of vancomycin-resistance vanD gene clusters in the human intestinal microbiota by metagenomics and culture-enriched metagenomics.},
journal = {JAC-antimicrobial resistance},
volume = {5},
number = {2},
pages = {dlad026},
pmid = {36968950},
issn = {2632-1823},
abstract = {OBJECTIVES: To characterize vancomycin-resistance vanD gene clusters and potential vanD-carrying bacteria in the intestinal microbiota of healthy volunteers exposed or not to β-lactam antibiotics.

METHODS: Stool samples were collected before and after 7 days of cefprozil β-lactam antibiotic exposure of 18 participants and six control participants who were not exposed to the antibiotic at the same time points. Metagenomic sequencing and culture-enriched metagenomic sequencing (with and without β-lactam selection) were used to characterize vanD gene clusters and determine potential vanD-carrying bacteria. Alteration by antimicrobials was also examined.

RESULTS: Culture enrichment allowed detection of vanD genes in a large number of participants (11/24; 46%) compared to direct metagenomics (2/24; 8%). vanD genes were detected in stool cultures only following β-lactam exposure, either after β-lactam treatment of participants or after culture of stools with β-lactam selection. Six types of vanD gene clusters were identified. Two types of vanD cluster highly similar to those of enterococci were found in two participants. Other vanD genes or vanD clusters were nearly identical to those identified in commensal anaerobic bacteria of the families Lachnospiraceae and Oscillospiraceae and/or bordered by genomic sequences similar or related to these anaerobes, suggesting that they are the origin or carriers of vanD.

CONCLUSIONS: This study showed that culture-enriched metagenomics allowed detection of vanD genes not detected by direct metagenomics and revealed collateral enrichment of bacteria containing vancomycin-resistance vanD genes following exposure to β-lactams, with a higher prevalence of the most likely gut commensal anaerobes carrying vanD. These commensal anaerobes could be the reservoir of vanD genes carried by enterococci.},
}

@article {pmid36968356,
year = {2023},
author = {Zhang, M and Xiao, N and Yang, H and Li, Y and Gao, F and Li, J and Zhang, Z},
title = {The layout measures of micro-sprinkler irrigation under plastic film regulate tomato soil bacterial community and root system.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1136439},
pmid = {36968356},
issn = {1664-462X},
abstract = {INTRODUCTION: The change in rhizosphere soil bacterial community and root system under new water-saving device is not clear.

METHODS: A completely randomized experimental design was used to explore the effects of different micropore group spacing (L1: 30 cm micropore group spacing, L2: 50 cm micropore group spacing) and capillary arrangement density (C1: one pipe for one row, C2: one pipe for two rows, C3: one pipe for three rows) on tomato rhizosphere soil bacteria community, roots and tomato yield under MSPF. The bacteria in tomato rhizosphere soil were sequenced by 16S rRNA gene amplicon metagenomic sequencing technology, the interaction of bacterial community, root system and yield in tomato rhizosphere soil was quantitatively described based on regression analysis.

RESULTS: Results showed that L1 was not only beneficial to the development of tomato root morphology, but also promoted the ACE index of tomato soil bacterial community structure and the abundance of nitrogen and phosphorus metabolism functional genes. The yield and crop water use efficiency (WUE) of spring tomato and autumn tomato in L1 were about 14.15% and 11.27%, 12.64% and 10.35% higher than those in L2. With the decrease of capillary arrangement density, the diversity of bacterial community structure in tomato rhizosphere soil decreased, and the abundance of nitrogen and phosphorus metabolism functional genes of soil bacteria also decreased. The small abundance of soil bacterial functional genes limited the absorption of soil nutrients by tomato roots and roots morphological development. The yield and crop water use efficiency of spring and autumn tomato in C2 were significantly higher than those in C3 about 34.76% and 15.23%, 31.94% and 13.91%, respectively. The positive interaction between soil bacterial community and root morphological development of tomato was promoted by the capillary layout measures of MSPF.

DISCUSSION: The L1C2 treatment had a stable bacterial community structure and good root morphological development, which positively promoted the increase of tomato yield. The interaction between soil microorganisms and roots of tomato was regulated by optimizing the layout measures of MSPF to provide data support for water-saving and yield-increasing of tomato in Northwest China.},
}

@article {pmid36968018,
year = {2023},
author = {Muñoz-Barrera, A and Ciuffreda, L and Alcoba-Florez, J and Rubio-Rodríguez, LA and Rodríguez-Pérez, H and Gil-Campesino, H and García-Martínez de Artola, D and Salas-Hernández, J and Rodríguez-Núñez, J and Íñigo-Campos, A and García-Olivares, V and Díez-Gil, O and González-Montelongo, R and Valenzuela-Fernández, A and Lorenzo-Salazar, JM and Flores, C},
title = {Bioinformatic approaches to draft the viral genome sequence of Canary Islands cases related to the multicountry mpox virus 2022-outbreak.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {2197-2203},
pmid = {36968018},
issn = {2001-0370},
abstract = {On July 23, 2022, monkeypox disease (mpox) was declared a Public Emergency of International Concern (PHEIC) by the World Health Organization (WHO) due to a multicountry outbreak. In Europe, several cases of mpox virus (MPXV) infection related to this outbreak were detected in the Canary Islands (Spain). Here we describe the combination of viral DNA sequencing and bioinformatic approaches, including methods for de novo genome assembly and short- and long-read technologies, used to reconstruct the first MPXV genome isolated in the Canary Islands on the 31st of May 2022 from a male adult patient with mild symptoms. The same sequencing and bioinformatic approaches were then validated with three other positive cases of MPXV infection from the same mpox outbreak. We obtained the best results using a reference-based approach with short reads, evidencing 46-79 nucleotide variants against viral sequences from the 2018-2019 mpox outbreak and placing the viral sequences in the new B.1 sublineage of clade IIb of the MPXV classification. This study of MPXV demonstrates the potential of metagenomics sequencing for rapid and precise pathogen identification.},
}

@article {pmid36967692,
year = {2023},
author = {Niu, J and Kong, X and Li, Q and Zhang, Y and Yuan, J and Liu, J and Zhang, Y},
title = {Deciphering different effects of ZVI and NaOH on metabolic characteristics in the process of methanogenesis recovery from VFA suppression.},
journal = {Journal of environmental management},
volume = {336},
number = {},
pages = {117686},
doi = {10.1016/j.jenvman.2023.117686},
pmid = {36967692},
issn = {1095-8630},
abstract = {Dosing zero valent iron (ZVI) or sodium hydroxide (NaOH) is the common method of addressing acidification in anaerobic digestion (AD) systems; however, few studies have discussed and compared their effects on microbial metabolism. In the present study, microbial syntrophy and metabolic pathways under ZVI and NaOH regulation are comparatively analyzed through microbial network analysis and metagenomic/metaproteomic analyses. CH4 yield in the ZVI reactor was 414 mL/gVS, an increase of 23% when compared with that in the reactor with NaOH dosing (336 mL/gVS). The methanogenesis recovery period in the ZVI reactor (37 days) was shorter than that in the NaOH reactor (48 days). Co-occurrence networks indicated that ZVI promoted Methanoculleus and Methanosarcina to establish a complex syntrophic association with SAO bacteria (Syntrophaceticus and Aminobacterium) and syntrophic acetogens (Syntrophomonas), strengthening SAO-hydrogenotrophic methanogenesis (HM) and acetoclastic methanogenesis (AM) pathways simultaneously. Metagenomic analysis showed that the relative abundance of mcrA and fwdB in the ZVI reactor was higher 27% than that in the NaOH reactor. Furthermore, through metaproteomics analysis, much more enzymes related to glucose degradation, bioconversion of butyric acid and pyruvate, conversion of formate and acetate to CO2, and production of CH4 from acetate and CO2 were significantly upregulated under ZVI regulation than under NaOH regulation (fold change relative to control [FC] > 1.5, p < 0.05). The results of the present study enhance our understanding of methanogenic mechanisms under the regulation of ZVI, providing a theoretical basis for its practical application in AD systems experiencing VFA suppression.},
}

@article {pmid36967247,
year = {2023},
author = {O'Connor, L and Heyderman, R},
title = {The challenges of defining the human nasopharyngeal resistome.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2023.02.008},
pmid = {36967247},
issn = {1878-4380},
abstract = {The nasopharynx is an important microbial reservoir for the emergence and spread of antibiotic-resistant organisms. The nasopharyngeal resistome is an extensive, adaptable reservoir of antibiotic-resistance genes (ARGs) within this niche. Metagenomic sequencing decodes the genetic material of all organisms within a sample using next-generation technologies, permitting unbiased discovery of novel ARGs and associated mobile genetic elements (MGEs). The challenges of sequencing a low-biomass bacterial sample have limited exploration of the nasopharyngeal resistome. Here, we explore the current understanding of the nasopharyngeal resistome, particularly the role of MGEs in propagating antimicrobial resistance (AMR), explore the advantages and limitations of metagenomic sequencing technologies and bioinformatic pipelines for nasopharyngeal resistome analysis, and highlight the key outstanding questions for future research.},
}

@article {pmid36967003,
year = {2023},
author = {Li, J and Xu, X and Chen, C and Xu, L and Du, Z and Gu, L and Xiang, P and Shi, D and Huangfu, X and Liu, F},
title = {Conductive materials enhance microbial salt-tolerance in anaerobic digestion of food waste: Microbial response and metagenomics analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {115779},
doi = {10.1016/j.envres.2023.115779},
pmid = {36967003},
issn = {1096-0953},
abstract = {Previous studies have shown that high salinity environments can inhibit anaerobic digestion (AD) of food waste (FW). Finding ways to alleviate salt inhibition is important for the disposal of the growing amount of FW. We selected three common conductive materials (powdered activated carbon, magnetite, and graphite) to understand their performance and individual mechanisms that relieve salinity inhibition. Digester performances and related enzyme parameters were compared. Our data revealed that under normal and low salinity stress conditions, the anaerobic digester ran steady without significant inhibitions. Further, the presence of conductive materials promoted conversion rate of methanogenesis. This promotion effect was highest from magnetite > powdered activated carbon (PAC) > graphite. At 1.5% salinity, PAC and magnetite are beneficial in maintaining high methane production efficiency while control and the graphite added digester acidified and failed rapidly. Additionally, metagenomics and binning were used to analyze the metabolic capacity of the microorganisms. Some species enriched by PAC and magnetite possessed higher cation transport capacities and were to accumulate compatible solutes. PAC and magnetite promoted direct interspecies electron transference (DIET) and syntrophic oxidation of butyrate and propionate. Also, the microorganisms had more energy available to cope with salt inhibition in the PAC and magnetite added digesters. Our data imply that the promotion of Na+/H+ antiporter, K+ uptake, and osmoprotectant synthesis or transport by conductive materials may be crucial for their proliferation in highly stressful environments. These findings will help to understand the mechanisms of alleviate salt inhibition by conductive materials and help to recover methane from high-salinity FW.},
}

@article {pmid36966989,
year = {2023},
author = {Chen, Z and Song, B and Guo, H and Xia, D and Cai, Y and Wang, Y and Zhao, W},
title = {Metagenomic characterization of biomethane transformation by lipid-catalyzed anaerobic fermentation of lignite.},
journal = {Environmental research},
volume = {},
number = {},
pages = {115777},
doi = {10.1016/j.envres.2023.115777},
pmid = {36966989},
issn = {1096-0953},
abstract = {The present study aims at using lipid in a novel way to improve the efficiency of methane production from lignite anaerobic digestion. The obtained results showed an increase by 3.13 times of the cumulative biomethane content of lignite anaerobic fermentation, when 1.8 g lipid was added. The gene expression of functional metabolic enzymes was also found to be enhanced during the anaerobic fermentation. Moreover, the enzymes related to fatty acid degradation such as long-chain Acyl-CoA synthetase and Acyl-CoA dehydrogenase were increased by 1.72 and 10.48 times, respectively, which consequently, accelerated the conversion of fatty acid. Furthermore, the addition of lipid enhanced the carbon dioxide trophic and acetic acid trophic metabolic pathways. Hence, the addition of lipids was argued to promote the production of methane from lignite anaerobic fermentation, which provided a new insight for the conversion and utilization of lipid waste.},
}

@article {pmid36966826,
year = {2023},
author = {Zhao, Z and Yu, C and Yang, C and Gao, B and Jiménez, N and Wang, C and Li, F and Ao, Y and Zheng, L and Huang, F and Tomberlin, JK and Ren, Z and Yu, Z and Zhang, J and Cai, M},
title = {Mitigation of antibiotic resistome in swine manure by black soldier fly larval conversion combined with composting.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {163065},
doi = {10.1016/j.scitotenv.2023.163065},
pmid = {36966826},
issn = {1879-1026},
abstract = {The increasing prevalence of antibiotic resistance genes (ARGs) in animal manure has attracted considerable attention because of their potential contribution to the development of multidrug resistance worldwide. Insect technology may be a promising alternative for the rapid attenuation of ARGs in manure; however, the underlying mechanism remains unclear. This study aimed to evaluate the effects of black soldier fly (BSF, Hermetia illucens [L.]) larvae conversion combined with composting on ARGs dynamics in swine manure and to uncover the mechanisms through metagenomic analysis. Compared to natural composting (i.e. without BSF), BSFL conversion combined with composting reduced the absolute abundance of ARGs by 93.2 % within 28 days. The rapid degradation of antibiotics and nutrient reformulation during BSFL conversion combined with composting indirectly altered manure bacterial communities, resulting in a lower abundance and richness of ARGs. The number of main antibiotic-resistant bacteria (e.g., Prevotella, Ruminococcus) decreased by 74.9 %, while their potential antagonistic bacteria (e.g., Bacillus, Pseudomonas) increased by 128.7 %. The number of antibiotic-resistant pathogenic bacteria (e.g., Selenomonas, Paenalcaligenes) decreased by 88.3 %, and the average number of ARGs carried by each human pathogenic bacterial genus declined by 55.8 %. BSF larvae gut microbiota (e.g., Clostridium butyricum, C. bornimense) could help reduce the risk of multidrug-resistant pathogens. These results provide insight into a novel approach to mitigate multidrug resistance from the animal industry in the environment by using insect technology combined with composting, in particular in light of the global "One Health" requirements.},
}

@article {pmid36966821,
year = {2023},
author = {Zhang, H and Gong, W and Xue, Y and Zeng, W and Wang, H and Wang, J and Tang, X and Li, G and Liang, H},
title = {Municipal wastewater contains antibiotic treatment using O2 transfer membrane based biofilm reactor: Interaction between regular pollutants metabolism and sulfamethoxazole degradation.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {163060},
doi = {10.1016/j.scitotenv.2023.163060},
pmid = {36966821},
issn = {1879-1026},
abstract = {The antibiotic sulfamethoxazole (SMX) is frequently detected in wastewater treatment plant effluents and has attracted significant attention owing to its significant potential environmental effects. We present a novel O2 transfer membrane based biofilm reactor (O2TM-BR) to treat municipal wastewater to eliminate containing SMX. Furthermore, conducting metagenomics analyses, the interactions in biodegradation process between SMX and regular pollutants (NH4[+]-N and COD) were studied. Results suggest that O2TM-BR yields evident advantages in SMX degradation. Increasing SMX concentrations did not affect the efficiency of the system, and the effluent concentration remained consistent at approximately 17.0 μg/L. The interaction experiment showed that heterotrophic bacteria tend to consume easily degradable COD for metabolism, resulting in a delay (>36 h) in complete SMX degradation, which is 3-times longer than without COD. It is worth noting that the taxonomic and functional structure and composition in nitrogen metabolism were significantly shifted upon the SMX. NH4[+]-N removal remained unaffected by SMX in O2TM-BR, and the expression of K10944 and K10535 has no significant difference under the stress of SMX (P > 0.02). However, the K00376 and K02567 required in the nitrate reductase is inhibited by SMX (P < 0.01), which hinders the reduction of NO3[-]-N and hence the accumulation of TN. This study provides a new method for SMX treatment and reveals the interaction between SMX and conventional pollutants in O2TM-BR as well as the microbial community function and assembly mechanism.},
}

@article {pmid36966280,
year = {2023},
author = {Zhao, Y and Yi, J and Xiang, J and Jia, W and Chen, A and Chen, L and Zheng, L and Zhou, W and Wu, M and Yu, Z and Tang, J},
title = {Exploration of lung mycobiome in the patients with non-small-cell lung cancer.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {81},
pmid = {36966280},
issn = {1471-2180},
abstract = {As the Human Microbiome Project (HMP) progresses, the relationship between microbes and human health has been receiving increasing attention. A growing number of reports support the correlation between cancer and microbes. However, most studies have focused on bacteria, rather than fungal communities. In this study, we studied the alteration in lung mycobiome in patients with non-small-cell lung cancer (NSCLC) using metagenomic sequencing and qPCR. The higher fungal diversity and more complex network were observed in the patients with NSCLC. In addition, Alternaria arborescens was found as the most relevant fungus to NSCLC, and the enrichment of it in cancerous tissue was also detected. This study proposes that the changes in fungal communities may be closely related to lung cancer, and provides insights into further exploration the relationship between lung cancer and fungi.},
}

@article {pmid36966258,
year = {2023},
author = {Deng, L and Li, Q and Hu, W and Chen, X and Chen, T and Song, S and Mo, P and Zou, S and Zhang, Y and Gao, S and Chen, L and Zhuang, K and Yang, R and Xiong, Y},
title = {Metagenomic next-generation sequencing versus traditional laboratory methods for the diagnosis of central nervous system opportunistic infections in HIV-infected Chinese adults.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {4921},
pmid = {36966258},
issn = {2045-2322},
abstract = {To evaluate clinical value of metagenomic next-generation sequencing (mNGS) in people living with HIV/AIDS (PLWHA) who had CNS disorders. Cerebrospinal fluid (CSF) samples from 48 PLWHA presenting with CNS disorders were sequenced using mNGS and compared with clinical conventional diagnostic methods. In total, 36/48 ss(75%) patients were diagnosed with pathogen(s) infection by mNGS, and the positive detection proportion by mNGS was higher than that by clinical conventional diagnostic methods (75% vs 52.1%, X[2] = 5.441, P = 0.020). Thirteen out of 48 patients (27.1%) were detected with 3-7 pathogens by mNGS. Moreover, 77 pathogen strains were detected, of which 94.8% (73/77) by mNGS and 37.0% (30/77) by clinical conventional methods (X[2] = 54.206, P < 0.001). The sensitivity and specificity of pathogens detection by mNGS were 63.9% (23/36) and 66.7% (8/12), respectively, which were superior to that by clinical conventional methods (23/36 vs 9/25, X[2] = 4.601, P = 0.032; 8/12 vs 5/23, X[2] = 5.029, P = 0.009). The application of mNGS was superior for its ability to detect a variety of unknown pathogens and multiple pathogens infection, and relatively higher sensitivity and specificity in diagnosis of CNS disorders in PLWHA.},
}

@article {pmid36966231,
year = {2023},
author = {Berglund, F and Ebmeyer, S and Kristiansson, E and Larsson, DGJ},
title = {Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge.},
journal = {Communications biology},
volume = {6},
number = {1},
pages = {321},
pmid = {36966231},
issn = {2399-3642},
abstract = {The emergence and spread of mobile antibiotic resistance genes (ARGs) in pathogens have become a serious threat to global health. Still little is known about where ARGs gain mobility in the first place. Here, we aimed to collect evidence indicating where such initial mobilization events of clinically relevant ARGs may have occurred. We found that the majority of previously identified origin species did not carry the mobilizing elements that likely enabled intracellular mobility of the ARGs, suggesting a necessary interplay between different bacteria. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements. Most origin species were only occasionally detected in other environments. Co-occurrence of origin species and corresponding mobilizing elements were rare in human microbiota. Our results identify wastewaters and wastewater-impacted environments as plausible arenas for the initial mobilization of resistance genes.},
}

@article {pmid36966151,
year = {2023},
author = {Lin, X and Hu, T and Chen, J and Liang, H and Zhou, J and Wu, Z and Ye, C and Jin, X and Xu, X and Zhang, W and Jing, X and Yang, T and Wang, J and Yang, H and Kristiansen, K and Xiao, L and Zou, Y},
title = {The genomic landscape of reference genomes of cultivated human gut bacteria.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1663},
pmid = {36966151},
issn = {2041-1723},
abstract = {Culture-independent metagenomic studies have revolutionized our understanding of the gut microbiota. However, the lack of full genomes from cultured species is still a limitation for in-depth studies of the gut microbiota. Here we present a substantially expanded version of our Cultivated Genome Reference (CGR), termed CGR2, providing 3324 high-quality draft genomes from isolates selected from a large-scale cultivation of bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (179 previously unidentified species) from 8 phyla, and uncovers a genomic and functional diversity of Collinsella aerofaciens. The CGR2 genomes match 126 metagenome-assembled genomes without cultured representatives in the Unified Human Gastrointestinal Genome (UHGG) collection and harbor 3767 unidentified secondary metabolite biosynthetic gene clusters, providing a source of natural compounds with pharmaceutical potentials. We uncover accurate phage-bacterium linkages providing information on the evolutionary characteristics of interaction between bacteriophages and bacteria at the strain level.},
}

@article {pmid36965360,
year = {2023},
author = {Li, Z and Qing, Y and Cui, G and Li, M and Liu, T and Zeng, Y and Zhou, C and Hu, X and Jiang, J and Wang, D and Gao, Y and Zhang, J and Cai, C and Wang, T and Wan, C},
title = {Shotgun metagenomics reveals abnormal short-chain fatty acid-producing bacteria and glucose and lipid metabolism of the gut microbiota in patients with schizophrenia.},
journal = {Schizophrenia research},
volume = {255},
number = {},
pages = {59-66},
doi = {10.1016/j.schres.2023.03.005},
pmid = {36965360},
issn = {1573-2509},
abstract = {Evidence has shown that the gut microbiota is closely related to the pathogenesis of schizophrenia, but temporal changes in the gut microbiota of patients with schizophrenia (SZ) during treatment remain unclear. Here, to evaluate temporal changes in the gut microbiota in schizophrenia, we performed whole-genome shotgun metagenomics on fecal samples from 36 healthy controls (HCs) and 19 baseline-period patients, and followed up with patients upon treatment. Compared to that in HCs, beta diversity in SZ was significantly distinct. The genera Bacteroides, Prevotella and Clostridium were the top 3 altered genera between SZ and HCs, and the Bacteroides-Prevotella ratio was significantly increased in SZ. Thirty-three percent of differentially abundant species were short-chain fatty acid (SCFA)-producing bacteria. Functional analysis showed that glucose and lipid metabolism of the gut microbiota was decreased in SZ compared with those in HCs. The abundances of two rate-limiting enzymes in glucose and lipid metabolism, phosphofructokinase (PFK) and acetyl-CoA carboxylase (ACC), were significantly decreased in SZ, and differentially abundant metabolism-related enzymes were significantly associated with SCFA-producing bacteria. Next, we found that the abundance of SCFA-producing bacteria also changed after treatment and that Clostridium was significantly negatively correlated with the total positive and negative syndrome scale (PANSS) score in patients. Functional analysis showed that glycoside hydrolase family 30 incrementally increased in abundance during treatment and were significantly associated with SCFA-producing bacteria. Our findings help to provide evidence for the role of gut microbiota in the occurrence and development of schizophrenia.},
}

@article {pmid36965294,
year = {2023},
author = {Hu, P and Qian, Y and Liu, J and Gao, L and Li, Y and Xu, Y and Wu, J and Hong, Y and Ford, T and Radian, A and Yang, Y and Gu, JD},
title = {Delineation of the complex microbial nitrogen-transformation network in an anammox-driven full-scale wastewater treatment plant.},
journal = {Water research},
volume = {235},
number = {},
pages = {119799},
doi = {10.1016/j.watres.2023.119799},
pmid = {36965294},
issn = {1879-2448},
abstract = {Microbial-driven nitrogen removal is a crucial step in modern full-scale wastewater treatment plants (WWTPs), and the complexity of nitrogen transformation is integral to the various wastewater treatment processes. A full understanding of the overall nitrogen cycling networks in WWTPs is therefore a prerequisite for the further enhancement and optimization of wastewater treatment processes. In this study, metagenomics and metatranscriptomics were used to elucidate the microbial nitrogen removal processes in an ammonium-enriched full-scale WWTP, which was configured as an anaerobic-anoxic-anaerobic-oxic system for efficient nitrogen removal (99.63%) on a duck breeding farm. A typical simultaneous nitrification-anammox-denitrification (SNAD) process was established in each tank of this WWTP. Ammonia was oxidized by ammonia-oxidizing bacteria (AOB), archaea (AOA), and nitrite-oxidizing bacteria (NOB), and the produced nitrite and nitrate were further reduced to dinitrogen gas (N2) by anammox and denitrifying bacteria. Visible red anammox biofilms were formed successfully on the sponge carriers submerged in the anoxic tank, and the nitrogen removal rate by anammox reaction was 4.85 times higher than that by denitrification based on [15]N isotope labeling and analysis. This supports the significant accumulation of anammox bacteria on the carriers responsible for efficient nitrogen removal. Two distinct anammox bacteria, named "Ca. Brocadia sp. PF01" and "Ca. Jettenia sp. PF02", were identified from the biofilm in this investigation. By recovering their genomic features and their metabolic capabilities, our results indicate that the highly active core anammox process found in PF01, suggests extending its niche within the plant. With the possible contribution of the dissimilatory nitrate reduction to ammonium (DNRA) reaction, enriching PF02 within the biofilm may also be warranted. Collectively, this study highlights the effective design strategies of a full-scale WWTP with enrichment of anammox bacteria on the carrier materials for nitrogen removal and therefore the biochemical reaction mechanisms of the contributing members.},
}

@article {pmid36965279,
year = {2023},
author = {Viver, T and Conrad, RE and Lucio, M and Harir, M and Urdiain, M and Gago, JF and Suárez-Suárez, A and Bustos-Caparros, E and Sanchez-Martinez, R and Mayol, E and Fassetta, F and Pang, J and Mădălin Gridan, I and Venter, S and Santos, F and Baxter, B and Llames, ME and Cristea, A and Banciu, HL and Hedlund, BP and Stott, MB and Kämpfer, P and Amann, R and Schmitt-Kopplin, P and Konstantinidis, KT and Rossello-Mora, R},
title = {Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov.},
journal = {Systematic and applied microbiology},
volume = {46},
number = {3},
pages = {126416},
doi = {10.1016/j.syapm.2023.126416},
pmid = {36965279},
issn = {1618-0984},
abstract = {Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31[T], respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31[T], respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.},
}

@article {pmid36965198,
year = {2023},
author = {Ceylani, T and Allahverdi, H and Teker, HT},
title = {Role of age-related plasma in the diversity of gut bacteria.},
journal = {Archives of gerontology and geriatrics},
volume = {111},
number = {},
pages = {105003},
doi = {10.1016/j.archger.2023.105003},
pmid = {36965198},
issn = {1872-6976},
abstract = {Recent studies have demonstrated the efficacy of young blood plasma factors in reversing aging-related deformities. However, the impact of plasma exchange between young and old individuals on gut microbiota remains understudied. To investigate this, we evaluated the effects of plasma exchange between 5-week-old and 24-month-old rats on gut microbiota composition. In this study, old rats were administered 0.5 ml of young plasma, while young rats were administered 0.25 ml of old plasma daily for 30 days. Metagenome analysis was performed on the contents of the cecum after completing plasma transfer. Results showed that transferring young plasma to old rats significantly increased the alpha diversity indices (Shannon and Simpson values), while the Firmicutes to Bacteroidetes ratio decreased significantly. Conversely, transferring aged plasma to young rats led to a significant decrease in Shannon value and F/B ratio but no change in Simpson value. Plasma exchange also caused substantial changes in the top ten dominant genera and species found in the gut microbiota of young and old rats. After young blood plasma transfer, the dominant bacterial profile in the old gut microbiota shifted toward the bacterial profile found in the young control group. Notably, old plasma also altered the gut microbiota structure of young rats toward that of old rats. Our findings suggest that age-related changes in plasma play a crucial role in gut microbiota species diversity and their presence rates.},
}

@article {pmid36964623,
year = {2023},
author = {Manabe, Y and Ishibashi, T and Asano, R and Tonomura, S and Maeda, Y and Motooka, D and Ueda, J and Yanagawa, M and Edamoto-Taira, Y and Chikaishi-Kirino, T and Masaki, T and Inagaki, T and Nakamura, S and Katada, Y and Okazawa, M and Narazaki, M and Ogo, T and Kumanogoh, A and Nakaoka, Y},
title = {Gut dysbiosis is associated with aortic aneurysm formation and progression in Takayasu arteritis.},
journal = {Arthritis research & therapy},
volume = {25},
number = {1},
pages = {46},
pmid = {36964623},
issn = {1478-6362},
abstract = {BACKGROUND: Takayasu arteritis (TAK) is an autoimmune large vessel vasculitis that affects the aorta and its major branches, eventually leading to the development of aortic aneurysm and vascular stenosis or occlusion. This retrospective and prospective study aimed to investigate whether the gut dysbiosis exists in patients with TAK and to identify specific gut microorganisms related to aortic aneurysm formation/progression in TAK.

METHODS: We analysed the faecal microbiome of 76 patients with TAK and 56 healthy controls (HCs) using 16S ribosomal RNA sequencing. We examined the relationship between the composition of the gut microbiota and clinical parameters.

RESULTS: The patients with TAK showed an altered gut microbiota with a higher abundance of oral-derived bacteria, such as Streptococcus and Campylobacter, regardless of the disease activity, than HCs. This increase was significantly associated with the administration of a proton pump inhibitor used for preventing gastric ulcers in patients treated with aspirin and glucocorticoids. Among patients taking a proton pump inhibitor, Campylobacter was more frequently detected in those who underwent vascular surgeries and endovascular therapy for aortic dilatation than in those who did not. Among the genus of Campylobacter, Campylobacter gracilis in the gut microbiome was significantly associated with clinical events related to aortic aneurysm formation/worsening in patients with TAK. In a prospective analysis, patients with a gut microbiome positive for Campylobacter were significantly more likely to require interventions for aortic dilatation than those who were negative for Campylobacter. Furthermore, patients with TAK who were positive for C. gracilis by polymerase chain reaction showed a tendency to have severe aortic aneurysms.

CONCLUSIONS: A specific increase in oral-derived Campylobacter in the gut may be a novel predictor of aortic aneurysm formation/progression in patients with TAK.},
}

@article {pmid36964199,
year = {2023},
author = {Kavagutti, VS and Chiriac, MC and Ghai, R and Salcher, MM and Haber, M},
title = {Isolation of phages infecting the abundant freshwater Actinobacteriota order 'Ca. Nanopelagicales'.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {36964199},
issn = {1751-7370},
abstract = {Low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of 'Ca. Nanopelagicales' we isolated a novel species of its genus 'Ca. Planktophila'. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host's metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting 'Ca. Nanopelagicales'. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.},
}

@article {pmid36964154,
year = {2023},
author = {Zimmermann, HH and Stoof-Leichsenring, KR and Dinkel, V and Harms, L and Schulte, L and Hütt, MT and Nürnberg, D and Tiedemann, R and Herzschuh, U},
title = {Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1650},
pmid = {36964154},
issn = {2041-1723},
abstract = {Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.},
}

@article {pmid36963658,
year = {2023},
author = {Xing, X and Liu, Q and Yuan, W and Zhu, C and Yang, J},
title = {Pulmonary scedosporiosis caused by Lomentospora prolificans in an immunocompetent patient: a rare case report.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijid.2023.03.037},
pmid = {36963658},
issn = {1878-3511},
abstract = {Infections with Scedosporium and Lomentospora species are usually found in immunodeficient patients, particularly in the transplant population. However, they are relatively rare in immunocompetent patients, which is especially useful in ruling out near-drowning and aspiration situations. Here, we report a case of an immunocompetent patient with clinically suspected community-acquired pneumonia caused by Lomentospora prolificans detected by metagenomics next-generation sequencing (mNGS) and polymerase chain reaction from bronchoalveolar lavage fluid. This case highlights mNGS in the clinical diagnosis of pulmonary invasive fungal disease. mNGS is proposed as an important adjunctive diagnostic approach for rare pathogens.},
}

@article {pmid36963586,
year = {2023},
author = {Dahiya, S and Mohan, SV},
title = {Co-fermenting lactic acid and glucose towards caproic acid production.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {138491},
doi = {10.1016/j.chemosphere.2023.138491},
pmid = {36963586},
issn = {1879-1298},
abstract = {The functional role of lactate (HLac), as a co-substrate along with glucose (Glu) as well as an electron donor for the synthesis of caproic acid (HCa) a medium chain fatty acids (MCFAs) was studied. A varied HLac and Glu ratios were thus investigated in fed-batch anaerobic reactors (R1-R5) operating at pH 6 with a heat-treated anaerobic consortium. R1 and R5 were noted as controls and operated with sole Glu and HLac, respectively. Strategically, ethanol (HEth) was additionally supplemented as co-electron donor after the production of short chain carboxylic acids (SCCAs) for chain elongation in all the reactors. The reactor operated with HLac and Glu in a ratio of 0.25:0.75 (1.25 g/L (HLac) and 3.75 g/L (Glu)) showed the highest HCa production of 1.86 g/L. R5 operated with solely HLac yielded propionic acid (HPr) as the major product which further led to the higher valeric acid (HVa) production of 1.1 g/L within the reactor. Butyric acid (HBu) was observed in R1, which used Glu as carbon source alone indicating the importance of HLac as electron co-donor. Clostridium observed as the most dominant genera in shotgun metagenome sequencing in R2 and R3, the reactors that produced the highest HCa in comparison to other studied reactors. The study thus provided insight into the importance of substrate and electron donor and their supplementation strategies during the production of MCFAs.},
}

@article {pmid36963164,
year = {2023},
author = {Beliaeva, MA and Wilmanns, M and Zimmermann, M},
title = {Decipher enzymes from human microbiota for drug discovery and development.},
journal = {Current opinion in structural biology},
volume = {80},
number = {},
pages = {102567},
doi = {10.1016/j.sbi.2023.102567},
pmid = {36963164},
issn = {1879-033X},
abstract = {The human microbiota plays an important role in human health and contributes to the metabolism of therapeutic drugs affecting their potency. However, the current knowledge on human gut bacterial metabolism is limited and lacks an understanding of the underlying mechanisms of observed drug biotransformations. Despite the complexity of the gut microbial community, genomic and metagenomic sequencing provides insights into the diversity of chemical reactions that can be carried out by the microbiota and poses new challenges to functionally annotate thousands of bacterial enzymes. Here, we outline methods to systematically address the structural and functional space of the human microbiome, highlighting a combination of in silico and in vitro approaches. Systematic knowledge about microbial enzymes could eventually be applied for personalized therapy, the development of prodrugs and modulators of unwanted bacterial activity, and the further discovery of new antibiotics.},
}

@article {pmid36962260,
year = {2022},
author = {Muthanje, EM and Kimita, G and Nyataya, J and Njue, W and Mulili, C and Mugweru, J and Mutai, B and Kituyi, SN and Waitumbi, J},
title = {March 2019 dengue fever outbreak at the Kenyan south coast involving dengue virus serotype 3, genotypes III and V.},
journal = {PLOS global public health},
volume = {2},
number = {3},
pages = {e0000122},
pmid = {36962260},
issn = {2767-3375},
abstract = {The first description of a disease resembling dengue fever (DF) was in the 15th century slave trade era by Spanish sailors visiting the Tanzania coast. The disease, then associated with evil spirits is now known to be caused by four serotypes of dengue virus (DENV1-4) that are transmitted by Aedes mosquitoes. Kenya has experienced multiple outbreaks, mostly associated with DENV-2. In this study, plasma samples obtained from 37 febrile patients during a DF outbreak at Kenya's south coast in March 2019 were screened for DENV. Total RNA was extracted and screened for the alpha- and flavi-viruses by real-time polymerase chain reaction (qPCR). DENV-3 was the only virus detected. Shotgun metagenomics and targeted sequencing were used to obtain DENV whole genomes and the complete envelope genes (E gene) respectively. Sequences were used to infer phylogenies and time-scaled genealogies. Following Maximum likelihood and Bayesian phylogenetic analysis, two DENV-3 genotypes (III, n = 15 and V, n = 2) were found. We determined that the two genotypes had been in circulation since 2015, and that both had been introduced independently. Genotype III's origin was estimated to have been from Pakistan. Although the origin of genotype V could not be ascertained due to rarity of these sequences globally, it was most related to a 2006 Brazilian isolate. Unlike genotype III that has been described in East and West Africa multiple times, this was the second description of genotype V in Kenya. Of note, there was marked amino acid variances in the E gene between study samples and the Thailand DENV-3 strain used in the approved Dengvaxia vaccine. It remains to be seen whether these variances negatively impact the efficacy of the Dengvaxia or future vaccines.},
}

@article {pmid36961862,
year = {2023},
author = {Yan, W and Zhu, Y and Liu, W and Zou, C and Jia, B and Chen, ZQ and Han, Y and Wu, J and Yang, DL and Zhang, Z and Xie, L and Chen, B and Li, R and Ding, SW and Wu, Q and Guo, Z},
title = {Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing.},
journal = {PLoS pathogens},
volume = {19},
number = {3},
pages = {e1011238},
doi = {10.1371/journal.ppat.1011238},
pmid = {36961862},
issn = {1553-7374},
abstract = {A major threat to rice production is the disease epidemics caused by insect-borne viruses that emerge and re-emerge with undefined origins. It is well known that some human viruses have zoonotic origins from wild animals. However, it remains unknown whether native plants host uncharacterized endemic viruses with spillover potential to rice (Oryza sativa) as emerging pathogens. Here, we discovered rice tiller inhibition virus (RTIV), a novel RNA virus species, from colonies of Asian wild rice (O. rufipogon) in a genetic reserve by metagenomic sequencing. We identified the specific aphid vector that is able to transmit RTIV and found that RTIV would cause low-tillering disease in rice cultivar after transmission. We further demonstrated that an infectious molecular clone of RTIV initiated systemic infection and causes low-tillering disease in an elite rice variety after Agrobacterium-mediated inoculation or stable plant transformation, and RTIV can also be transmitted from transgenic rice plant through its aphid vector to cause disease. Finally, global transcriptome analysis indicated that RTIV may disturb defense and tillering pathway to cause low tillering disease in rice cultivar. Thus, our results show that new rice viral pathogens can emerge from native habitats, and RTIV, a rare aphid-transmitted rice viral pathogen from native wild rice, can threaten the production of rice cultivar after spillover.},
}

@article {pmid36961286,
year = {2023},
author = {López-Islas, JJ and Méndez-Olvera, ET and Reyes C, T and Martínez-Gómez, D},
title = {Identification of antimicrobial resistance genes in intestinal content from Coyote (Canis latrans).},
journal = {Polish journal of veterinary sciences},
volume = {26},
number = {1},
pages = {143-149},
doi = {10.24425/pjvs.2023.145016},
pmid = {36961286},
issn = {2300-2557},
abstract = {Antibiotic resistance has become a global public health concern in the last few years. Given the widespread rate of recurrence, increasing attention is being turned toward environmental pathways that potentially contribute to antibiotic resistance genes (ARGs) dissemination outside the clinical realm. In this study, a metagenome analysis of intestinal virus-like particle fraction (VLPs) from a wild coyote (Canis latrans) revealed for the first time, multiple ARGs, such as B-lactamases and multidrug efflux pumps. Description of ARGs presence in natural environments is critical to understand the emergence of resistant strains.},
}

@article {pmid36960290,
year = {2023},
author = {Marini, S and Boucher, C and Noyes, N and Prosperi, M},
title = {The K-mer antibiotic resistance gene variant analyzer (KARGVA).},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1060891},
pmid = {36960290},
issn = {1664-302X},
abstract = {Characterization of antibiotic resistance genes (ARGs) from high-throughput sequencing data of metagenomics and cultured bacterial samples is a challenging task, with the need to account for both computational (e.g., string algorithms) and biological (e.g., gene transfers, rearrangements) aspects. Curated ARG databases exist together with assorted ARG classification approaches (e.g., database alignment, machine learning). Besides ARGs that naturally occur in bacterial strains or are acquired through mobile elements, there are chromosomal genes that can render a bacterium resistant to antibiotics through point mutations, i.e., ARG variants (ARGVs). While ARG repositories also collect ARGVs, there are only a few tools that are able to identify ARGVs from metagenomics and high throughput sequencing data, with a number of limitations (e.g., pre-assembly, a posteriori verification of mutations, or specification of species). In this work we present the k-mer, i.e., strings of fixed length k, ARGV analyzer - KARGVA - an open-source, multi-platform tool that provides: (i) an ad hoc, large ARGV database derived from multiple sources; (ii) input capability for various types of high-throughput sequencing data; (iii) a three-way, hash-based, k-mer search setup to process data efficiently, linking k-mers to ARGVs, k-mers to point mutations, and ARGVs to k-mers, respectively; (iv) a statistical filter on sequence classification to reduce type I and II errors. On semi-synthetic data, KARGVA provides very high accuracy even in presence of high sequencing errors or mutations (99.2 and 86.6% accuracy within 1 and 5% base change rates, respectively), and genome rearrangements (98.2% accuracy), with robust performance on ad hoc false positive sets. On data from the worldwide MetaSUB consortium, comprising 3,700+ metagenomics experiments, KARGVA identifies more ARGVs than Resistance Gene Identifier (4.8x) and PointFinder (6.8x), yet all predictions are below the expected false positive estimates. The prevalence of ARGVs is correlated to ARGs but ecological characteristics do not explain well ARGV variance. KARGVA is publicly available at https://github.com/DataIntellSystLab/KARGVA under MIT license.},
}

@article {pmid36960043,
year = {2023},
author = {Lin, T},
title = {Editorial: New techniques in microbiome research.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1158392},
doi = {10.3389/fcimb.2023.1158392},
pmid = {36960043},
issn = {2235-2988},
}

@article {pmid36959975,
year = {2023},
author = {Baltoumas, FA and Karatzas, E and Paez-Espino, D and Venetsianou, NK and Aplakidou, E and Oulas, A and Finn, RD and Ovchinnikov, S and Pafilis, E and Kyrpides, NC and Pavlopoulos, GA},
title = {Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.},
journal = {Frontiers in bioinformatics},
volume = {3},
number = {},
pages = {1157956},
pmid = {36959975},
issn = {2673-7647},
abstract = {Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.},
}

@article {pmid36959686,
year = {2023},
author = {Yang, Y and Han, Z and Gao, Z and Chen, J and Song, C and Xu, J and Wang, H and Huang, A and Shi, J and Gu, J},
title = {Metagenomic and targeted metabolomic analyses reveal distinct phenotypes of the gut microbiota in patients with colorectal cancer and type 2 diabetes mellitus.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {36959686},
issn = {2542-5641},
abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is an independent risk factor for colorectal cancer (CRC), and the patients with CRC and T2DM have worse survival. The human gut microbiota (GM) is linked to the development of CRC and T2DM, respectively. However, the GM characteristics in patients with CRC and T2DM remain unclear.

METHODS: We performed fecal metagenomic and targeted metabolomics studies on 36 samples from CRC patients with T2DM (DCRC group, n = 12), CRC patients without diabetes (CRC group, n = 12), and healthy controls (Health group, n = 12). We analyzed the fecal microbiomes, characterized the composition and function based on the metagenomics of DCRC patients, and detected the short-chain fatty acids (SCFAs) and bile acids (BAs) levels in all fecal samples. Finally, we performed a correlation analysis of the differential bacteria and metabolites between different groups.

RESULTS: Compared with the CRC group, LefSe analysis showed that there is a specific GM community in DCRC group, including an increased abundance of Eggerthella, Hungatella, Peptostreptococcus, and Parvimonas, and decreased Butyricicoccus, Lactobacillus, and Paraprevotella. The metabolomics analysis results revealed that the butyric acid level was lower but the deoxycholic acid and 12-keto-lithocholic acid levels were higher in the DCRC group than other groups (P < 0.05). The correlation analysis showed that the dominant bacterial abundance in the DCRC group (Parvimonas, Desulfurispora, Sebaldella, and Veillonellales, among others) was negatively correlated with butyric acid, hyodeoxycholic acid, ursodeoxycholic acid, glycochenodeoxycholic acid, chenodeoxycholic acid, cholic acid and glycocholate. However, the abundance of mostly inferior bacteria was positively correlated with these metabolic acid levels, including Faecalibacterium, Thermococci, and Cellulophaga.

CONCLUSIONS: Unique fecal microbiome signatures exist in CRC patients with T2DM compared to those with non-diabetic CRC. Alterations in GM composition and SCFAs and secondary BAs levels may promote CRC development.},
}

@article {pmid36959175,
year = {2023},
author = {Bjerg, JJ and Lustermans, JJM and Marshall, IPG and Mueller, AJ and Brokjær, S and Thorup, CA and Tataru, P and Schmid, M and Wagner, M and Nielsen, LP and Schramm, A},
title = {Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {1614},
pmid = {36959175},
issn = {2041-1723},
abstract = {Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.},
}

@article {pmid36958817,
year = {2023},
author = {Vich Vila, A and Hu, S and Andreu-Sánchez, S and Collij, V and Jansen, BH and Augustijn, HE and Bolte, LA and Ruigrok, RAAA and Abu-Ali, G and Giallourakis, C and Schneider, J and Parkinson, J and Al-Garawi, A and Zhernakova, A and Gacesa, R and Fu, J and Weersma, RK},
title = {Faecal metabolome and its determinants in inflammatory bowel disease.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2022-328048},
pmid = {36958817},
issn = {1468-3288},
abstract = {OBJECTIVE: Inflammatory bowel disease (IBD) is a multifactorial immune-mediated inflammatory disease of the intestine, comprising Crohn's disease and ulcerative colitis. By characterising metabolites in faeces, combined with faecal metagenomics, host genetics and clinical characteristics, we aimed to unravel metabolic alterations in IBD.

DESIGN: We measured 1684 different faecal metabolites and 8 short-chain and branched-chain fatty acids in stool samples of 424 patients with IBD and 255 non-IBD controls. Regression analyses were used to compare concentrations of metabolites between cases and controls and determine the relationship between metabolites and each participant's lifestyle, clinical characteristics and gut microbiota composition. Moreover, genome-wide association analysis was conducted on faecal metabolite levels.

RESULTS: We identified over 300 molecules that were differentially abundant in the faeces of patients with IBD. The ratio between a sphingolipid and L-urobilin could discriminate between IBD and non-IBD samples (AUC=0.85). We found changes in the bile acid pool in patients with dysbiotic microbial communities and a strong association between faecal metabolome and gut microbiota. For example, the abundance of Ruminococcus gnavus was positively associated with tryptamine levels. In addition, we found 158 associations between metabolites and dietary patterns, and polymorphisms near NAT2 strongly associated with coffee metabolism.

CONCLUSION: In this large-scale analysis, we identified alterations in the metabolome of patients with IBD that are independent of commonly overlooked confounders such as diet and surgical history. Considering the influence of the microbiome on faecal metabolites, our results pave the way for future interventions targeting intestinal inflammation.},
}