@article {pmid38664737,
year = {2024},
author = {Dang, YR and Cha, QQ and Liu, SS and Wang, SY and Li, PY and Li, CY and Wang, P and Chen, XL and Tian, JW and Xin, Y and Chen, Y and Zhang, YZ and Qin, QL},
title = {Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {77},
pmid = {38664737},
issn = {2049-2618},
abstract = {BACKGROUND: The deep sea represents the largest marine ecosystem, driving global-scale biogeochemical cycles. Microorganisms are the most abundant biological entities and play a vital role in the cycling of organic matter in such ecosystems. The primary food source for abyssal biota is the sedimentation of particulate organic polymers. However, our knowledge of the specific biopolymers available to deep-sea microbes remains largely incomplete. One crucial rate-limiting step in organic matter cycling is the depolymerization of particulate organic polymers facilitated by extracellular enzymes (EEs). Therefore, the investigation of active EEs and the microbes responsible for their production is a top priority to better understand the key nutrient sources for deep-sea microbes.

RESULTS: In this study, we conducted analyses of extracellular enzymatic activities (EEAs), metagenomics, and metatranscriptomics from seawater samples of 50-9305 m from the Mariana Trench. While a diverse array of microbial groups was identified throughout the water column, only a few exhibited high levels of transcriptional activities. Notably, microbial populations actively transcribing EE genes involved in biopolymer processing in the abyssopelagic (4700 m) and hadopelagic zones (9305 m) were primarily associated with the class Actinobacteria. These microbes actively transcribed genes coding for enzymes such as cutinase, laccase, and xyloglucanase which are capable of degrading phytoplankton polysaccharides as well as GH23 peptidoglycan lyases and M23 peptidases which have the capacity to break down peptidoglycan. Consequently, corresponding enzyme activities including glycosidases, esterase, and peptidases can be detected in the deep ocean. Furthermore, cell-specific EEAs increased at 9305 m compared to 4700 m, indicating extracellular enzymes play a more significant role in nutrient cycling in the deeper regions of the Mariana Trench.

CONCLUSIONS: Transcriptomic analyses have shed light on the predominant microbial population actively participating in organic matter cycling in the deep-sea environment of the Mariana Trench. The categories of active EEs suggest that the complex phytoplankton polysaccharides (e.g., cutin, lignin, and hemicellulose) and microbial peptidoglycans serve as the primary nutrient sources available to deep-sea microbes. The high cell-specific EEA observed in the hadal zone underscores the robust polymer-degrading capacities of hadal microbes even in the face of the challenging conditions they encounter in this extreme environment. These findings provide valuable new insights into the sources of nutrition, the key microbes, and the EEs crucial for biopolymer degradation in the deep seawater of the Mariana Trench. Video Abstract.},
}

@article {pmid38664402,
year = {2024},
author = {Zheng, Y and Cao, X and Zhou, Y and Ma, S and Wang, Y and Li, Z and Zhao, D and Yang, Y and Zhang, H and Meng, C and Xie, Z and Sui, X and Xu, K and Li, Y and Zhang, CS},
title = {Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3520},
pmid = {38664402},
issn = {2041-1723},
support = {32101289//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32171948//National Natural Science Foundation of China (National Science Foundation of China)/ ; ZR2021QD026//Natural Science Foundation of Shandong Province (Shandong Provincial Natural Science Foundation)/ ; },
mesh = {*Pseudomonas/genetics/metabolism ; *Glycine max/microbiology/metabolism/genetics ; *Plant Roots/microbiology/metabolism ; *Rhizosphere ; Microbiota/drug effects ; Purines/metabolism/pharmacology ; Salt Stress/genetics ; Chemotaxis/genetics ; Salt Tolerance/genetics ; Soil Microbiology ; Xanthine/metabolism ; Bacterial Proteins/metabolism/genetics ; },
abstract = {The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.},
}

*Pseudomonas/genetics/metabolism
*Glycine max/microbiology/metabolism/genetics
*Plant Roots/microbiology/metabolism
*Rhizosphere
Microbiota/drug effects
Purines/metabolism/pharmacology
Salt Stress/genetics
Chemotaxis/genetics
Salt Tolerance/genetics
Soil Microbiology
Xanthine/metabolism
Bacterial Proteins/metabolism/genetics

@article {pmid38664180,
year = {2024},
author = {Knorr, J and Lone, Z and Werneburg, G and Adler, A and Agudelo, J and Suryavanshi, M and Campbell, RA and Ericson, K and Qiu, H and Bajic, P and Haber, GP and Weight, CJ and Ahern, PP and Almassi, N and Miller, AW and Lee, BH},
title = {An exploratory study investigating the impact of the bladder tumor microbiome on Bacillus Calmette Guerin (BCG) response in non-muscle invasive bladder cancer.},
journal = {Urologic oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urolonc.2024.04.011},
pmid = {38664180},
issn = {1873-2496},
abstract = {PURPOSE: Intravesical Bacillus Calmette-Guerin (BCG) is standard of care for intermediate- and high-risk non-muscle invasive bladder cancer (NMIBC). The effect of the bladder microbiome on response to BCG is unclear. We sought to characterize the microbiome of bladder tumors in BCG-responders and non-responders and identify potential mechanisms that drive treatment response.

MATERIALS AND METHODS: Patients with archival pre-treatment biopsy samples (2012-2018) were identified retrospectively. Prospectively, urine and fresh tumor samples were collected from individuals with high-risk NMIBC (2020-2023). BCG response was defined as tumor-free 2 years from induction therapy. Extracted DNA was sequenced for 16S rRNA and shotgun metagenomics. Primary outcomes were species richness (α-diversity) and microbial composition (β-diversity). Paired t-tests were performed for α-diversity (Observed species/Margalef). Statistical analysis for β-diversity (weighted and unweighted UniFrac distances, weighted Bray-Curtis dissimilarity) were conducted through Permanova, with 999 permutations.

RESULTS: Microbial species richness (P < 0.001) and composition (P = 0.001) differed between BCG responders and non-responders. Lactobacillus spp. were significantly enriched in BCG-responders. Shotgun metagenomics identified possible mechanistic pathways such as assimilatory sulfate reduction.

CONCLUSION: A compositional difference exists in the tumor microbiome of BCG responders and non-responders with Lactobacillus having increased abundance in BCG responders.},
}

@article {pmid38663298,
year = {2024},
author = {Rout, AK and Dixit, S and Tripathy, PS and Rout, SS and Parida, SN and Parida, PK and Sarkar, DJ and Kumar Das, B and Singh, AK and Behera, BK},
title = {Metagenomic landscape of sediments of river Ganga reveals microbial diversity, potential plastic and xenobiotic degradation enzymes.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134377},
doi = {10.1016/j.jhazmat.2024.134377},
pmid = {38663298},
issn = {1873-3336},
abstract = {The Ganga is the largest river in India, serves as a lifeline for agriculture, drinking water, and religious rites. However, it became highly polluted due to the influx of industrial wastes and untreated sewages, leading to the decline of aquatic biodiversity. This study investigated the microbial diversity and plastic-xenobiotic degrading enzymes of six sediment metagenomes of river Ganga at Prayagraj (RDG, TSG, SDG) and Devprayag (KRG, BNG, BRG). The water quality parameters, higher values of BOD (1.8-3.7 ppm), COD (23-29.2 ppm) and organic carbon (0.18-0.51%) were recorded at Prayagraj. Comparative analysis of microbial community structure between Prayagraj and Devprayag revealed significant differences between Bacteroidetes and Firmicutes, which emerging as the predominant bacterial phyla across six sediment samples. Notably, their prevalence was highest in the BRG samples. Furthermore, 25 OTUs at genus level were consistent across all six samples. Alpha diversity exhibited minimal variation among samples, while beta diversity indicated an inverse relationship between species richness and diversity. Co-occurrence network analysis established that genera from the same and different groups of phyla show positive co-relations with each other. Thirteen plastic degrading enzymes, including Laccase, Alkane-1 monooxygenase and Alkane monooxygenase, were identified from six sediment metagenomes of river Ganga, which can degrade non-biodegradable plastic viz. Polyethylene, Polystyrene and Low-density Polyethelene. Further, 18 xenobiotic degradation enzymes were identified for the degradation of Bisphenol, Xylene, Toluene, Polycyclic aromatic hydrocarbon, Styrene, Atrazene and Dioxin etc. This is the first report on the identification of non-biodegradable plastic degrading enzymes from sediment metagenomes of river Ganga, India. The findings of this study would help in pollution abatement and sustainable management of riverine ecosystem.},
}

@article {pmid38664337,
year = {2024},
author = {Ullah Khan, N and Sadiq, A and Khan, J and Basharat, N and Hassan, ZU and Ali, I and Shah, TA and Bourhia, M and Bin Jardan, YA and Wondmie, GF},
title = {Molecular characterization of plasma virome of hepatocellular carcinoma (HCC) patients.},
journal = {AMB Express},
volume = {14},
number = {1},
pages = {46},
pmid = {38664337},
issn = {2191-0855},
abstract = {Hepatocellular carcinoma (HCC) stands as the most common cancer type, arising from various causes, and responsible for a substantial number of cancer-related fatalities. Recent advancements in viral metagenomics have empowered scientists to delve into the intricate diversity of the virosphere, viral evolution, interactions between viruses and their hosts, and the identification of viral causes behind disease outbreaks, the development of specific symptoms, and their potential role in altering the host's physiology. The present study had the objective of "Molecular Characterization of HBV, HCV, anelloviruses, CMV, SENV-D, SENV-H, HEV, and HPV viruses among individuals suffering from HCC." A total of 381 HCC patients contributed 10 cc of blood each for this study. The research encompassed the assessment of tumor markers, followed by molecular characterization of HBV, HCV, Anelloviruses (TTV, TTMV, and TTMDV), SENV-H and SENV-D viruses, HEV, CMV, and HPV, as well as histopathological examinations. The outcomes of this study revealed that majority of the HCC patients 72.4% (276/381) were male as compared to females. HCV infection, at 76.4% (291 out of 381), exhibited a significant association (p < 0.05) with HCC. Most patients displayed singular lesions in the liver, with Child Pugh Score Type B being the predominant finding in 45.2% of cases. Plasma virome analysis indicated the prevalence of TTMDV (75%), followed by TTMV (70%) and TTV (42.1%) among anelloviruses in HCC patients. Similarly, SENV-H (52%) was followed by SENV-D (20%), with co-infections at 15%. The presence of CMV and HEV among the HCC patients was recorded 5% each however 3.5% of the patients showed the presence of HPV. In conclusion, this study underscores that HCC patients serve as reservoirs for various pathogenic and non-pathogenic viruses, potentially contributing to the development, progression, and severity of the disease.},
}

@article {pmid38664270,
year = {2024},
author = {Cadena, S and Cerqueda-García, D and Uribe-Flores, MM and Ramírez, SI},
title = {Metagenomic profiling of halites from the Atacama Desert: an extreme environment with natural perchlorate does not promote high diversity of perchlorate reducing microorganisms.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {2},
pages = {25},
pmid = {38664270},
issn = {1433-4909},
support = {377887//Consejo Nacional de Humanidades Ciencias y Tecnologías/ ; 570049-2022-2023//Consejo Nacional de Humanidades Ciencias y Tecnologías/ ; 88//Consejo de Ciencia y Tecnología del Estado de Morelos/ ; },
mesh = {*Perchlorates/metabolism ; *Oxidation-Reduction ; *Desert Climate ; *Extreme Environments ; Metagenome ; Microbiota ; },
abstract = {We surveyed the presence of perchlorate-reducing microorganisms in available metagenomic data of halite environments from the Atacama Desert, an extreme environment characterized by high perchlorate concentrations, intense ultraviolet radiation, saline and oxidizing soils, and severe desiccation. While the presence of perchlorate might suggest a broad community of perchlorate reducers or a high abundance of a dominant taxa, our search reveals a scarce presence. In fact, we identified only one halophilic species, Salinibacter sp003022435, carrying the pcrA and pcrC genes, represented in low abundance. Moreover, we also discovered some napA genes and organisms carrying the nitrate reductase nasB gene, which hints at the possibility of cryptic perchlorate reduction occurring in these ecosystems. Our findings contribute with the knowledge of perchlorate reduction metabolism potentially occurring in halites from Atacama Desert and point towards promising future research into the perchlorate-reducing mechanism in Salinibacter, a common halophilic bacterium found in hypersaline ecosystems, whose metabolic potential remains largely unknown.},
}

*Perchlorates/metabolism
*Oxidation-Reduction
*Desert Climate
*Extreme Environments
Metagenome
Microbiota

@article {pmid38664214,
year = {2024},
author = {Feng, JC and Gao, MX and Chen, SL and Zhang, W and Luo, WY},
title = {[A case of treatment for severe hip trauma].},
journal = {Zhongguo gu shang = China journal of orthopaedics and traumatology},
volume = {37},
number = {4},
pages = {411-413},
doi = {10.12200/j.issn.1003-0034.20220780},
pmid = {38664214},
issn = {1003-0034},
mesh = {Humans ; Male ; *Hip Injuries/therapy/surgery ; Adult ; Middle Aged ; },
}

Humans
Male
*Hip Injuries/therapy/surgery
Adult
Middle Aged

@article {pmid38663623,
year = {2024},
author = {Liang, X and Zhu, Y and Liu, H and Xie, Z and Li, G and Li, D and Liang, Y and Peng, C},
title = {Nitrogen-fixing cyanobacteria enhance microbial carbon utilization by modulating the microbial community composition in paddy soils of the Mollisols region.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172609},
doi = {10.1016/j.scitotenv.2024.172609},
pmid = {38663623},
issn = {1879-1026},
abstract = {Nitrogen-fixing cyanobacteria (NFC) are photosynthetic prokaryotic microorganisms capable of nitrogen fixation. They can be used as biofertilizers in paddy fields, thereby improving the rice tillering capacity and yield. To reveal the microbiological mechanisms by which nitrogen-fixing cyanobacteria alter soil carbon storage, we conducted a field experiment using NFC as a partial substitute for nitrogen fertilizer in paddy fields in the Sanjiang Plain of Northeast China's Mollisols region. Using metagenomic sequencing technology and Biolog Ecoplate™ carbon matrix metabolism measurements, we explored the changes in the soil microbial community structure and carbon utilization in paddy fields. The results indicated that the replacement of nitrogen fertilizer with NFC predisposed the soil microbial community to host a great number of copiotrophic bacterial taxa, and Proteobacteria and Actinobacteria were closely associated with the metabolism of soil carbon sources. Moreover, through co-occurrence network analysis, we found that copiotrophic bacteria clustered in modules that were positively correlated with the metabolic level of carbon sources. The addition of NFC promoted the growth of copiotrophic bacteria, which increased the carbon utilization level of soil microorganisms, improved the diversity of the microbial communities, and had a potential impact on the soil carbon stock. The findings of this study are helpful for assessing the impact of NFC on the ecological function of soil microbial communities in paddy fields in the black soil area of Northeast China, which is highly important for promoting sustainable agricultural development and providing scientific reference for promoting the use of algal-derived nitrogen fertilizers.},
}

@article {pmid38662518,
year = {2024},
author = {Lages da Silva, DH and Marques da Silva, RL and Rios, DL and Glória de Souza, DD and Aburjaile, F and de Freitas Neto, OC and Camargos Lara, LJ and Araújo, MD and Ecco, R},
title = {Intestinal microbiota diversity from broilers with runting and stunting syndrome performed by metagenomics.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/03079457.2024.2348509},
pmid = {38662518},
issn = {1465-3338},
abstract = {Runting and stunting syndrome (RSS) is an enteric viral disease in commercial poultry that directly affects gut health; however, its influence on gut microbiota remains unknown. This study aimed to investigate the compositional changes in the bacterial community of the ileum of 7-day-old broiler chicks naturally affected and not affected by RSS, using next-generation sequencing (NGS) technology. Twenty-one samples were obtained from the ileal contents and mucosa of 11 chicks with RSS and 10 healthy chicks, raised in a dark house system located on a farm in the state of Minas Gerais, Brazil. The results revealed overall changes in the gut microbiota of the chicks with RSS, including a decrease in microbial richness and diversity. In particular, there was a decrease in Lactobacillus and an increase in Candidatus Arthromitus and Clostridium sensu stricto 1. These results indicate a relationship between viral infection and the gut microbial composition, which can cause gut dysbiosis and may influence inflammation in this organ.RESEARCH HIGHLIGHTSRSS causes dysbiosis of the gut microbiota of the ilea of chicks.A difference was found in gut microbiota between chicks with and without RSS.Candidatus Arthromitus was predominant in chicks with RSS.Clostridium sensu stricto 1 was strictly associated with chicks with RSS.},
}

@article {pmid38662307,
year = {2024},
author = {Wang, Z and Zhou, H and Cheng, Y and An, L and Yan, D and Chao, H and Wu, J},
title = {Novel small multidrug resistance protein Tmt endows the Escherichia coli with triphenylmethane dyes bioremediation capability.},
journal = {Biotechnology letters},
volume = {},
number = {},
pages = {},
pmid = {38662307},
issn = {1573-6776},
support = {31800111//National Natural Science Foundation of China/ ; },
abstract = {Dye contamination in printing and dyeing wastewater has long been a major concern due to its serious impact on both the environment and human health. In the quest for bioremediation of these hazardous dyes, biological resources such as biodegradation bacteria and enzymes have been investigated in severely polluted environments. In this context, the triphenylmethane transporter gene (tmt) was identified in six distinct clones from a metagenomic library of the printing and dyeing wastewater treatment system. Escherichia coli expressing tmt revealed 98.1% decolorization efficiency of triphenylmethane dye malachite green within 24 h under shaking culture condition. The tolerance to malachite green was improved over eightfold in the Tmt strain compared of the none-Tmt expressed strain. Similarly, the tolerance of Tmt strain to other triphenylmethane dyes like crystal violet and brilliant green, was improved by at least fourfold. Site-directed mutations, including A75G, A75S and V100G, were found to reinforce the tolerance of malachite green, and double mutations of these even further improve the tolerance. Therefore, the tmt has been demonstrated to be a specific efflux pump for triphenylmethane dyes, particularly the malachite green. By actively pumping out toxic triphenylmethane dyes, it significantly extends the cells tolerance in a triphenylmethane dye-rich environment, which may provide a promising strategy for bioremediation of triphenylmethane dye pollutants in the environments.},
}

@article {pmid38662153,
year = {2024},
author = {Choudhary, G and Kumari, S and Anu, K and Devi, S},
title = {Deciphering the microbial communities of alkaline hot spring in Panamik, Ladakh, India using a high-throughput sequencing approach.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38662153},
issn = {1678-4405},
abstract = {Due to their distinctive physicochemical characteristics, hot springs are extremely important. The whole genome metagenomic sequencing technology can be utilized to analyze the diverse microbial community that thrives in this habitat due to the particular selection pressure that prevails there. The current investigation emphasizes on culture-independent metagenomic study of the Panamik hot spring and its nearby areas from Ladakh, India. Based on different diversity indices, sequence analysis of the soil reservoir showed higher species richness and diversity in comparison to water and sediment samples. The mineral content and various physicochemical pameters like temperature, pH had an impact on the composition of the microbial community of the geothermal springs. The phyla Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacter, Firmicutes, and Verrucomicrobia in bacterial domain dominate the thermos-alkaline spring at Panamik in different concentrations. Economically significant microbes from the genera Actinobacter, Thermosynechoccus, Candidatus Solibacter, Chthoniobacter, Synechoccus, Pseudomonas and Sphingomonas, were prevalent in hot spring. In the archaeal domain, the most dominant phylum and genera were Euryarchaeota and Thermococcus in all the samples. Further, the most abundant species were Methanosarcina barkeri, Nitrospumilus maritimus and Methanosarcina acetivorans. The present study which only examined one of the several thermal springs present in the Himalayan geothermal area, should be regarded as a preliminary investigation of the microbiota that live in the hot springs on these remote areas. These findings suggest that further investigations should be undertaken to characterize the ecosystems of the Panamik hot spring, which serve as a repository for unidentified microbial lineages.},
}

@article {pmid38661581,
year = {2024},
author = {Suarez, SA and Martiny, AC},
title = {Intraspecific variation in antibiotic resistance potential within E. coli.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0316223},
doi = {10.1128/spectrum.03162-23},
pmid = {38661581},
issn = {2165-0497},
abstract = {Intraspecific genomic diversity brings the potential for an unreported and diverse reservoir of cryptic antibiotic resistance genes in pathogens, as cryptic resistance can occur without major mutations and horizontal transmission. Here, we predicted the differences in the types of antibiotics and genes that induce cryptic and latent resistance between micro-diverse Escherichia coli strains. For example, we hypothesize that known resistance genes will be the culprit of latent resistance within clinical strains. We used a modified functional metagenomics method to induce expression in eight E. coli strains. We found a total of 66 individual genes conferring phenotypic resistance to 11 out of 16 antibiotics. A total of 14 known antibiotic resistance genes comprised 21% of total identified genes, whereas the majority (52 genes) were unclassified cryptic resistance genes. Between the eight strains, 1.2% of core orthologous genes were positive (conferred resistance in at least one strain). Sixty-four percent of positive orthologous genes conferred resistance to only one strain, demonstrating high intraspecific variability of latent resistance genes. Cryptic resistance genes comprised most resistance genes among laboratory and clinical strains as well as natural, semisynthetic, and synthetic antibiotics. Known antibiotic resistance genes primarily conferred resistance to multiple antibiotics from varying origins and within multiple strains. Hence, it is uncommon for E. coli to develop cross-cryptic resistance to antibiotics from multiple origins or within multiple strains. We have uncovered prospective and previously unknown resistance genes as well as antibiotics that have the potential to trigger latent antibiotic resistance in E. coli strains from varying origins.IMPORTANCEIntraspecific genomic diversity may be a driving force in the emergence of adaptive antibiotic resistance. Adaptive antibiotic resistance enables sensitive bacterial cells to acquire temporary antibiotic resistance, creating an optimal window for the development of permanent mutational resistance. In this study, we investigate cryptic resistance, an adaptive resistance mechanism, and unveil novel (cryptic) antibiotic resistance genes that confer resistance when amplified within eight E. coli strains derived from clinical and laboratory origins. We identify the potential of cryptic resistance genes to confer cross-resistance to antibiotics from varying origins and within multiple strains. We discern antibiotic characteristics that promote latent resistance in multiple strains, considering intraspecific diversity. This study may help detect novel resistance genes and functional genes that could become responsible for cryptic resistance among diverse strains and antibiotics, thus also identifying potential novel antibiotic targets and mechanisms.},
}

@article {pmid38661445,
year = {2024},
author = {Sánchez-Terrón, G and Martínez, R and Morcuende, D and Caballero, V and Estévez, M},
title = {Pomegranate supplementation alleviates dyslipidemia and the onset of non-alcoholic fatty liver disease in Wistar rats by shifting microbiota and producing urolithin-like microbial metabolites.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo00688g},
pmid = {38661445},
issn = {2042-650X},
abstract = {Non-alcoholic fatty liver disease (NAFLD), obesity and related chronic diseases are major non-communicable diseases with high mortality rates worldwide. While dietary sugars are known to be responsible for insulin resistance and metabolic syndrome (MetS), the underlying pathophysiological effects of sustained fructose consumption require further elucidation. We hypothesize that certain bioactive compounds (i.e. punicalagin and ellagic acid) from dietary pomegranate could counteract the harmful effects of sustained fructose consumption in terms of obesity and liver damage. The present study aimed to elucidate both the molecular mechanisms involved in the pathophysiology associated with fructose intake and the effect of a punicalagin-rich commercial pomegranate dietary supplement (P) used as a nutritional strategy to alleviate fructose-induced metabolic impairments. Thus, nineteen Wistar rats fed on a basal commercial feed were supplemented with either 30% (w/v) fructose in drinking water (F; n = 7) or 30% (w/v) fructose solution plus 0.2% (w/v) P (F + P; n = 6) for 10 weeks. The results were compared to those from a control group fed on the basal diet and provided with drinking water (C; n = 6). Body weight and energy intake were registered weekly. P supplementation decreased fat depots, counteracted the dyslipidemia caused by F and improved markers of liver injury including steatosis. The study of the microbiota by metagenomics and urine by untargeted MS-based metabolomics revealed microbial metabolites from P that may be responsible for these health benefits.},
}

@article {pmid38661414,
year = {2024},
author = {Alexander, CC and Gaudier-Diaz, MM and Kleinschmit, AJ and Dihle, PJ and Salger, SA and Vega, N and Robertson, SD},
title = {A case study to engage students in the research design and ethics of high-throughput metagenomics.},
journal = {Journal of microbiology & biology education},
volume = {25},
number = {1},
pages = {e0007423},
doi = {10.1128/jmbe.00074-23},
pmid = {38661414},
issn = {1935-7877},
abstract = {Case studies present students with an opportunity to learn and apply course content through problem solving and critical thinking. Supported by the High-throughput Discovery Science & Inquiry-based Case Studies for Today's Students (HITS) Research Coordination Network, our interdisciplinary team designed, implemented, and assessed two case study modules entitled "You Are What You Eat." Collectively, the case study modules present students with an opportunity to engage in experimental research design and the ethical considerations regarding microbiome research and society. In this manuscript, we provide instructors with tools for adopting or adapting the research design and/or the ethics modules. To date, the case has been implemented using two modalities (remote and in-person) in three courses (Microbiology, Physiology, and Neuroscience), engaging over 200 undergraduate students. Our assessment data demonstrate gains in content knowledge and students' perception of learning following case study implementation. Furthermore, when reflecting on our experiences and student feedback, we identified ways in which the case study could be modified for different settings. In this way, we hope that the "You Are What You Eat" case study modules can be implemented widely by instructors to promote problem solving and critical thinking in the traditional classroom or laboratory setting when discussing next-generation sequencing and/or metagenomics research.},
}

@article {pmid38661357,
year = {2023},
author = {Chen, XX and Zeng, MX and Cai, D and Zhou, HH and Wang, YJ and Liu, Z},
title = {Correlation between APOE4 gene and gut microbiota in Alzheimer's disease.},
journal = {Beneficial microbes},
volume = {14},
number = {4},
pages = {349-360},
doi = {10.1163/18762891-20220116},
pmid = {38661357},
issn = {1876-2891},
mesh = {*Alzheimer Disease/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome ; *Apolipoprotein E4/genetics ; Aged ; Male ; Female ; China ; *Bacteria/genetics/classification/isolation & purification ; Dysbiosis/microbiology ; United States ; Middle Aged ; Aged, 80 and over ; Feces/microbiology ; Case-Control Studies ; },
abstract = {Gut microbiota (GM) dysbiosis has been increasingly associated with Alzheimer's disease (AD). However, the association between APOE4, the most common genetic risk factor for sporadic AD, and GM in AD remains unclear. In this study, we conducted a comparative analysis of the GM of participants from China and the USA, with and without APOE4 genes and with or without AD (67 AD cases, 67 control cases). Our results revealed that the GM alpha diversity was not different between groups (AD_APOE4, Control_APOE4, AD_non-APOE4, and Control_non-APOE4) (419.031 ± 143.631 vs 391.091 ± 126.081, 351.086 ± 169.174 and 386.089 ± 177.200, respectively. P > 0.05). Interestingly, individuals in the AD_APOE4 group had different bacterial compositions and bacterial biomarkers. The Kruskal-Wallis rank sum test indicated that the abundances of many bacterial species in the AD_APOE4 patients differed from those in control individuals, including decreases in unclassified_g__Escherichia-Shigella (1.763 ± 6.73, 4.429 ± 11.13, 8.245 ± 16.55, and 5.69 ± 13.91 in four groups, respectively; P < 0.05), and unclassified_g_Clostridium_sensu_stricto_1 (0.1519 ± 0.348, 2.502 ± 5.913, 0.5146 ± 0.9487, 1.063 ± 3.428 in four groups, respectively; P < 0.05), and increases in gut_metagenome_g_Faecalibacterium (2.885 ± 4.47, 2.174 ± 3.957, 0.5765 ± 1.784, 1.582 ± 2.92 in four groups, respectively. P < 0.01) and unclassified_g_Bacteroides (3.875 ± 3.738, 2.47 ± 2.748, 2.046 ± 3.674, 3.206 ± 3.446 in four groups, respectively; P < 0.05). In the KEGG pathway level 2 analysis, we identified three significant differences in relative abundances of predicted functions between AD_APOE4 and AD_non-APOE4_carrier groups: neurodegenerative diseases (0.0007 ± 0.0005 vs 0.0009 ± 0.0004; P < 0.01), metabolism (0.0240 ± 0.0003 vs 0.0250 ± 0.0003; P < 0.05), and biosynthesis of other secondary metabolites (0.0094 ± 0.0002 vs 0.0090 ± 0.0002; P < 0.05). Receiver operating characteristic curves further demonstrated an area under the curve (AUC) of 0.74 for the discrimination of AD_APOE4_carrier and AD_non-APOE4_carrier individuals.},
}

*Alzheimer Disease/microbiology/genetics
Humans
*Gastrointestinal Microbiome
*Apolipoprotein E4/genetics
Aged
Male
Female
China
*Bacteria/genetics/classification/isolation & purification
Dysbiosis/microbiology
United States
Middle Aged
Aged, 80 and over
Feces/microbiology
Case-Control Studies

@article {pmid38661344,
year = {2024},
author = {Phan, J and Calvo, DC and Nair, D and Jain, S and Montagne, T and Dietsche, S and Blanchard, K and Treadwell, S and Adams, J and Krajmalnik-Brown, R},
title = {Precision synbiotics increase gut microbiome diversity and improve gastrointestinal symptoms in a pilot open-label study for autism spectrum disorder.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0050324},
doi = {10.1128/msystems.00503-24},
pmid = {38661344},
issn = {2379-5077},
abstract = {UNLABELLED: The efficacy of prebiotics and probiotics (synbiotics when combined) to improve symptoms associated with autism spectrum disorder (ASD) has shown considerable inter-study variation, likely due to the complex, heterogeneous nature of the disorder and its associated behavioral, developmental, and gastrointestinal symptoms. Here, we present a precision synbiotic supplementation study in 296 children and adults diagnosed with ASD versus 123 age-matched neurotypical controls. One hundred seventy ASD participants completed the study. Baseline and post-synbiotic assessment of ASD and gastrointestinal (GI) symptoms and deep metagenomic sequencing were performed. Within the ASD cohort, there were significant differences in microbes between subpopulations based on the social responsiveness scale (SRS2) survey (Prevotella spp., Bacteroides, Fusicatenibacter, and others) and gluten and dairy-free diets (Bifidobacterium spp., Lactococcus, Streptococcus spp., and others). At the baseline, the ASD cohort maintained a lower taxonomic alpha diversity and significant differences in taxonomic composition, metabolic pathways, and gene families, with a greater proportion of potential pathogens, including Shigella, Klebsiella, and Clostridium, and lower proportions of beneficial microbes, including Faecalibacterium compared to controls. Following the 3-month synbiotic supplementation, the ASD cohort showed increased taxonomic alpha diversity, shifts in taxonomy and metabolic pathway potential, and improvements in some ASD-related symptoms, including a significant reduction in GI discomfort and overall improved language, comprehension, cognition, thinking, and speech. However, the open-label study design may include some placebo effects. In summary, we found that precision synbiotics modulated the gut microbiome and could be used as supplementation to improve gastrointestinal and ASD-related symptoms.

IMPORTANCE: Autism spectrum disorder (ASD) is prevalent in 1 out of 36 children in the United States and contributes to health, financial, and psychological burdens. Attempts to identify a gut microbiome signature of ASD have produced varied results. The limited pre-clinical and clinical population sizes have hampered the success of these trials. To understand the microbiome associated with ASD, we employed whole metagenomic shotgun sequencing to classify microbial composition and genetic functional potential. Despite being one of the most extensive ASD post-synbiotic assessment studies, the results highlight the complexity of performing such a case-control supplementation study in this population and the potential for a future therapeutic approach in ASD.},
}

@article {pmid38660910,
year = {2024},
author = {Mao, WY and Lan, JE and Gan, MY and Zhang, XJ and Yu, H and Hu, LY and Zhang, R and Cao, Y and Xiao, ML},
title = {[Moxifloxacin treatment for Mycoplasma hominis meningitis in an extremely preterm infant].},
journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics},
volume = {26},
number = {4},
pages = {432-436},
pmid = {38660910},
issn = {1008-8830},
mesh = {Humans ; *Mycoplasma hominis/isolation & purification ; Infant, Newborn ; Male ; *Infant, Extremely Premature ; *Moxifloxacin/therapeutic use/administration & dosage ; Meningitis, Bacterial/drug therapy/microbiology/diagnosis ; Mycoplasma Infections/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; },
abstract = {The patient, a male newborn, was admitted to the hospital 2 hours after birth due to prematurity (gestational age 27[+5] weeks) and respiratory distress occurring 2 hours postnatally. After admission, the infant developed fever and elevated C-reactive protein levels. On the fourth day after birth, metagenomic next-generation sequencing of cerebrospinal fluid indicated a positive result for Mycoplasma hominis (9 898 reads). On the eighth day, a retest of cerebrospinal fluid metagenomics confirmed Mycoplasma hominis (56 806 reads). The diagnosis of purulent meningitis caused by Mycoplasma hominis was established, and the antibiotic treatment was switched to moxifloxacin [5 mg/(kg·day)] administered intravenously for a total of 4 weeks. After treatment, the patient's cerebrospinal fluid tests returned to normal, and he was discharged as cured on the 76th day after birth. This article focuses on the diagnosis and treatment of neonatal Mycoplasma hominis purulent meningitis, introducing the multidisciplinary diagnosis and treatment of the condition in extremely preterm infants.},
}

Humans
*Mycoplasma hominis/isolation & purification
Infant, Newborn
Male
*Infant, Extremely Premature
*Moxifloxacin/therapeutic use/administration & dosage
Meningitis, Bacterial/drug therapy/microbiology/diagnosis
Mycoplasma Infections/drug therapy/diagnosis
Anti-Bacterial Agents/therapeutic use/administration & dosage

@article {pmid38660245,
year = {2024},
author = {Qian, X and Chen, Z and Ji, XM and Ji, YL and Wang, J and Liu, YC and Zhou, XC and Li, QL and Li, CY and Zhang, AQ},
title = {Qingfei mixture modulates the immune responses in lung cancer through modulating mTOR signaling and gut microbiota-derived short-chain fatty acids.},
journal = {Heliyon},
volume = {10},
number = {8},
pages = {e29404},
pmid = {38660245},
issn = {2405-8440},
abstract = {Lung cancer ranks among the primary contributors to cancer-related fatalities on a global scale. Multiple research investigations have demonstrated that there exists a dysbiosis within the intestinal bacteria and short-chain fatty acids (SCFAs) is linked with immune responses in lung cancer. Qingfei mixture (QFM) has been widely used in treating lung cancer, yet the active ingredients and roles of the QFM on immune responses by targeting gut microbiota remain to be elucidated. The chemical constituents of QFM were qualitatively examined by UPLC/Q-TOF-MS. Additionally, we evaluated the therapeutic impact of the organic substance QFM on lung cancer, aiming to elucidate its mechanisms for improving the tumor-immune microenvironment. Herein, we constructed a Lewis lung carcinoma (LLC)-bearing mice model with QFM treatment to observe tumor growth and immune cell changes. Then, the feces were collected and a combinatory study using metagenomes, non-targeted metabonomics, and targeted metabonomics of SCFAs was performed. In vitro experiments have been conducted to estimate the roles of acetate and sodium propionate in CD8[+] T cells. Furthermore, we treated tumor-bearing mice with QFM, QFM + MHY1485 (an mTOR activator), and QFM + an antibiotic mixture (ABX) to explore the potential therapeutic benefit of regulation of the tumor microenvironment. A total of 96 compounds were obtained from QFM by UPLC/Q-TOF-MS. Besides, the findings demonstrated that QFM exhibited significant efficacy against lung cancer, manifesting in reduced tumor growth and improved immune responses. In investigating its mechanisms, we integrated gut microbiota sequencing and fecal metabolomics, revealing that QFM effectively restored disruptions in gut microbiota and SCFAs in mice with lung cancer. QFM, acetate, or sodium propionate contributed to the up-regulation of IFN-γ, Gzms-B, perforin, IL-17, IL-6, IL-12, TNF-α expressions and decreased HDAC and IL-10 levels in vitro and in vivo. Moreover, MHY1485 and ABX weakened the effects of QFM on immunomodulation. Collectively, these results suggest that QFM may facilitate immune responses in the LLC-bearing mice via regulating the gut microbiota-derived SCFAs at least partially through targeting the mTOR signaling pathway.},
}

@article {pmid38660073,
year = {2024},
author = {Yang, XL and Zhang, JY and Ren, JM},
title = {Successful treatment of Purpureocillium lilacinum pulmonary infection with isavuconazole: A case report.},
journal = {World journal of clinical cases},
volume = {12},
number = {10},
pages = {1772-1777},
pmid = {38660073},
issn = {2307-8960},
abstract = {BACKGROUND: Purpureocillium lilacinum (P. lilacinum) is a saprophytic fungus widespread in soil and vegetation. As a causative agent, it is very rarely detected in humans, most commonly in the skin.

CASE SUMMARY: In this article, we reported the case of a 72-year-old patient with chronic lymphocytic leukemia who was admitted with cough and fever. Computed tomography revealed an infection in the right lower lobe. Bronchoalveolar lavage fluid culture and metagenomic next-generation sequencing were ultimately confirmed to have a pulmonary infection with P. lilacinum. She was eventually discharged with good outcomes after treatment with isavuconazole.

CONCLUSION: Pulmonary infection with P. lilacinum was exceedingly rare. While currently there are no definitive therapeutic agents, there are reports of high resistance to amphotericin B and fluconazole and good sensitivity to second-generation triazoles. The present report is the first known use of isavuconazole for pulmonary P. lilacinum infection. It provides new evidence for the characterization and treatment of clinical P. lilacinum lung infections.},
}

@article {pmid38659981,
year = {2024},
author = {Gand, M and Navickaite, I and Bartsch, LJ and Grützke, J and Overballe-Petersen, S and Rasmussen, A and Otani, S and Michelacci, V and Matamoros, BR and González-Zorn, B and Brouwer, MSM and Di Marcantonio, L and Bloemen, B and Vanneste, K and Roosens, NHCJ and AbuOun, M and De Keersmaecker, SCJ},
title = {Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1336532},
pmid = {38659981},
issn = {1664-302X},
abstract = {Metagenomic sequencing is a promising method that has the potential to revolutionize the world of pathogen detection and antimicrobial resistance (AMR) surveillance in food-producing environments. However, the analysis of the huge amount of data obtained requires performant bioinformatics tools and databases, with intuitive and straightforward interpretation. In this study, based on long-read metagenomics data of chicken fecal samples with a spike-in mock community, we proposed confidence levels for taxonomic identification and AMR gene detection, with interpretation guidelines, to help with the analysis of the output data generated by KMA, a popular k-mer read alignment tool. Additionally, we demonstrated that the completeness and diversity of the genomes present in the reference databases are key parameters for accurate and easy interpretation of the sequencing data. Finally, we explored whether KMA, in a two-step procedure, can be used to link the detected AMR genes to their bacterial host chromosome, both detected within the same long-reads. The confidence levels were successfully tested on 28 metagenomics datasets which were obtained with sequencing of real and spiked samples from fecal (chicken, pig, and buffalo) or food (minced beef and food enzyme products) origin. The methodology proposed in this study will facilitate the analysis of metagenomics sequencing datasets for KMA users. Ultimately, this will contribute to improvements in the rapid diagnosis and surveillance of pathogens and AMR genes in food-producing environments, as prioritized by the EU.},
}

@article {pmid38659779,
year = {2024},
author = {Moraes, JGN and Gull, TB and Ericsson, AC and Caldeira, MO and Evans, TJ and Poock, SE and Lucy, MC},
title = {Systemic antibiotic treatment of cows with metritis early postpartum does not change the progression of uterine disease or the uterine microbiome at 1 month postpartum.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4233045/v1},
pmid = {38659779},
abstract = {Background: Postpartum uterine disease (metritis) is common in dairy cows. The disease develops within 1 week after calving and is associated with microbial dysbiosis, fever, and fetid uterine discharge. Cows with metritis have a greater likelihood of developing endometritis and infertility later postpartum. Antibiotic treatment is used to relieve symptoms of metritis but the capacity of antibiotic treatment to improve fertility later postpartum is inconsistent across published studies. We hypothesized that an antibiotic has only a short-term effect on the uterine microbiome and does not change the progression of disease from metritis to endometritis. To test this hypothesis, we studied the effects of systemic antibiotic given to cows diagnosed with metritis and healthy cows early postpartum on the development of endometritis and the uterine microbiome at 1 month postpartum. Results: Cows diagnosed with metritis were compared to healthy ones in a 2 x 2 factorial design, where they were either treated with an antibiotic (ceftiofur hydrochloride) at 7 to 10 days postpartum or left untreated. Cows were slaughtered at one month postpartum and the uterus was assessed for endometritis (presence of purulent material in the uterine lumen and inflammation in the endometrium) and uterine samples were collected for bacteriology and metagenomics (16S rRNA gene sequencing). As expected, the uterine microbiome at disease diagnosis had dysbiosis of typical metritis pathogens (e.g., Fusobacterium , Bacteroides , and Porphyromonas) in diseased compared with healthy cows. At one month postpartum, there was a tendency for more endometritis in metritis cows compared with healthy but antibiotic treatment had no effect on endometritis prevalence regardless of the original disease diagnosis. Likewise, when bacteria were cultured or sequenced, there were a greater number of species (culture) or amplicon sequence variants (ASV; sequencing) in the uterine lumen of cows with metritis. However, antibiotic treatment had no effect on the prevalence of cultured species or the composition of the detected ASV. The uterine microbiome at 1 month postpartum was associated with the clinical observation of the uterus (endometritis or healthy). Conclusions: Early postpartum antibiotic treatment only provides temporary resolution of uterine dysbiosis that is not sustained long-term. Failure to resolve the dysbiosis is associated with a greater prevalence of endometritis in cows with metritis, and the occurrence of endometritis significantly impacts fertility later postpartum.},
}

@article {pmid38659737,
year = {2024},
author = {Jiang, D and Soo, N and Tan, CY and Dankwa, S and Wang, HY and Theriot, BS and Ardeshir, A and Siddiqui, NY and Van Rompay, KKA and De Paris, K and Permar, SR and Goswami, R and Surana, NK},
title = {Commensal bacteria inhibit viral infections via a tryptophan metabolite.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.21.589969},
pmid = {38659737},
abstract = {There is growing appreciation that commensal bacteria impact the outcome of viral infections, though the specific bacteria and their underlying mechanisms remain poorly understood. Studying a simian-human immunodeficiency virus (SHIV)-challenged cohort of pediatric nonhuman primates, we bioinformatically associated Lactobacillus gasseri and the bacterial family Lachnospiraceae with enhanced resistance to infection. We experimentally validated these findings by demonstrating two different Lachnospiraceae isolates, Clostridium immunis and Ruminococcus gnavus, inhibited HIV replication in vitro and ex vivo. Given the link between tryptophan catabolism and HIV disease severity, we found that an isogenic mutant of C. immunis that lacks the aromatic amino acid aminotransferase (ArAT) gene, which is key to metabolizing tryptophan into 3-indolelactic acid (ILA), no longer inhibits HIV infection. Intriguingly, we confirmed that a second commensal bacterium also inhibited HIV in an ArAT-dependent manner, thus establishing the generalizability of this finding. In addition, we found that purified ILA inhibited HIV infection by agonizing the aryl hydrocarbon receptor (AhR). Given that the AhR has been implicated in the control of multiple viral infections, we demonstrated that C. immunis also inhibited human cytomegalovirus (HCMV) infection in an ArAT-dependent manner. Importantly, metagenomic analysis of individuals at-risk for HIV revealed that those who ultimately acquired HIV had a lower fecal abundance of the bacterial ArAT gene compared to individuals who did not, which indicates our findings translate to humans. Taken together, our results provide mechanistic insights into how commensal bacteria decrease susceptibility to viral infections. Moreover, we have defined a microbiota-driven antiviral pathway that offers the potential for novel therapeutic strategies targeting a broad spectrum of viral pathogens.},
}

@article {pmid38659344,
year = {2024},
author = {Wang, L and Zhu, Y and Zhao, C and Zhao, M and Li, Z and Xu, W and Mu, W},
title = {Engineering Escherichia coli for Highly Efficient Biosynthesis of Lacto-N-difucohexaose II through De Novo GDP-l-fucose Pathway.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c01264},
pmid = {38659344},
issn = {1520-5118},
abstract = {Lacto-N-difucohexaose II (LNDFH II) is a typical fucosylated human milk oligosaccharide and can be enzymatically produced from lacto-N-tetraose (LNT) by a specific α1,3/4-fucosyltransferase from Helicobacter pylori DMS 6709, referred to as FucT14. Previously, we constructed an engineered Escherichia coli BL21(DE3) with a single plasmid for highly efficient biosynthesis of LNT. In this study, two additional plasmids harboring the de novo GDP-L-fucose pathway module and FucT14, respectively, were further introduced to construct the strain for successful biosynthesis of LNDFH II. FucT14 was actively expressed, and the engineered strain produced LNDFH II as the major product, lacto-N-fucopentaose (LNFP) V as the minor product, and a trace amount of LNFP II and 3-fucosyllactose as very minor products. Additional expression of the α1,3-fucosyltransferase FutM1 from a Bacteroidaceae bacterium from the gut metagenome could obviously enhance the LNDFH II biosynthesis. After optimization of induction conditions, the maximum titer reached 3.011 g/L by shake-flask cultivation. During the fed-batch cultivation, LNDFH II was highly efficiently produced with the highest titer of 18.062 g/L and the productivity yield of 0.301 g/L·h.},
}

@article {pmid38659188,
year = {2024},
author = {Pérez-Castillo, ÍM and Sabag-Daigle, A and López-Chicharro, J and Mihic, N and Rueda, R and Bouzamondo, H},
title = {The athlete gut microbiota: state of the art and practical guidance.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-30},
doi = {10.1163/18762891-bja00007},
pmid = {38659188},
issn = {1876-2891},
abstract = {The gut microbiota has been proposed to grant the athlete a metabolic advantage that might be key when optimising performance. While a taxonomic core set of microorganisms characterising the athlete's gut microbiota has not been delineated, some compositional features might be associated with improved metabolic efficiency, which appears to be driven by the production of bacterial metabolites, such as short-chain fatty acids. Not only long-term exercise but also dietary patterns associated with high-level sports practice contribute to this microbial environment, yet isolating the impact of individual dietary components is challenging. The present review synthetises the available evidence on the compositional aspects of the athlete's gut microbiota, discusses mechanisms involved in the bidirectional association between exercise and the gut environment, and evaluates the role of athletes' diet in this interplay. Additionally, a practical approach to indicators commonly reported in metagenomic and metabolomic analyses is provided to explore how these insights can translate to support dietary protocols.},
}

@article {pmid38659008,
year = {2024},
author = {Santos, JD and Sobral, D and Pinheiro, M and Isidro, J and Bogaardt, C and Pinto, M and Eusébio, R and Santos, A and Mamede, R and Horton, DL and Gomes, JP and , and Borges, V},
title = {INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {61},
pmid = {38659008},
issn = {1756-994X},
support = {101102733//EU4Health Programme (DURABLE)/ ; 773830//European Union's Horizon 2020 Research and Innovation program/ ; EU4H-2022-DGA-MS-IBA-1//EU4H programme (GENEO)/ ; },
mesh = {*Metagenomics/methods ; Humans ; *SARS-CoV-2/genetics/classification ; *Genome, Viral ; *Software ; *COVID-19/virology ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Internet ; Genomics/methods ; },
abstract = {BACKGROUND: Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification.

RESULTS: The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a "generic" build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis.

CONCLUSIONS: The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).},
}

*Metagenomics/methods
Humans
*SARS-CoV-2/genetics/classification
*Genome, Viral
*Software
*COVID-19/virology
*Computational Biology/methods
High-Throughput Nucleotide Sequencing/methods
Internet
Genomics/methods

@article {pmid38658858,
year = {2024},
author = {Liu, C and Liu, F and Nie, D and Xiao, Y and Wu, W and Jia, Y and Jin, L and Qiao, N and Cai, K and Ru, S and Liu, X and Song, Y and Xu, J and Cao, L and Gui, S},
title = {Gut microbiota composition and metabolic characteristics in patients with Craniopharyngioma.},
journal = {BMC cancer},
volume = {24},
number = {1},
pages = {521},
pmid = {38658858},
issn = {1471-2407},
mesh = {Humans ; *Craniopharyngioma/metabolism ; *Gastrointestinal Microbiome ; Male ; Female ; Adult ; *Pituitary Neoplasms/metabolism/microbiology ; *Feces/microbiology ; Middle Aged ; Case-Control Studies ; Young Adult ; Adolescent ; Metabolomics/methods ; Metagenomics/methods ; Metabolome ; },
abstract = {BACKGROUND: Emerging evidence suggests that the gut microbiota is associated with various intracranial neoplastic diseases. It has been observed that alterations in the gut microbiota are present in gliomas, meningiomas, and pituitary neuroendocrine tumors (Pit-NETs). However, the correlation between gut microbiota and craniopharyngioma (CP), a rare embryonic malformation tumor in the sellar region, has not been previously mentioned. Consequently, this study aimed to investigate the gut microbiota composition and metabolic patterns in CP patients, with the goal of identifying potential therapeutic approaches.

METHODS: We enrolled 15 medication-free and non-operated patients with CP and 15 healthy controls (HCs), conducting sequential metagenomic and metabolomic analyses on fecal samples to investigate changes in the gut microbiota of CP patients.

RESULTS: The composition of gut microbiota in patients with CP compared to HCs show significant discrepancies at both the genus and species levels. The CP group exhibits greater species diversity. And the metabolic patterns between the two groups vary markedly.

CONCLUSIONS: The gut microbiota composition and metabolic patterns in patients with CP differ significantly from the healthy population, presenting potential new therapeutic opportunities.},
}

Humans
*Craniopharyngioma/metabolism
*Gastrointestinal Microbiome
Male
Female
Adult
*Pituitary Neoplasms/metabolism/microbiology
*Feces/microbiology
Middle Aged
Case-Control Studies
Young Adult
Adolescent
Metabolomics/methods
Metagenomics/methods
Metabolome

@article {pmid38658841,
year = {2024},
author = {Jeong, S and Liao, YT and Tsai, MH and Wang, YK and Wu, IC and Liu, CJ and Wu, MS and Chan, TS and Chen, MY and Hu, PJ and Kao, WY and Liu, HC and Tsai, MJ and Liu, CY and Chang, CC and Wu, DC and Hsu, YH},
title = {Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {139},
pmid = {38658841},
issn = {1471-2180},
abstract = {BACKGROUND: Gastric cancer is one of the global health concerns. A series of studies on the stomach have confirmed the role of the microbiome in shaping gastrointestinal diseases. Delineation of microbiome signatures to distinguish chronic gastritis from gastric cancer will provide a non-invasive preventative and treatment strategy. In this study, we performed whole metagenome shotgun sequencing of fecal samples to enhance the detection of rare bacterial species and increase genome sequence coverage. Additionally, we employed multiple bioinformatics approaches to investigate the potential targets of the microbiome as an indicator of differentiating gastric cancer from chronic gastritis.

RESULTS: A total of 65 patients were enrolled, comprising 33 individuals with chronic gastritis and 32 with gastric cancer. Within each group, the chronic gastritis group was sub-grouped into intestinal metaplasia (n = 15) and non-intestinal metaplasia (n = 18); the gastric cancer group, early stage (stages 1 and 2, n = 13) and late stage (stages 3 and 4, n = 19) cancer. No significant differences in alpha and beta diversities were detected among the patient groups. However, in a two-group univariate comparison, higher Fusobacteria abundance was identified in phylum; Fusobacteria presented higher abundance in gastric cancer (LDA scored 4.27, q = 0.041 in LEfSe). Age and sex-adjusted MaAsLin and Random Forest variable of importance (VIMP) analysis in species provided meaningful features; Bacteria_caccae was the most contributing species toward gastric cancer and late-stage cancer (beta:2.43, se:0.891, p:0.008, VIMP score:2.543). In contrast, Bifidobacterium_longum significantly contributed to chronic gastritis (beta:-1.8, se:0.699, p:0.009, VIMP score:1.988). Age, sex, and BMI-adjusted MasAsLin on metabolic pathway analysis showed that GLCMANNANAUT-PWY degradation was higher in gastric cancer and one of the contributing species was Fusobacterium_varium.

CONCLUSION: Microbiomes belonging to the pathogenic phylum Fusobacteria and species Bacteroides_caccae and Streptococcus_anginosus can be significant targets for monitoring the progression of gastric cancer. Whereas Bifidobacterium_longum and Lachnospiraceae_bacterium_5_1_63FAA might be protection biomarkers against gastric cancer.},
}

@article {pmid38658578,
year = {2024},
author = {Pedrazzoli, E and Demozzi, M and Visentin, E and Ciciani, M and Bonuzzi, I and Pezzè, L and Lucchetta, L and Maule, G and Amistadi, S and Esposito, F and Lupo, M and Miccio, A and Auricchio, A and Casini, A and Segata, N and Cereseto, A},
title = {CoCas9 is a compact nuclease from the human microbiome for efficient and precise genome editing.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3478},
pmid = {38658578},
issn = {2041-1723},
support = {825825//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101071041//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 1U01CA230551//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; MetaPG-716575//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {The expansion of the CRISPR-Cas toolbox is highly needed to accelerate the development of therapies for genetic diseases. Here, through the interrogation of a massively expanded repository of metagenome-assembled genomes, mostly from human microbiomes, we uncover a large variety (n = 17,173) of type II CRISPR-Cas loci. Among these we identify CoCas9, a strongly active and high-fidelity nuclease with reduced molecular size (1004 amino acids) isolated from an uncultivated Collinsella species. CoCas9 is efficiently co-delivered with its sgRNA through adeno associated viral (AAV) vectors, obtaining efficient in vivo editing in the mouse retina. With this study we uncover a collection of previously uncharacterized Cas9 nucleases, including CoCas9, which enriches the genome editing toolbox.},
}

@article {pmid38658176,
year = {2024},
author = {Ramachandran, P and Grose, C},
title = {Serious neurological adverse events in immunocompetent children and adolescents caused by viral reactivation in the years following varicella vaccination.},
journal = {Reviews in medical virology},
volume = {34},
number = {3},
pages = {e2538},
doi = {10.1002/rmv.2538},
pmid = {38658176},
issn = {1099-1654},
support = {AI153817//National Institutes of Health Bethesda/ ; },
mesh = {Humans ; *Chickenpox Vaccine/adverse effects/administration & dosage/immunology ; Child ; Adolescent ; Virus Activation/drug effects ; Vaccination/adverse effects ; Child, Preschool ; Herpesvirus 3, Human/immunology ; Acyclovir/therapeutic use/adverse effects ; Antiviral Agents/therapeutic use/adverse effects ; Meningitis, Viral/virology/etiology ; Chickenpox/prevention & control/virology ; Male ; Nervous System Diseases/virology/etiology ; Female ; },
abstract = {Serious adverse events following vaccination include medical complications that require hospitalisation. The live varicella vaccine that was approved by the Food and Drug Administration in the United States in 1995 has an excellent safety record. Since the vaccine is a live virus, adverse events are more common in immunocompromised children who are vaccinated inadvertently. This review includes only serious adverse events in children considered to be immunocompetent. The serious adverse event called varicella vaccine meningitis was first reported in a hospitalised immunocompetent child in 2008. When we carried out a literature search, we found 15 cases of immunocompetent children and adolescents with varicella vaccine meningitis; the median age was 11 years. Eight of the children had received two varicella vaccinations. Most of the children also had a concomitant herpes zoster rash, although three did not. The children lived in the United States, Greece, Germany, Switzerland, and Japan. During our literature search, we found five additional cases of serious neurological events in immunocompetent children; these included 4 cases of progressive herpes zoster and one case of acute retinitis. Pulses of enteral corticosteroids as well as a lack of herpes simplex virus antibody may be risk factors for reactivation in immunocompetent children. All 20 children with adverse events were treated with acyclovir and recovered; 19 were hospitalised and one child was managed as an outpatient. Even though the number of neurological adverse events remains exceedingly low following varicella vaccination, we recommend documentation of those caused by the vaccine virus.},
}

Humans
*Chickenpox Vaccine/adverse effects/administration & dosage/immunology
Child
Adolescent
Virus Activation/drug effects
Vaccination/adverse effects
Child, Preschool
Herpesvirus 3, Human/immunology
Acyclovir/therapeutic use/adverse effects
Antiviral Agents/therapeutic use/adverse effects
Meningitis, Viral/virology/etiology
Chickenpox/prevention & control/virology
Male
Nervous System Diseases/virology/etiology
Female

@article {pmid38657817,
year = {2024},
author = {Gong, W and Guo, L and Huang, C and Xie, B and Jiang, M and Zhao, Y and Zhang, H and Wu, Y and Liang, H},
title = {A systematic review of antibiotics and antibiotic resistance genes (ARGs) in mariculture wastewater: Antibiotics removal by microalgal-bacterial symbiotic system (MBSS), ARGs characterization on the metagenomic.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172601},
doi = {10.1016/j.scitotenv.2024.172601},
pmid = {38657817},
issn = {1879-1026},
abstract = {Antibiotic residues in mariculture wastewater seriously affect the aquatic environment. Antibiotic Resistance Genes (ARGs) produced under antibiotic stress flow through the environment and eventually enter the human body, seriously affecting human health. Microalgal-bacterial symbiotic system (MBSS) can remove antibiotics from mariculture and reduce the flow of ARGs into the environment. This review encapsulates the present scenario of mariculture wastewater, the removal mechanism of MBSS for antibiotics, and the biomolecular information under metagenomic assay. When confronted with antibiotics, there was a notable augmentation in the extracellular polymeric substances (EPS) content within MBSS, along with a concurrent elevation in the proportion of protein (PN) constituents within the EPS, which limits the entry of antibiotics into the cellular interior. Quorum sensing stimulates the microorganisms to produce biological responses (DNA synthesis - for adhesion) through signaling. Oxidative stress promotes gene expression (coupling, conjugation) to enhance horizontal gene transfer (HGT) in MBSS. The microbial community under metagenomic detection is dominated by aerobic bacteria in the bacterial-microalgal system. Compared to aerobic bacteria, anaerobic bacteria had the significant advantage of decreasing the distribution of ARGs. Overall, MBSS exhibits remarkable efficacy in mitigating the challenges posed by antibiotics and resistant genes from mariculture wastewater.},
}

@article {pmid38657605,
year = {2024},
author = {Su, Q and Lau, RI and Liu, Q and Li, MKT and Yan Mak, JW and Lu, W and Lau, ISF and Lau, LHS and Yeung, GTY and Cheung, CP and Tang, W and Liu, C and Ching, JYL and Cheong, PK and Chan, FKL and Ng, SC},
title = {The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.04.005},
pmid = {38657605},
issn = {1934-6069},
abstract = {The mechanisms underlying the many phenotypic manifestations of post-acute COVID-19 syndrome (PACS) are poorly understood. Herein, we characterized the gut microbiome in heterogeneous cohorts of subjects with PACS and developed a multi-label machine learning model for using the microbiome to predict specific symptoms. Our processed data covered 585 bacterial species and 500 microbial pathways, explaining 12.7% of the inter-individual variability in PACS. Three gut-microbiome-based enterotypes were identified in subjects with PACS and associated with different phenotypic manifestations. The trained model showed an accuracy of 0.89 in predicting individual symptoms of PACS in the test set and maintained a sensitivity of 86% and a specificity of 82% in predicting upcoming symptoms in an independent longitudinal cohort of subjects before they developed PACS. This study demonstrates that the gut microbiome is associated with phenotypic manifestations of PACS, which has potential clinical utility for the prediction and diagnosis of PACS.},
}

@article {pmid38657391,
year = {2024},
author = {Bains, RK and Nasseri, SA and Wardman, JF and Withers, SG},
title = {Advances in the understanding and exploitation of carbohydrate-active enzymes.},
journal = {Current opinion in chemical biology},
volume = {80},
number = {},
pages = {102457},
doi = {10.1016/j.cbpa.2024.102457},
pmid = {38657391},
issn = {1879-0402},
abstract = {Carbohydrate-active enzymes (CAZymes) are responsible for the biosynthesis, modification and degradation of all glycans in Nature. Advances in genomic and metagenomic methodologies, in conjunction with lower cost gene synthesis, have provided access to a steady stream of new CAZymes with both well-established and novel mechanisms. At the same time, increasing access to cryo-EM has resulted in exciting new structures, particularly of transmembrane glycosyltransferases of various sorts. This improved understanding has resulted in widespread progress in applications of CAZymes across diverse fields, including therapeutics, organ transplantation, foods, and biofuels. Herein, we highlight a few of the many important advances that have recently been made in the understanding and applications of CAZymes.},
}

@article {pmid38658654,
year = {2024},
author = {Han, G and Huang, T and Liu, X and Liu, R},
title = {Bacteriophage EPP-1, a potential antibiotic alternative for controlling edwardsiellosis caused by Edwardsiella piscicida while mitigating drug-resistant gene dissemination.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9399},
pmid = {38658654},
issn = {2045-2322},
support = {42377120//the National Natural Science Foundation of China/ ; },
abstract = {Edwardsiella piscicida causes significant economic losses to the aquaculture industry worldwide. Phage-based biocontrol methods are experiencing a renaissance because of the spread of drug-resistant genes and bacteria resulting from the heavy use of antibiotics. Here, we showed that the novel Edwardsiella phage EPP-1 could achieve comparable efficacy to florfenicol using a zebrafish model of Edwardsiella piscicida infection and could reduce the content of the floR resistance gene in zebrafish excreta. Specifically, phage EPP-1 inhibited bacterial growth in vitro and significantly improved the zebrafish survival rate in vivo (P = 0.0035), achieving an efficacy comparable to that of florfenicol (P = 0.2304). Notably, integrating the results of 16S rRNA sequencing, metagenomic sequencing, and qPCR, although the effects of phage EPP-1 converged with those of florfenicol in terms of the community composition and potential function of the zebrafish gut microbiota, it reduced the floR gene content in zebrafish excreta and aquaculture water. Overall, our study highlights the feasibility and safety of phage therapy for edwardsiellosis control, which has profound implications for the development of antibiotic alternatives to address the antibiotic crisis.},
}

@article {pmid38658559,
year = {2024},
author = {Chen, KH and Feng, J and Bodelier, PLE and Yang, Z and Huang, Q and Delgado-Baquerizo, M and Cai, P and Tan, W and Liu, YR},
title = {Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3471},
pmid = {38658559},
issn = {2041-1723},
support = {32071595//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371731//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177022//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH4) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH4 oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and [13]CH4-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH4 oxidation in supporting denitrification. Our results reveal positive relationships between CH4 oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH4 and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, [13]CH4-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating [13]C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of [13]C-metagenome-assembled genomes and [13]C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH4 oxidation, for the coupling of CH4 oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH4 oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.},
}

@article {pmid38658525,
year = {2024},
author = {Arthofer, P and Panhölzl, F and Delafont, V and Hay, A and Reipert, S and Cyran, N and Wienkoop, S and Willemsen, A and Sifaoui, I and Arberas-Jiménez, I and Schulz, F and Lorenzo-Morales, J and Horn, M},
title = {A giant virus infecting the amoeboflagellate Naegleria.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3307},
pmid = {38658525},
issn = {2041-1723},
support = {P37198-B//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 891572//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 101039843//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Giant viruses (Nucleocytoviricota) are significant lethality agents of various eukaryotic hosts. Although metagenomics indicates their ubiquitous distribution, available giant virus isolates are restricted to a very small number of protist and algal hosts. Here we report on the first viral isolate that replicates in the amoeboflagellate Naegleria. This genus comprises the notorious human pathogen Naegleria fowleri, the causative agent of the rare but fatal primary amoebic meningoencephalitis. We have elucidated the structure and infection cycle of this giant virus, Catovirus naegleriensis (a.k.a. Naegleriavirus, NiV), and show its unique adaptations to its Naegleria host using fluorescence in situ hybridization, electron microscopy, genomics, and proteomics. Naegleriavirus is only the fourth isolate of the highly diverse subfamily Klosneuvirinae, and like its relatives the NiV genome contains a large number of translation genes, but lacks transfer RNAs (tRNAs). NiV has acquired genes from its Naegleria host, which code for heat shock proteins and apoptosis inhibiting factors, presumably for host interactions. Notably, NiV infection was lethal to all Naegleria species tested, including the human pathogen N. fowleri. This study expands our experimental framework for investigating giant viruses and may help to better understand the basic biology of the human pathogen N. fowleri.},
}

@article {pmid38657818,
year = {2024},
author = {Stewart, DI and Vasconcelos, EJR and Burke, IT and Baker, A},
title = {Metagenomes from microbial populations beneath a chromium waste tip give insight into the mechanism of Cr (VI) reduction.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172507},
doi = {10.1016/j.scitotenv.2024.172507},
pmid = {38657818},
issn = {1879-1026},
abstract = {Dumped Chromium Ore Processing Residue (COPR) at legacy sites poses a threat to health through leaching of toxic Cr(VI) into groundwater. Previous work implicates microbial activity in reducing Cr(VI) to less mobile and toxic Cr(III), but the mechanism has not been explored. To address this question a combined metagenomic and geochemical study was undertaken. Soil samples from below the COPR waste were used to establish anaerobic microcosms which were challenged with Cr(VI), with or without acetate as an electron donor, and incubated for 70 days. Cr was rapidly reduced in both systems, which also reduced nitrate, nitrite then sulfate, but this sequence was accelerated in the acetate amended microcosms. 16S rRNA gene sequencing revealed that the original soil sample was diverse but both microcosm systems became less diverse by the end of the experiment. A high proportion of 16S rRNA gene reads and metagenome-assembled genomes (MAGs) with high completeness could not be taxonomically classified, highlighting the distinctiveness of these alkaline Cr impacted systems. Examination of the coding capacity revealed widespread capability for metal tolerance and Fe uptake and storage, and both populations possessed metabolic capability to degrade a wide range of organic molecules. The relative abundance of genes for fatty acid degradation was 4× higher in the unamended compared to the acetate amended system, whereas the capacity for dissimilatory sulfate metabolism was 3× higher in the acetate amended system. We demonstrate that naturally occurring in situ bacterial populations have the metabolic capability to couple acetate oxidation to sequential reduction of electron acceptors which can reduce Cr(VI) to less mobile and toxic Cr(III), and that microbially produced sulfide may be important in reductive precipitation of chromate. This capability could be harnessed to create a Cr(VI) trap-zone beneath COPR tips without the need to disturb the waste.},
}

@article {pmid38656971,
year = {2024},
author = {Alahdal, H and Almuneef, G and Alkhulaifi, MM and Aldibasi, O and Aljouie, A and Alharbi, O and Almohawes, ZN and Basingab, F and Rejili, M},
title = {Gut microbiota composition in patients with Crohn's disease in Saudi Arabia.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0299749},
doi = {10.1371/journal.pone.0299749},
pmid = {38656971},
issn = {1932-6203},
mesh = {Humans ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome ; Saudi Arabia/epidemiology ; Male ; Female ; Adult ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Dysbiosis/microbiology ; Young Adult ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Quality of Life ; },
abstract = {Crohn's disease (CD) entails intricate interactions with gut microbiome diversity, richness, and composition. The relationship between CD and gut microbiome is not clearly understood and has not been previously characterized in Saudi Arabia. We performed statistical analysis about various factors influencing CD activity and microbiota dysbiosis, including diagnosis, treatment, and its impact on their quality of life as well as high-throughput metagenomic V3-V4 16S rRNA encoding gene hypervariable region of a total of eighty patients with CD, both in its active and inactive state with healthy controls. The results were correlated with the demographic and lifestyle information, which the participants provided via a questionnaire. α-diversity measures indicated lower bacterial diversity and richness in the active and inactive CD groups compared to the control group. Greater dysbiosis was observed in the active CD patients compared to the inactive form of the disease, showed by a reduction in microbial diversity. Specific pathogenic bacteria such as Filifactor, Peptoniphilus, and Sellimonas were identified as characteristic of CD groups. In contrast, anti-inflammatory bacteria like Defluviitalea, Papillibacter, and Petroclostridium were associated with the control group. Among the various factors influencing disease activity and microbiota dysbiosis, smoking emerged as the most significant, with reduced α-diversity and richness for the smokers in all groups, and proinflammatory Fusobacteria was more present (p<0.05). Opposite to the control group, microbial diversity and richness were lower in CD participants of older age compared to younger ones, and male CD participants showed less diversity compared to women participants from the same groups. Our results describe the first report on the relationship between microbiota and Crohn's disease progress in Saudi Arabia, which may provide a theoretical basis for the application of therapeutic methods to regulate gut microbes in CD.},
}

Humans
*Crohn Disease/microbiology
*Gastrointestinal Microbiome
Saudi Arabia/epidemiology
Male
Female
Adult
*RNA, Ribosomal, 16S/genetics
Middle Aged
Dysbiosis/microbiology
Young Adult
Bacteria/genetics/classification/isolation & purification
Case-Control Studies
Quality of Life

@article {pmid38656275,
year = {2024},
author = {Divilov, K},
title = {Whole-genome assembly of a novel invertebrate herpesvirus from the gastropod Babylonia areolata.},
journal = {Microbial genomics},
volume = {10},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001237},
pmid = {38656275},
issn = {2057-5858},
mesh = {Animals ; *Genome, Viral ; *Gastropoda/virology ; *Phylogeny ; *Herpesviridae/genetics/classification ; Whole Genome Sequencing/methods ; Genomics/methods ; Synteny ; },
abstract = {Molluscan herpesviruses cause disease in species of major importance to aquaculture and are the only known herpesviruses to infect invertebrates, which lack an adaptive immune system. Understanding the evolution of malacoherpesviruses in relation to their hosts will likely require comparative genomic studies on multiple phylogenetic scales. Currently, only two malacoherpesvirus species have genomes that have been fully assembled, which limits the ability to perform comparative genomic studies on this family of viruses. In the present study, we fully assemble a herpesvirus from Illumina and Nanopore sequence data that were previously used to assemble the genome of the gastropod Babylonia areolata. We tentatively assign this novel herpesvirus to the genus Aurivirus within the family Malacoherpesviridae based on a phylogenetic analysis of DNA polymerase. While structurally similar to other malacoherpesvirus genomes, a synteny analysis of the novel herpesvirus with another Aurivirus species indicates that genomic rearrangements might be an important process in the evolution of this genus. We anticipate that future complete assemblies of malacoherpesviruses will be a valuable resource in comparative herpesvirus research.},
}

Animals
*Genome, Viral
*Gastropoda/virology
*Phylogeny
*Herpesviridae/genetics/classification
Whole Genome Sequencing/methods
Genomics/methods
Synteny

@article {pmid38655538,
year = {2024},
author = {Tay, HW and Tay, KS},
title = {Future directions for early detection of fracture related infections.},
journal = {Journal of orthopaedics},
volume = {55},
number = {},
pages = {64-68},
pmid = {38655538},
issn = {0972-978X},
abstract = {INTRODUCTION: Fracture related infection (FRI) refers to pathogens infecting a fracture site and hence impeding fracture healing. It is a significant complication that carries substantial disease burden and socio-economic costs, but has had limited scientific development. Hence, this paper will review the existing strategies for early detection of FRI, in the form of serum markers, molecular diagnostics and imaging modalities, and further discuss potential future directions for improved detection of FRI.

The Anti-infection Global Expert Committee (AIGEC) developed a consensus definition for FRI in 2017, which includes confirmatory and suggestive criteria for diagnosis of FRI. Existing strategies for diagnosis include clinical, laboratory, histopathological, microbiological and radiological investigations.

With increasing recognition of FRI, early detection is crucial for early treatment to be enforced. We have identified potential areas for future development in diagnostics for early detection of FRI, which are discussed in this manuscript. They include inflammatory cytokines, serum calcium levels, platelet count, improved management of histopathological and microbiological specimens, metagenomics, wound biomarkers, gut microbiota analysis, and novel imaging technologies.},
}

@article {pmid38655084,
year = {2024},
author = {Orf, GS and Ahouidi, AD and Mata, M and Diedhiou, C and Mboup, A and Padane, A and Manga, NM and Dela-Del Lawson, AT and Averhoff, F and Berg, MG and Cloherty, GA and Mboup, S},
title = {Next-generation sequencing survey of acute febrile illness in Senegal (2020-2022).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1362714},
pmid = {38655084},
issn = {1664-302X},
abstract = {INTRODUCTION: Acute febrile illnesses (AFI) in developing tropical and sub-tropical nations are challenging to diagnose due to the numerous causes and non-specific symptoms. The proliferation of rapid diagnostic testing and successful control campaigns against malaria have revealed that non-Plasmodium pathogens still contribute significantly to AFI burden. Thus, a more complete understanding of local trends and potential causes is important for selecting the correct treatment course, which in turn will reduce morbidity and mortality. Next-generation sequencing (NGS) in a laboratory setting can be used to identify known and novel pathogens in individuals with AFI.

METHODS: In this study, plasma was collected from 228 febrile patients tested negative for malaria at clinics across Senegal from 2020-2022. Total nucleic acids were extracted and converted to metagenomic NGS libraries. To identify viral pathogens, especially those present at low concentration, an aliquot of each library was processed with a viral enrichment panel and sequenced. Corresponding metagenomic libraries were also sequenced to identify non-viral pathogens.

RESULTS AND DISCUSSION: Sequencing reads for pathogens with a possible link to febrile illness were identified in 51/228 specimens, including (but not limited to): Borrelia crocidurae (N = 7), West Nile virus (N = 3), Rickettsia felis (N = 2), Bartonella quintana (N = 1), human herpesvirus 8 (N = 1), and Saffold virus (N = 1). Reads corresponding to Plasmodium falciparum were detected in 19 specimens, though their presence in the cohort was likely due to user error of rapid diagnostic testing or incorrect specimen segregation at the clinics. Mosquito-borne pathogens were typically detected just after the conclusion of the rainy season, while tick-borne pathogens were mostly detected before the rainy season. The three West Nile virus strains were phylogenetically characterized and shown to be related to both European and North American clades. Surveys such as this will increase the understanding of the potential causes of non-malarial AFI, which may help inform diagnostic and treatment options for clinicians who provide care to patients in Senegal.},
}

@article {pmid38655082,
year = {2024},
author = {Thøgersen, MS and Zervas, A and Stougaard, P and Ellegaard-Jensen, L},
title = {Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1358787},
pmid = {38655082},
issn = {1664-302X},
abstract = {The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.},
}

@article {pmid38654702,
year = {2024},
author = {Hewel, C and Schmidt, H and Runkel, S and Kohnen, W and Schweiger-Seemann, S and Michel, A and Bikar, SE and Lieb, B and Plachter, B and Hankeln, T and Linke, M and Gerber, S},
title = {Nanopore adaptive sampling of a metagenomic sample derived from a human monkeypox case.},
journal = {Journal of medical virology},
volume = {96},
number = {5},
pages = {e29610},
doi = {10.1002/jmv.29610},
pmid = {38654702},
issn = {1096-9071},
mesh = {Humans ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Mpox (monkeypox)/epidemiology/virology ; *Monkeypox virus/genetics/isolation & purification ; *Whole Genome Sequencing/methods ; Nanopores ; DNA, Viral/genetics ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Setup of proper genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore (PromethION P24) and Illumina (NextSeq. 2000) Whole Genome Sequencing (WGS) of a monkeypox sample. Adaptive sampling was applied for in silico depletion of the human host genome, allowing for the enrichment of low abundance viral DNA without a priori knowledge of sample composition. Nanopore sequencing allowed for high viral genome coverage, tracking of sample composition during sequencing, strain determination, and preliminary assessment of mutational pattern. In addition to that, only Nanopore data allowed us to resolve the entire monkeypox virus genome, with respect to two structural variants belonging to the genes OPG015 and OPG208. These SVs in important host range genes seem stable throughout the outbreak and are frequently misassembled and/or misannotated due to the prevalence of short read sequencing or short read first assembly. Ideally, standalone standard Illumina sequencing should not be used for Monkeypox WGS and de novo assembly, since it will obfuscate the structure of the genome, which has an impact on the quality and completeness of the genomes deposited in public databases and thus possibly on the ability to evaluate the complete genetic reason for the host range change of monkeypox in the current pandemic.},
}

Humans
*Genome, Viral/genetics
*Metagenomics/methods
*Nanopore Sequencing/methods
*Mpox (monkeypox)/epidemiology/virology
*Monkeypox virus/genetics/isolation & purification
*Whole Genome Sequencing/methods
Nanopores
DNA, Viral/genetics
High-Throughput Nucleotide Sequencing/methods

@article {pmid38653968,
year = {2024},
author = {Serra Moncadas, L and Hofer, C and Bulzu, PA and Pernthaler, J and Andrei, AS},
title = {Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3421},
pmid = {38653968},
issn = {2041-1723},
support = {PZ00P3_193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {*Genome, Bacterial ; *Bacteria/genetics/classification ; *Fresh Water/microbiology ; *Phylogeny ; *Adaptation, Physiological/genetics ; Metagenomics/methods ; Evolution, Molecular ; Genome Size ; Proteome/genetics/metabolism ; },
abstract = {The emergence of bacterial species is rooted in their inherent potential for continuous evolution and adaptation to an ever-changing ecological landscape. The adaptive capacity of most species frequently resides within the repertoire of genes encoding the secreted proteome (SP), as it serves as a primary interface used to regulate survival/reproduction strategies. Here, by applying evolutionary genomics approaches to metagenomics data, we show that abundant freshwater bacteria exhibit biphasic adaptation states linked to the eco-evolutionary processes governing their genome sizes. While species with average to large genomes adhere to the dominant paradigm of evolution through niche adaptation by reducing the evolutionary pressure on their SPs (via the augmentation of functionally redundant genes that buffer mutational fitness loss) and increasing the phylogenetic distance of recombination events, most of the genome-reduced species exhibit a nonconforming state. In contrast, their SPs reflect a combination of low functional redundancy and high selection pressure, resulting in significantly higher levels of conservation and invariance. Our findings indicate that although niche adaptation is the principal mechanism driving speciation, freshwater genome-reduced bacteria often experience extended periods of adaptive stasis. Understanding the adaptive state of microbial species will lead to a better comprehension of their spatiotemporal dynamics, biogeography, and resilience to global change.},
}

*Genome, Bacterial
*Bacteria/genetics/classification
*Fresh Water/microbiology
*Phylogeny
*Adaptation, Physiological/genetics
Metagenomics/methods
Evolution, Molecular
Genome Size
Proteome/genetics/metabolism

@article {pmid38653418,
year = {2024},
author = {Yu, T and Liu, Z and Hu, B and Zhu, L},
title = {Field-based investigation reveals selective enrichment of companion microbes in vegetables leading to specific accumulation of antibiotic resistance genes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172636},
doi = {10.1016/j.scitotenv.2024.172636},
pmid = {38653418},
issn = {1879-1026},
abstract = {Vegetables capture antibiotic resistance genes (ARGs) from the soil and then pass them on to consumers through the delivery chain and food chain, and are therefore the key node that may increase the risk of human exposure to ARGs. This study investigates the patterns and driving forces behind the transmission of ARGs from soil to vegetables by the commonly planted cash crops in the coastal region of southern China, i.e. broccoli, pumpkin, and broad bean, to investigate. The study used metagenomic data to reveal the microbial and ARGs profiles of various vegetables and the soil they are grown. The results indicate significant differences in the accumulation of ARGs among different vegetables harvested in the same area at the same time frame, and the ARGs accumulation ability of the three vegetables was in the order of broccoli, broad bean, and pumpkin. In addition, broccoli collected the highest number of ARGs in types (n = 14), while pumpkin (n = 13) does not obtain trimethoprim resistance genes and broad beans (n = 10) do not obtain chloramphenicol, fosmidomycin, quinolone, rifamycin, or trimethoprim resistance genes. Host tracking analysis shows a strong positive correlation (|rho| > 0.8, p < 0.05) between enriched ARGs and plant companion microbes. Enrichment analysis of metabolic pathways of companion microbes shows that vegetables exhibit a discernible enrichment of companion microbes, with significant differences among vegetables. This phenomenon is primarily due to the screening of carbohydrate metabolism capabilities among companion microbes and leads varied patterns of ARGs that spread from the soil to vegetables. This offers a novel insight into the intervention of foodborne transmission of ARGs.},
}

@article {pmid38653417,
year = {2024},
author = {Haobo, G and Zhaofeng, C and Zhiyong, L and Qipeng, D and Mingdeng, X and Tong, Z and Zhenchi, L and Zijuan, Z and Yunjiang, Y},
title = {Enhanced humification of full-scale apple wood and cow manure by promoting lignocellulose degradation via biomass pretreatments.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172646},
doi = {10.1016/j.scitotenv.2024.172646},
pmid = {38653417},
issn = {1879-1026},
abstract = {Agroforestry waste and cow manure pollute the environment, of which, agroforestry waste is difficult to degrade. Compost is an effective way to dispose agroforestry waste; however, the low degradation efficiency of lignocellulose in agroforestry waste affects the process of composting humification. This study investigated lignocellulose degradation and composting humification in full-size apple wood and cow manure composting processes by applying different pretreatments (acidic, alkaline, and high-temperature) to apple wood. Simultaneously, physicochemical characterization and metagenome sequencing were combined to analyze the function of carbohydrate-active enzymes database (CAZy). Therefore, microbial communities and functions were linked during the composting process and the lignocellulose degradation mechanism was elaborated. The results showed that the addition of apple wood increased the compost humus (HS) yield, and pretreatment of apple wood enhanced the lignocellulose degradation during composting processes. In addition, pretreatment improved the physicochemical properties, such as temperature, pH, electric conductivity (EC), ammonium nitrogen (NH4[+]), and nitrate nitrogen (NO3[-]) in the compost, of which, acid treated apple wood compost (AcAWC) achieved the highest temperature of 58.4 °C, effectively promoting nitrification with NO3[-] ultimately reaching 0.127 g/kg. In all composts, microbial networks constructed a high proportion of positively correlated connections, and microorganisms promoted the composting process through cooperation. The proportions of glycosyltransferase (GT) and glycoside hydrolase (GH) promoted the separation and degradation of lignocellulose during composting to form HS. Notably, the adverse effects of the alkali-treated apple wood compost on bacteria were greater. AcAWC showed significant correlations between bacterial and fungal communities and both lignin and hemicellulose, and had more biomarkers associated with lignocellulose degradation and humification. The lignin degradation rate was 24.57 % and the HS yield increased by 27.49 %. Therefore, AcAWC has been confirmed to enhance lignocellulose degradation and promote compost humification by altering the properties of the apple wood and establishing a richer microbial community.},
}

@article {pmid38652444,
year = {2024},
author = {Li, D and Wang, H and Chen, N and Jiang, H and Chen, N},
title = {Metagenomic analysis of soil microbial communities associated with Poa alpigena Lindm in Haixin Mountain, Qinghai Lake.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38652444},
issn = {1678-4405},
support = {WXBSH2021001//Postdoctoral Science Foundation of West Anhui University/ ; WGKQ2021021//The High-level Talent Project of West Anhui University/ ; GXYQ2020127//the Provincial Level Nature Science Foundation of Anhui Education Department/ ; 2022AH010090//Anhui Scientific Research and Innovation Team of Quality Evaluation and Improvement of Traditional Chinese Medicine/ ; KJ2021A0924//Natural Science Research Project of Anhui Provincial Colleges and Universities/ ; },
abstract = {To investigate the impact of Poa alpigena Lindm on rhizosphere and bulk soil microorganisms in Haixin Mountain, Qinghai Lake, this study employed metagenomics technology to analyze the microbial communities of the samples. Results showed that 65 phyla, 139 classes, 278 orders, 596 families, 2376 genera, and 5545 species of soil microorganisms were identified from rhizosphere and bulk soil samples. Additionally, a microbial gene library specific to Poa alpigena Lindm was established for Qinghai Lake. Through α-diversity analysis, the richness and diversity of bulk microorganisms both significantly had a higher value than that in rhizosphere soil. The indicator microorganisms of rhizosphere and bulk soil at class level were Actinobacteria and Alphaproteobacteria, respectively. KEGG pathway analysis indicated that Carotenoid biosynthesis, Starch and sucrose metabolism, Bacterial chemotaxis, MAPK signaling pathway, Terpenoid backbone biosynthesis, and vancomycin resistance were the key differential metabolic pathways of rhizosphere soil microorganisms; in contrast, in bulk soil, the key differential metabolic were Benzoate degradation, Glycolysis gluconeogenesis, Aminobenzoate degradation, ABC transporters, Glyoxylate and dicarboxylate metabolism, oxidative phosphorylation, Degradation of aromatic compounds, Methane metabolism, Pyruvate metabolism and Microbial metabolism diverse environments. Our results indicated that Poa alpigena Lindm rhizosphere soil possessed selectivity for microorganisms in Qinghai Lake Haixin Mountain, and the rhizosphere soil also provided a suitable survival environment for microorganisms.},
}

@article {pmid38651930,
year = {2024},
author = {Reygner, J and Delannoy, J and Barba-Goudiaby, M-T and Gasc, C and Levast, B and Gaschet, E and Ferraris, L and Paul, S and Kapel, N and Waligora-Dupriet, A-J and Barbut, F and Thomas, M and Schwintner, C and Laperrousaz, B and Corvaïa, N},
title = {Reduction of product composition variability using pooled microbiome ecosystem therapy and consequence in two infectious murine models.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0001624},
doi = {10.1128/aem.00016-24},
pmid = {38651930},
issn = {1098-5336},
abstract = {Growing evidence demonstrates the key role of the gut microbiota in human health and disease. The recent success of microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on its potential in conditions associated with gut dysbiosis, such as acute graft-versus-host disease, intestinal bowel diseases, neurodegenerative diseases, or even cancer. However, the difficulty in defining a "good" donor as well as the intrinsic variability of donor-derived products' taxonomic composition limits the translatability and reproducibility of these studies. Thus, the pooling of donors' feces has been proposed to homogenize product composition and achieve higher taxonomic richness and diversity. In this study, we compared the metagenomic profile of pooled products to corresponding single donor-derived products. We demonstrated that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria known to produce anti-inflammatory short chain fatty acids compared to single donor-derived products. We then evaluated pooled products' efficacy compared to corresponding single donor-derived products in Salmonella and C. difficile infectious mouse models. We were able to demonstrate that pooled products decreased pathogenicity by inducing a structural change in the intestinal microbiota composition. Single donor-derived product efficacy was variable, with some products failing to control disease progression. We further performed in vitro growth inhibition assays of two extremely drug-resistant bacteria, Enterococcus faecium vanA and Klebsiella pneumoniae oxa48, supporting the use of pooled microbiotherapies. Altogether, these results demonstrate that the heterogeneity of donor-derived products is corrected by pooled fecal microbiotherapies in several infectious preclinical models.IMPORTANCEGrowing evidence demonstrates the key role of the gut microbiota in human health and disease. Recent Food and Drug Administration approval of fecal microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on their potential to treat pathological conditions associated with gut dysbiosis. In this study, we combined metagenomic analysis with in vitro and in vivo studies to compare the efficacy of pooled microbiotherapy products to corresponding single donor-derived products. We demonstrate that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria compared to single donor-derived products. We further reveal that pooled products decreased Salmonella and Clostridioides difficile pathogenicity in mice, while single donor-derived product efficacy was variable, with some products failing to control disease progression. Altogether, these findings support the development of pooled microbiotherapies to overcome donor-dependent treatment efficacy.},
}

@article {pmid38651915,
year = {2024},
author = {Jia, C and Wu, C and Li, Y and Wang, S and Liu, J and Liu, J and Su, H and Tian, X and Li, J},
title = {Metagenome-assembled genomes from enrichment cultures grown on xenobiotic solvents.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0010724},
doi = {10.1128/mra.00107-24},
pmid = {38651915},
issn = {2576-098X},
abstract = {Microbes play a significant role in the cleanup of xenobiotic contaminants. Based on metagenomes derived from long-term enrichment cultures grown on xenobiotic solvents, we report 166 metagenome-assembled genomes, of which 137 are predicted to be more than 90% complete. These genomes broaden the representation of xenobiotic degraders.},
}

@article {pmid38651910,
year = {2024},
author = {Rodríguez-Ramos, J and Nicora, CD and Purvine, SO and Borton, MA and McGivern, BB and Hoyt, DW and Lipton, MS and Wrighton, KC},
title = {Untargeted, tandem mass spectrometry metaproteome of Columbia River sediments.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0003324},
doi = {10.1128/mra.00033-24},
pmid = {38651910},
issn = {2576-098X},
abstract = {Rivers are critical ecosystems that impact global biogeochemical cycles. Nonetheless, a mechanistic understanding of river microbial metabolisms and their influences on geochemistry is lacking. Here, we announce metaproteomes of river sediments that are paired with metagenomes and metabolites, enabling an understanding of the microbial underpinnings of river respiration.},
}

@article {pmid38651859,
year = {2024},
author = {Cai, X and Yi, P and Chen, X and Wu, J and Lan, G and Li, S and Luo, S and Huang, F and Huang, J and Shen, P},
title = {Intake of compound probiotics accelerates the construction of immune function and gut microbiome in Holstein calves.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0190923},
doi = {10.1128/spectrum.01909-23},
pmid = {38651859},
issn = {2165-0497},
abstract = {UNLABELLED: Acquired immunity is an important way to construct the intestinal immune barrier in mammals, which is almost dependent on suckling. To develop a new strategy for accelerating the construction of gut microbiome, newborn Holstein calves were continuously fed with 40 mL of compound probiotics (containing Lactobacillus plantarum T-14, Enterococcus faecium T-11, Saccharomyces cerevisiae T-209, and Bacillus licheniformis T-231) per day for 60 days. Through diarrhea rate monitoring, immune index testing, antioxidant capacity detection, and metagenome sequencing, the changes in diarrhea incidence, average daily gain, immune index, and gut microbiome of newborn calves within 60 days were investigated. Results indicated that feeding the compound probiotics reduced the average diarrhea rate of calves by 42.90%, increased the average daily gain by 43.40%, raised the antioxidant indexes of catalase, superoxide dismutase, total antioxidant capacity, and Glutathione peroxidase by 22.81%, 6.49%, 8.33%, and 13.67%, respectively, and increased the immune indexes of IgA, IgG, and IgM by 10.44%, 4.85%, and 6.12%, respectively. Moreover, metagenome sequencing data showed that feeding the compound probiotics increased the abundance of beneficial strains (e.g., Lactococcus lactis and Bacillus massionigeriensis) and decreased the abundance of some harmful strains (e.g., Escherichia sp. MOD1-EC5189 and Mycobacterium brisbane) in the gut microbiome of calves, thus contributing to accelerating the construction of healthy gut microbiome in newborn Holstein calves.

IMPORTANCE: The unstable gut microbiome and incomplete intestinal function of newborn calves are important factors for the high incidence of early diarrhea. This study presents an effective strategy to improve the overall immunity and gut microbiome in calves and provides new insights into the application of compound probiotics in mammals.},
}

@article {pmid38651173,
year = {2024},
author = {Xu, L and Yue, XL and Li, HZ and Jian, SL and Shu, WS and Cui, L and Xu, XW},
title = {Aerobic Anoxygenic Phototrophic Bacteria in the Marine Environments Revealed by Raman/Fluorescence-Guided Single-Cell Sorting and Targeted Metagenomics.},
journal = {Environmental science & technology},
volume = {58},
number = {16},
pages = {7087-7098},
doi = {10.1021/acs.est.4c02881},
pmid = {38651173},
issn = {1520-5851},
abstract = {Aerobic anoxygenic phototrophic bacteria (AAPB) contribute profoundly to the global carbon cycle. However, most AAPB in marine environments are uncultured and at low abundance, hampering the recognition of their functions and molecular mechanisms. In this study, we developed a new culture-independent method to identify and sort AAPB using single-cell Raman/fluorescence spectroscopy. Characteristic Raman and fluorescent bands specific to bacteriochlorophyll a (Bchl a) in AAPB were determined by comparing multiple known AAPB with non-AAPB isolates. Using these spectroscopic biomarkers, AAPB in coastal seawater, pelagic seawater, and hydrothermal sediment samples were screened, sorted, and sequenced. 16S rRNA gene analysis and functional gene annotations of sorted cells revealed novel AAPB members and functional genes, including one species belonging to the genus Sphingomonas, two genera affiliated to classes Betaproteobacteria and Gammaproteobacteria, and function genes bchCDIX, pucC2, and pufL related to Bchl a biosynthesis and photosynthetic reaction center assembly. Metagenome-assembled genomes (MAGs) of sorted cells from pelagic seawater and deep-sea hydrothermal sediment belonged to Erythrobacter sanguineus that was considered as an AAPB and genus Sphingomonas, respectively. Moreover, multiple photosynthesis-related genes were annotated in both MAGs, and comparative genomic analysis revealed several exclusive genes involved in amino acid and inorganic ion metabolism and transport. This study employed a new single-cell spectroscopy method to detect AAPB, not only broadening the taxonomic and genetic contents of AAPB in marine environments but also revealing their genetic mechanisms at the single-genomic level.},
}

@article {pmid38650708,
year = {2024},
author = {Mosley, OE and Gios, E and Handley, KM},
title = {Implications for nitrogen and sulphur cycles: phylogeny and niche-range of Nitrospirota in terrestrial aquifers.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae047},
pmid = {38650708},
issn = {2730-6151},
abstract = {Increasing evidence suggests Nitrospirota are important contributors to aquatic and subsurface nitrogen and sulphur cycles. We determined the phylogenetic and ecological niche associations of Nitrospirota colonizing terrestrial aquifers. Nitrospirota compositions were determined across 59 groundwater wells. Distributions were strongly influenced by oxygen availability in groundwater, marked by a trade-off between aerobic (Nitrospira, Leptospirillum) and anaerobic (Thermodesulfovibrionia, unclassified) lineages. Seven Nitrospirota metagenome-assembled genomes (MAGs), or populations, were recovered from a subset of wells, including three from the recently designated class 9FT-COMBO-42-15. Most were relatively more abundant and transcriptionally active in dysoxic groundwater. These MAGs were analysed with 743 other Nitrospirota genomes. Results illustrate the predominance of certain lineages in aquifers (e.g. non-nitrifying Nitrospiria, classes 9FT-COMBO-42-15 and UBA9217, and Thermodesulfovibrionales family UBA1546). These lineages are characterized by mechanisms for nitrate reduction and sulphur cycling, and, excluding Nitrospiria, the Wood-Ljungdahl pathway, consistent with carbon-limited, low-oxygen, and sulphur-rich aquifer conditions. Class 9FT-COMBO-42-15 is a sister clade of Nitrospiria and comprises two families spanning a transition in carbon fixation approaches: f_HDB-SIOIB13 encodes rTCA (like Nitrospiria) and f_9FT-COMBO-42-15 encodes Wood-Ljungdahl CO dehydrogenase (like Thermodesulfovibrionia and UBA9217). The 9FT-COMBO-42-15 family is further differentiated by its capacity for sulphur oxidation (via DsrABEFH and SoxXAYZB) and dissimilatory nitrate reduction to ammonium, and gene transcription indicated active coupling of nitrogen and sulphur cycles by f_9FT-COMBO-42-15 in dysoxic groundwater. Overall, results indicate that Nitrospirota are widely distributed in groundwater and that oxygen availability drives the spatial differentiation of lineages with ecologically distinct roles related to nitrogen and sulphur metabolism.},
}

@article {pmid38650647,
year = {2024},
author = {Tunsakul, N and Wongsaroj, L and Janchot, K and Pongpirul, K and Somboonna, N},
title = {Non-significant influence between aerobic and anaerobic sample transport materials on gut (fecal) microbiota in healthy and fat-metabolic disorder Thai adults.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17270},
pmid = {38650647},
issn = {2167-8359},
abstract = {BACKGROUND: The appropriate sample handling for human fecal microbiota studies is essential to prevent changes in bacterial composition and quantities that could lead to misinterpretation of the data.

METHODS: This study firstly identified the potential effect of aerobic and anaerobic fecal sample collection and transport materials on microbiota and quantitative microbiota in healthy and fat-metabolic disorder Thai adults aged 23-43 years. We employed metagenomics followed by 16S rRNA gene sequencing and 16S rRNA gene qPCR, to analyze taxonomic composition, alpha diversity, beta diversity, bacterial quantification, Pearson's correlation with clinical factors for fat-metabolic disorder, and the microbial community and species potential metabolic functions.

RESULTS: Our study successfully obtained microbiota results in percent and quantitative compositions. Each sample exhibited quality sequences with a >99% Good's coverage index, and a relatively plateau rarefaction curve. Alpha diversity indices showed no statistical difference in percent and quantitative microbiota OTU richness and evenness, between aerobic and anaerobic sample transport materials. Obligate and facultative anaerobic species were analyzed and no statistical difference was observed. Supportively, the beta diversity analysis by non-metric multidimensional scale (NMDS) constructed using various beta diversity coefficients showed resembling microbiota community structures between aerobic and anaerobic sample transport groups (P = 0.86). On the other hand, the beta diversity could distinguish microbiota community structures between healthy and fat-metabolic disorder groups (P = 0.02), along with Pearson's correlated clinical parameters (i.e., age, liver stiffness, GGT, BMI, and TC), the significantly associated bacterial species and their microbial metabolic functions. For example, genera such as Ruminococcus and Bifidobacterium in healthy human gut provide functions in metabolisms of cofactors and vitamins, biosynthesis of secondary metabolites against gut pathogens, energy metabolisms, digestive system, and carbohydrate metabolism. These microbial functional characteristics were also predicted as healthy individual biomarkers by LEfSe scores. In conclusion, this study demonstrated that aerobic sample collection and transport (<48 h) did not statistically affect the microbiota and quantitative microbiota analyses in alpha and beta diversity measurements. The study also showed that the short-term aerobic sample collection and transport still allowed fecal microbiota differentiation between healthy and fat-metabolic disorder subjects, similar to anaerobic sample collection and transport. The core microbiota were analyzed, and the findings were consistent. Moreover, the microbiota-related metabolic potentials and bacterial species biomarkers in healthy and fat-metabolic disorder were suggested with statistical bioinformatics (i.e., Bacteroides plebeius).},
}

@article {pmid38650065,
year = {2024},
author = {Kharey, GS and Palace, V and Whyte, L and Greer, CW},
title = {Influence of heavy Canadian crude oil on pristine freshwater boreal lake ecosystems in an experimental oil spill.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae054},
pmid = {38650065},
issn = {1574-6941},
abstract = {The overall impact of a crude oil spill into a pristine freshwater environment in Canada is largely unknown. To evaluate the impact on the native microbial community, a large-scale in situ model experimental spill was conducted to assess the potential role of the natural community to attenuate hydrocarbons. A small volume of conventional heavy crude oil (CHV) was introduced within contained mesocosm enclosures deployed on the shoreline of a freshwater lake. The oil was left to interact with the shoreline for 72 h and then free-floating oil was recovered using common oil spill response methods (i.e. freshwater flushing and capture on oleophilic absorptive media). Residual PAH concentrations returned to near pre-oiling concentrations within 2 months, while the microbial community composition across the water, soil, and sediment matrices of the enclosed oligotrophic freshwater ecosystems did not shift significantly over this period. Metagenomic analysis revealed key polycyclic aromatic and alkane degradation mechanisms also did not change in their relative abundance over the monitoring period. These trends suggest that for small spills (<2 L of oil per 15 m2 of surface freshwater), physical oil recovery reduces PAH concentrations to levels tolerated by the native microbial community. Additionally, the native microbial community present in the monitored pristine freshwater ecosystem possesses the appropriate hydrocarbon degradation mechanisms without prior challenge by hydrocarbon substrates. This study corroborated trends found previously (Kharey et al. 2024) toward freshwater hydrocarbon degradation in an environmentally relevant scale and conditions on the tolerance of residual hydrocarbons in situ.},
}

@article {pmid38650064,
year = {2024},
author = {Kharey, GS and Palace, V and Whyte, L and Greer, CW},
title = {Native freshwater lake microbial community response to an in situ experimental dilbit spill.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae055},
pmid = {38650064},
issn = {1574-6941},
abstract = {With the increase in crude oil transport throughout Canada, the potential for spills into freshwater ecosystems has increased and additional research is needed in these sensitive environments. Large enclosures erected in a lake were used as mesocosms for this controlled experimental dilbit (diluted bitumen) spill under ambient environmental conditions. The microbial response to dilbit, the efficacy of standard remediation protocols on different shoreline types commonly found in Canadian freshwater lakes, including a testing of a shoreline washing agent were all evaluated. We found that the native microbial community did not undergo any significant shifts in composition after exposure to dilbit or the ensuing remediation treatments. Regardless of the treatment, sample type (soil, sediment, or water), or type of associated shoreline, the community remained relatively consistent over a 3-month monitoring period. Following this, metagenomic analysis of polycyclic aromatic and alkane hydrocarbon degradation mechanisms also showed that while many key genes identified in PAH and alkane biodegradation were present, their abundance did not change significantly over the course of the experiment. These results showed that the native microbial community present in a pristine freshwater lake has the prerequisite mechanisms for hydrocarbon degradation in place, and combined with standard remediation practices in use in Canada, has the genetic potential and resilience to potentially undertake bioremediation.},
}

@article {pmid38650051,
year = {2024},
author = {Song, X and Jiang, H and Zong, L and Shi, D and Zhu, H},
title = {The clinical value of mNGS of bronchoalveolar lavage fluid versus traditional microbiological tests for pathogen identification and prognosis of severe pneumonia (NT-BALF):study protocol for a prospective multi-center randomized clinical trial.},
journal = {Trials},
volume = {25},
number = {1},
pages = {276},
pmid = {38650051},
issn = {1745-6215},
support = {2022-PUMCH-D-005//National High Level Hospital Clinical Research Funding/ ; },
abstract = {BACKGROUND: Early, rapid, and accurate pathogen diagnosis can help clinicians select targeted treatment options, thus improving prognosis and reducing mortality rates of severe pneumonia. Metagenomic next-generation sequencing (mNGS) has a higher sensitivity and broader pathogen spectrum than traditional microbiological tests. However, the effects of mNGS-based antimicrobial treatment procedures on clinical outcomes and cost-effectiveness in patients with severe pneumonia have not been evaluated.

METHODS: This is a regional, multi-center, open, prospective, randomized controlled trial to evaluate that whether the combination of mNGS and traditional testing methods could decrease 28-day call-cause mortality with moderate cost-effectiveness. A total of 192 patients with severe pneumonia will be recruited from four large tertiary hospitals in China. Bronchoalveolar lavage fluid will be obtained in all patients and randomly assigned to the study group (mNGS combined with traditional microbiological tests) or the control group (traditional microbiological tests only) in a 1:1 ratio. Individualized antimicrobial treatment and strategy will be selected according to the analysis results. The primary outcome is 28-day all-cause mortality. The secondary outcomes are ICU and hospital length of stay (LOS), ventilator-free days and ICU-free days, consistency between mNGS and traditional microbiological tests, detective rate of mNGS and traditional microbiological tests, turn-out time, time from group allocation to start of treatment, duration of vasopressor support, types and duration of anti-infective regimens, source of drug-resistant bacteria or fungi, and ICU cost.

DISCUSSION: The clinical benefits of mNGS are potentially significant, but its limitations should also be considered.

TRIAL REGISTRATION: ChineseClinicalTrialRegistry.org, ChiCTR2300076853. Registered on 22 October 2023.},
}

@article {pmid38650043,
year = {2024},
author = {Wilson-Welder, JH and Han, S and Bayles, DO and Alt, DP and Kanipe, C and Garrison, K and Mansfield, KG and Olsen, SC},
title = {Correlation of lesion severity with bacterial changes in Treponeme-Associated Hoof Disease from free-roaming wild elk (Cervus canadensis).},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {20},
pmid = {38650043},
issn = {2524-4671},
abstract = {BACKGROUND: Treponeme-Associated Hoof Disease (TAHD) is a polybacterial, multifactorial disease affecting free-ranging wild elk (Cervus canadensis) in the Pacific Northwest. Previous studies have indicated a bacterial etiology similar to digital dermatitis in livestock, including isolation of Treponema species from lesions. The lesions appear to progress rapidly from ulcerative areas in the interdigital space or along the coronary band to severe, ulcerative, necrotic, proliferative lesions under-running the hoof wall, perforating the sole, and contributing to hoof elongation, deformity, and overgrowth. Eventually the lesions undermine the laminal structure leading to sloughing of the hoof horn capsule. The objective of this study was to characterize the bacterial communities associated with hoof lesions, which were categorized into 5 stages or disease grade severities, with 0 being unaffected tissue and 4 being sloughed hoof capsule. We also wanted to determine if the etiology of TAHD through morphological changes was dominated by Treponema, as observed in hoof diseases in livestock.

RESULTS: The bacterial 16S rRNA gene was sequenced from 66 hoof skin biopsy samples representing 5 lesion grades from samples collected by Washington Department of Fish and Wildlife as part of a voluntary hunter program. Analysis of the relative abundance of bacterial sequences showed that lesions were dominated by members of the bacterial phyla Proteobacteria, Firmicutes, Spirochaetes, Bacteroidetes and Actinobacteria. In lesion samples, members of the genus Treponema, Porphyromonas, and Mycoplasma increased with lesion severity. Association analysis indicated frequent identification of Treponema with Porphyromonas, Bacteroides and other anaerobic Gram-positive cocci.

CONCLUSIONS: The bacterial 16S rRNA gene sequencing confirmed the presence of Treponema species at all stages of TAHD lesions, treponeme specie-specific PCR and histopathology, indicating that the morphological changes are a continual progression of disease severity with similar bacterial communities. Association and abundance of these other pathogenic genera within lesions may mean synergistic role with Treponema in hoof disease pathogenesis. Characterizing bacteria involved in lesion development, and their persistence during disease progression, provides evidence for science-based management decisions in TAHD infected elk populations.},
}

@article {pmid38649836,
year = {2024},
author = {Zheng, A and Shaw, J and Yu, YW},
title = {Mora: abundance aware metagenomic read re-assignment for disentangling similar strains.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {161},
pmid = {38649836},
issn = {1471-2105},
support = {RGPIN-2022- 03074//Natural Sciences and Engineering Research Council of Canada/ ; CGS-D//Natural Sciences and Engineering Research Council of Canada/ ; DGDND-2022-03074//Ministère de la Défense Nationale/ ; },
abstract = {BACKGROUND: Taxonomic classification of reads obtained by metagenomic sequencing is often a first step for understanding a microbial community, but correctly assigning sequencing reads to the strain or sub-species level has remained a challenging computational problem.

RESULTS: We introduce Mora, a MetagenOmic read Re-Assignment algorithm capable of assigning short and long metagenomic reads with high precision, even at the strain level. Mora is able to accurately re-assign reads by first estimating abundances through an expectation-maximization algorithm and then utilizing abundance information to re-assign query reads. The key idea behind Mora is to maximize read re-assignment qualities while simultaneously minimizing the difference from estimated abundance levels, allowing Mora to avoid over assigning reads to the same genomes. On simulated diverse reads, this allows Mora to achieve F1 scores comparable to other algorithms while having less runtime. However, Mora significantly outshines other algorithms on very similar reads. We show that the high penalty of over assigning reads to a common reference genome allows Mora to accurately infer correct strains for real data in the form of E. coli reads.

CONCLUSIONS: Mora is a fast and accurate read re-assignment algorithm that is modularized, allowing it to be incorporated into general metagenomics and genomics workflows. It is freely available at https://github.com/AfZheng126/MORA .},
}

@article {pmid38649441,
year = {2024},
author = {Fedurek, P and Asiimwe, C and Rice, GK and Akankwasa, WJ and Reynolds, V and Hobaiter, C and Kityo, R and Muhanguzi, G and Zuberbühler, K and Crockford, C and Cer, RZ and Bennett, AJ and Rothman, JM and Bishop-Lilly, KA and Goldberg, TL},
title = {Selective deforestation and exposure of African wildlife to bat-borne viruses.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {470},
pmid = {38649441},
issn = {2399-3642},
support = {WUN A1417//United States Department of Defense | U.S. Navy (United States Navy)/ ; },
abstract = {Proposed mechanisms of zoonotic virus spillover often posit that wildlife transmission and amplification precede human outbreaks. Between 2006 and 2012, the palm Raphia farinifera, a rich source of dietary minerals for wildlife, was nearly extirpated from Budongo Forest, Uganda. Since then, chimpanzees, black-and-white colobus, and red duiker were observed feeding on bat guano, a behavior not previously observed. Here we show that guano consumption may be a response to dietary mineral scarcity and may expose wildlife to bat-borne viruses. Videos from 2017-2019 recorded 839 instances of guano consumption by the aforementioned species. Nutritional analysis of the guano revealed high concentrations of sodium, potassium, magnesium and phosphorus. Metagenomic analyses of the guano identified 27 eukaryotic viruses, including a novel betacoronavirus. Our findings illustrate how "upstream" drivers such as socioeconomics and resource extraction can initiate elaborate chains of causation, ultimately increasing virus spillover risk.},
}

@article {pmid38649365,
year = {2024},
author = {Kwon, D and Zhang, K and Paul, KC and Folle, AD and Del Rosario, I and Jacobs, JP and Keener, AM and Bronstein, JM and Ritz, B},
title = {Diet and the gut microbiome in patients with Parkinson's disease.},
journal = {NPJ Parkinson's disease},
volume = {10},
number = {1},
pages = {89},
pmid = {38649365},
issn = {2373-8057},
abstract = {It has been suggested that gut microbiota influence Parkinson's disease (PD) via the gut-brain axis. Here, we examine associations between diet and gut microbiome composition and its predicted functional pathways in patients with PD. We assessed gut microbiota in fecal samples from 85 PD patients in central California using 16S rRNA gene sequencing. Diet quality was assessed by calculating the Healthy Eating Index 2015 (HEI-2015) based on the Diet History Questionnaire II. We examined associations of diet quality, fiber, and added sugar intake with microbial diversity, composition, taxon abundance, and predicted metagenomic profiles, adjusting for age, sex, race/ethnicity, and sequencing platform. Higher HEI scores and fiber intake were associated with an increase in putative anti-inflammatory butyrate-producing bacteria, such as the genera Butyricicoccus and Coprococcus 1. Conversely, higher added sugar intake was associated with an increase in putative pro-inflammatory bacteria, such as the genera Klebsiella. Predictive metagenomics suggested that bacterial genes involved in the biosynthesis of lipopolysaccharide decreased with higher HEI scores, whereas a simultaneous decrease in genes involved in taurine degradation indicates less neuroinflammation. We found that a healthy diet, fiber, and added sugar intake affect the gut microbiome composition and its predicted metagenomic function in PD patients. This suggests that a healthy diet may support gut microbiome that has a positive influence on PD risk and progression.},
}

@article {pmid38649355,
year = {2024},
author = {Qin, Y and Tong, X and Mei, WJ and Cheng, Y and Zou, Y and Han, K and Yu, J and Jie, Z and Zhang, T and Zhu, S and Jin, X and Wang, J and Yang, H and Xu, X and Zhong, H and Xiao, L and Ding, PR},
title = {Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3396},
pmid = {38649355},
issn = {2041-1723},
support = {82073159//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The incidence of young-onset colorectal cancer (yCRC) has been increasing in recent decades, but little is known about the gut microbiome of these patients. Most studies have focused on old-onset CRC (oCRC), and it remains unclear whether CRC signatures derived from old patients are valid in young patients. To address this, we assembled the largest yCRC gut metagenomes to date from two independent cohorts and found that the CRC microbiome had limited association with age across adulthood. Differential analysis revealed that well-known CRC-associated taxa, such as Clostridium symbiosum, Peptostreptococcus stomatis, Parvimonas micra and Hungatella hathewayi were significantly enriched (false discovery rate <0.05) in both old- and young-onset patients. Similar strain-level patterns of Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli were observed for oCRC and yCRC. Almost all oCRC-associated metagenomic pathways had directionally concordant changes in young patients. Importantly, CRC-associated virulence factors (fadA, bft) were enriched in both oCRC and yCRC compared to their respective controls. Moreover, the microbiome-based classification model had similar predication accuracy for CRC status in old- and young-onset patients, underscoring the consistency of microbial signatures across different age groups.},
}

@article {pmid38648266,
year = {2024},
author = {Ramoneda, J and Fan, K and Lucas, JM and Chu, H and Bissett, A and Strickland, MS and Fierer, N},
title = {Ecological relevance of flagellar motility in soil bacterial communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae067},
pmid = {38648266},
issn = {1751-7370},
abstract = {Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26 192 genomes in total). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in environments with higher carbon availability. To test this hypothesis, we applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data, and quantified the prevalence of flagellar motility across 4 independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). As expected, we observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data acquired from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.},
}

@article {pmid38648214,
year = {2024},
author = {Lauber, C and Zhang, X and Vaas, J and Klingler, F and Mutz, P and Dubin, A and Pietschmann, T and Roth, O and Neuman, BW and Gorbalenya, AE and Bartenschlager, R and Seitz, S},
title = {Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates.},
journal = {PLoS pathogens},
volume = {20},
number = {4},
pages = {e1012163},
doi = {10.1371/journal.ppat.1012163},
pmid = {38648214},
issn = {1553-7374},
abstract = {Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.},
}

@article {pmid38647897,
year = {2022},
author = {Mon, ML and Marrero Díaz de Villegas, R and Campos, E and Soria, MA and Talia, PM},
title = {Characterization of a novel GH10 alkali-thermostable xylanase from a termite microbiome.},
journal = {Bioresources and bioprocessing},
volume = {9},
number = {1},
pages = {84},
pmid = {38647897},
issn = {2197-4365},
support = {PI 102//Instituto Nacional de Tecnología Agropecuaria/ ; 106//Instituto Nacional de Tecnología Agropecuaria/ ; 116//Instituto Nacional de Tecnología Agropecuaria/ ; 149//Instituto Nacional de Tecnología Agropecuaria/ ; 159//Instituto Nacional de Tecnología Agropecuaria/ ; (PICT) 2018-#4149//Agencia Nacional de Promoción Científica y Tecnológica/ ; 2020-#3570//Agencia Nacional de Promoción Científica y Tecnológica/ ; PIP-2021-2561//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; },
abstract = {The aim of the present study was to assess the biochemical and molecular structural characteristics of a novel alkali-thermostable GH10 xylanase (Xyl10B) identified in a termite gut microbiome by a shotgun metagenomic approach. This endoxylanase candidate was amplified, cloned, heterologously expressed in Escherichia coli and purified. The recombinant enzyme was active at a broad range of temperatures (37-60 ºC) and pH values (4-10), with optimal activity at 50 ºC and pH 9. Moreover, its activity remained at more than 80% of its maximum at 50 °C for 8 h. In addition, Xyl10B was found to be stable in the presence of salt and several ions and chemical reagents frequently used in the industry. These characteristics make this enzyme an interesting candidate for pulp and paper bleaching industries, since this process requires enzymes without cellulase activity and resistant to high temperatures and alkaline pH (thermo-alkaliphilic enzymes). The products of xylan hydrolysis by Xyl10B (short xylooligosaccharides, xylose and xylobiose) could be suitable for application as prebiotics and in the production of bioethanol.},
}

@article {pmid38647870,
year = {2024},
author = {Yang, F and Li, Q and Yin, X},
title = {Metagenomic analysis of the effects of salinity on microbial community and functional gene diversity in glacial meltwater estuary, Ny-Alesund, Arctic.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {38647870},
issn = {1678-4405},
support = {ZR2020KC036//Natural Science Foundation of Shandong Province/ ; },
abstract = {Due to the inflow of meltwater from the Midre Lovénbreen glacier upstream of Kongsfjorden, the nutrient concentration of Kongsfjorden change from the estuary to the interior of the fjord. Our objective was to explore the changes in bacterial community structure and metabolism-related genes from the estuary to fjord by metagenomic analysis. Our data indicate that glacial meltwater input has altered the physicochemical properties of the fjords, with a significant effect, in particular, on fjords salinity, thus altering the relative abundance of some specific bacterial groups. In addition, we suggest that the salinity of a fjord is an important factor affecting the abundance of genes associated with the nitrogen and sulfur cycles in the fjord. Changes in salinity may affect the relative abundance of microbial populations that carry metabolic genes, thus affecting the relative abundance of genes associated with the nitrogen and sulfur cycles.},
}

@article {pmid38647859,
year = {2024},
author = {Fernandez-Cassi, X and Kohn, T},
title = {Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics.},
journal = {Food and environmental virology},
volume = {},
number = {},
pages = {},
pmid = {38647859},
issn = {1867-0342},
support = {754462//Marie Skłodowska-Curie Grant Agreement/ ; },
abstract = {Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preamplification pipelines (specific to RNA viruses, DNA viruses or both) for viral genome sequencing using spiked-in Phosphate Buffered Saline and sewage samples containing known concentrations of viruses. We found that compared to the pipeline targeting all genome types, the RNA pipeline performed better in detecting RNA viruses in both spiked and unspiked sewage samples, allowing the detection of various mammalian viruses including members from the Reoviridae, Picornaviridae, Astroviridae and Caliciviridae. However, the DNA-specific pipeline did not improve the detection of mammalian DNA viruses. We also measured viral recovery by quantitative reverse transcription polymerase chain reaction and assessed the impact of genetic background (non-viral genetic material) on viral coverage. Our results indicate that viral recoveries were generally lower in sewage (average of 11.0%) and higher in Phosphate Buffered Saline (average of 23.4%) for most viruses. Additionally, spiked-in viruses showed lower genome coverage in sewage, demonstrating the negative effect of genetic background on sequencing. Finally, correlation analysis revealed a relationship between virus concentration and genome normalized reads per million, indicating that viral metagenomic sequencing can be semiquantitative.},
}

@article {pmid38647817,
year = {2023},
author = {Wang, Y and Luo, X and Chu, P and Shi, H and Wang, R and Li, J and Zheng, S},
title = {Cultivation and application of nicotine-degrading bacteria and environmental functioning in tobacco planting soil.},
journal = {Bioresources and bioprocessing},
volume = {10},
number = {1},
pages = {10},
pmid = {38647817},
issn = {2197-4365},
support = {20191307C04//Hubei Tobacco Company/ ; },
abstract = {Nicotine, a toxic and addictive alkaloid from tobacco, is an environmental pollutant. However, nicotine-degrading bacteria (NDB) and their function in tobacco planting soil are not fully understood. First, 52 NDB strains belonging to seven genera were isolated from tobacco soil. The most dominant genera were Flavobacterium (36.5%), Pseudomonas (30.8%), and Arthrobacter (15.4%), and Chitinophaga and Flavobacterium have not been previously reported. Then, two efficient NDB strains, Arthrobacter nitrophenolicus ND6 and Stenotrophomonas geniculata ND16, were screened and inoculated in the compost fertilizer from tobacco waste. The nicotine concentrations were reduced from 1.5 mg/g (DW) to below the safety threshold of 0.5 mg/g. Furthermore, strain ND6 followed the pyridine pathway of nicotine degradation, but the degrading pathway in strain ND16 could not be determined according to genomic analysis and color change. Finally, the abundance of nicotine-degrading genes in tobacco rhizosphere soil was investigated via metagenomic analysis. Five key genes, ndhA, nctB, kdhL, nboR, and dhponh, represent the whole process of nicotine degradation, and their abundance positively correlated with soil nicotine concentrations (p < 0.05). In conclusion, various NDB including unknown species live in tobacco soil and degrade nicotine efficiently. Some key nicotine-degrading genes could be used in monitoring nicotine degradation in the environment. The fermentation of compost from tobacco waste is a promising application of efficient NDB.},
}

@article {pmid38647787,
year = {2023},
author = {Xue, F and Yang, J and Luo, C and Li, D and Shi, G and Song, G and Li, Y},
title = {Metagenomic insight into the biodegradation of biomass and alkaloids in the aging process of cigar.},
journal = {Bioresources and bioprocessing},
volume = {10},
number = {1},
pages = {45},
pmid = {38647787},
issn = {2197-4365},
support = {110202101066(XJ-15)//Major Science and Technology Program of China National Tobacco Corporation/ ; (110202101014(XJ-06)//Major Science and Technology Program of China National Tobacco Corporation/ ; },
abstract = {A significant distinction between cigar production and tobacco lies in the necessary aging process, where intricate microbial growth, metabolic activities, enzymatic catalysis, and chemical reactions interact. Despite its crucial role in determining the final quality of cigars, our comprehension of the underlying chemical and biological mechanisms within this process remains insufficient. Biomass and alkaloids are the primary constituents that influence the flavor of cigars. Consequently, investigating the entire aging process could begin by exploring the involvement of microbes and enzymes in their biodegradation. In this study, handmade cigars were aged under different conditions. Metagenomic sequencing was employed to identify the microbes and enzymes responsible for the degradation of biomass and alkaloids derived from tobacco leaves. The results revealed that various environmental factors, including temperature, humidity, duration time, and turning frequency, yielded varying contents of total sugar and alkaloids in the cigars. Significant correlations were observed between microbial communities and starch, reducing sugars, total sugars, and alkaloids. Key species involved in the breakdown of biomass constituents, such as starch (Bacillus pumilus, Pseudomonas sp. 286, and Aspergillus cristatus), reducing sugars and total sugars (Aspergillus cristatus and Nitrolancea hollandica), were identified. Furthermore, Corynespora cassiicola and Pseudomonas fulva were found to potentially contribute to the degradation of alkaloid compounds, specifically nornicotine and neonicotinoid. Our work contributes to a deeper understanding of the microbial roles in the aging of cigars. Moreover, the selection of specific microbial strains or starter cultures can be employed to control and manipulate the aging process, thereby further refining the flavor development in cigar products.},
}

@article {pmid38647756,
year = {2022},
author = {Zhang, Y and Guan, F and Xu, G and Liu, X and Zhang, Y and Sun, J and Yao, B and Huang, H and Wu, N and Tian, J},
title = {A novel thermophilic chitinase directly mined from the marine metagenome using the deep learning tool Preoptem.},
journal = {Bioresources and bioprocessing},
volume = {9},
number = {1},
pages = {54},
pmid = {38647756},
issn = {2197-4365},
support = {2021YFC2100300//the National Key R&D Program of China/ ; Y2019XK19//the Central Public-interest Scientific Institution Basal Research Fund/ ; 1610392021008//the Central Public-interest Scientific Institution Basal Research Fund/ ; 1610392020001//the Central Public-interest Scientific Institution Basal Research Fund/ ; 19273201D//the Key Research and Development Plan Project of Hebei Province/ ; },
abstract = {Chitin is abundant in nature and its degradation products are highly valuable for numerous applications. Thermophilic chitinases are increasingly appreciated for their capacity to biodegrade chitin at high temperatures and prolonged enzyme stability. Here, using deep learning approaches, we developed a prediction tool, Preoptem, to screen thermophilic proteins. A novel thermophilic chitinase, Chi304, was mined directly from the marine metagenome. Chi304 showed maximum activity at 85 ℃, its Tm reached 89.65 ± 0.22℃, and exhibited excellent thermal stability at 80 and 90 °C. Chi304 had both endo- and exo-chitinase activities, and the (GlcNAc)2 was the main hydrolysis product of chitin-related substrates. The product yields of colloidal chitin degradation reached 97% within 80 min, and 20% over 4 days of reaction with crude chitin powder. This study thus provides a method to mine the novel thermophilic chitinase for efficient chitin biodegradation.},
}

@article {pmid38647577,
year = {2022},
author = {Wang, D and Unsal, T and Kumseranee, S and Punpruk, S and Saleh, MA and Alotaibi, MD and Xu, D and Gu, T},
title = {Mitigation of carbon steel biocorrosion using a green biocide enhanced by a nature-mimicking anti-biofilm peptide in a flow loop.},
journal = {Bioresources and bioprocessing},
volume = {9},
number = {1},
pages = {67},
pmid = {38647577},
issn = {2197-4365},
abstract = {Biocorrosion, also called microbiologically influenced corrosion (MIC), is a common operational threat to many industrial processes. It threatens carbon steel, stainless steel and many other metals. In the bioprocessing industry, reactor vessels in biomass processing and bioleaching are prone to MIC. MIC is caused by biofilms. The formation and morphology of biofilms can be impacted by fluid flow. Fluid velocity affects biocide distribution and MIC. Thus, assessing the efficacy of a biocide for the mitigation of MIC under flow condition is desired before a field trial. In this work, a benchtop closed flow loop bioreactor design was used to investigate the biocide mitigation of MIC of C1018 carbon steel at 25 °C for 7 days using enriched artificial seawater. An oilfield biofilm consortium was analyzed using metagenomics. The biofilm consortium was grown anaerobically in the flow loop which had a holding vessel for the culture medium and a chamber to hold C1018 carbon steel coupons. Peptide A (codename) was a chemically synthesized cyclic 14-mer (cys-ser-val-pro-tyr-asp-tyr-asn-trp-tyr-ser-asn-trp-cys) with its core 12-mer sequence originated from a biofilm dispersing protein secreted by a sea anemone which possesses a biofilm-free exterior. It was used as a biocide enhancer. The combination of 50 ppm (w/w) THPS (tetrakis hydroxymethyl phosphonium sulfate) biocide + 100 nM (180 ppb by mass) Peptide A resulted in extra 1-log reduction in the sulfate reducing bacteria (SRB) sessile cell count and the acid producing bacteria (APB) sessile cell count compared to 50 ppm THPS alone treatment. Furthermore, with the enhancement of 100 nM Peptide A, extra 44% reduction in weight loss and 36% abatement in corrosion pit depth were achieved compared to 50 ppm THPS alone treatment.},
}

@article {pmid38647315,
year = {2024},
author = {Chen, L-p and Zhang, L-f and Liu, S and Hua, H and Zhang, L and Liu, B-c and Wang, R-r},
title = {Ling-Gui-Zhu-Gan decoction ameliorates nonalcoholic fatty liver disease via modulating the gut microbiota.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0197923},
doi = {10.1128/spectrum.01979-23},
pmid = {38647315},
issn = {2165-0497},
abstract = {UNLABELLED: Numerous studies have supported that nonalcoholic fatty liver disease (NAFLD) is highly associated with gut microbiota dysbiosis. Ling-Gui-Zhu-Gan decoction (LG) has been clinically used to treat NAFLD, but the underlying mechanism remains unknown. This study investigated the therapeutic effect and mechanisms of LG in mice with NAFLD induced by a high-fat diet (HD). An HD-induced NAFLD mice model was established to evaluate the efficacy of LG followed by biochemical and histopathological analysis. Metagenomics, metabolomics, and transcriptomics were used to explore the structure and metabolism of the gut microbiota. LG significantly improved hepatic function and decreased lipid droplet accumulation in HD-induced NAFLD mice. LG reversed the structure of the gut microbiota that is damaged by HD and improved intestinal barrier function. Meanwhile, the LG group showed a lower total blood bile acids (BAs) concentration, a shifted BAs composition, and a higher fecal short-chain fatty acids (SCFAs) concentration. Furthermore, LG could regulate the hepatic expression of genes associated with the primary BAs biosynthesis pathway and peroxisome proliferator-activated receptor (PPAR) signaling pathway. Our study suggested that LG could ameliorate NAFLD by altering the structure and metabolism of gut microbiota, while BAs and SCFAs are considered possible mediating substances.

IMPORTANCE: Until now, there has still been no study on the gut microbiota and metabolomics of Ling-Gui-Zhu-Gan decoction (LG) in nonalcoholic fatty liver disease (NAFLD) mouse models. Our study is the first to report on the reshaping of the structure and metabolism of the gut microbiota by LG, as well as explore the potential mechanism underlying the improvement of NAFLD. Specifically, our study demonstrates the potential of gut microbial-derived short-chain fatty acids (SCFAs) and blood bile acids (BAs) as mediators of LG therapy for NAFLD in animal models. Based on the results of transcriptomics, we further verified that LG attenuates NAFLD by restoring the metabolic disorder of BAs via the up-regulation of Fgf15/FXR in the ileum and down-regulation of CYP7A1/FXR in the liver. LG also reduces lipogenesis in NAFLD mice by mediating the peroxisome proliferator-activated receptor (PPAR) signaling pathway, which then contributes to reducing hepatic inflammation and improving intestinal barrier function to treat NAFLD.},
}

@article {pmid38647296,
year = {2024},
author = {Barno, AR and Green, K and Rohwer, F and Silveira, CB},
title = {Snow viruses and their implications on red snow algal blooms.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0008324},
doi = {10.1128/msystems.00083-24},
pmid = {38647296},
issn = {2379-5077},
abstract = {Algal blooms can give snowmelt a red color, reducing snow albedo and creating a runaway effect that accelerates snow melting. The occurrence of red snow is predicted to grow in polar and subpolar regions with increasing global temperatures. We hypothesize that these algal blooms affect virus-bacteria interactions in snow, with potential effects on snowmelt dynamics. A genomic analysis of double-stranded DNA virus communities in red and white snow from the Whistler region of British Columbia, Canada, identified 792 putative viruses infecting bacteria. The most abundant putative snow viruses displayed low genomic similarity with known viruses. We recovered the complete circular genomes of nine putative viruses, two of which were classified as temperate. Putative snow viruses encoded genes involved in energy metabolisms, such as NAD[+] synthesis and salvage pathways. In model phages, these genes facilitate increased viral particle production and lysis rates. The frequency of temperate phages was positively correlated with microbial abundance in the snow samples. These results suggest the increased frequency of temperate virus-bacteria interactions as microbial densities increase during snowmelt. We propose that this virus-bacteria dynamic may facilitate the red snow algae growth stimulated by bacteria.IMPORTANCEMicrobial communities in red snow algal blooms contribute to intensifying snowmelt rates. The role of viruses in snow during this environmental shift, however, has yet to be elucidated. Here, we characterize novel viruses extracted from snow viral metagenomes and define the functional capacities of snow viruses in both white and red snow. These results are contextualized using the composition and functions observed in the bacterial communities from the same snow samples. Together, these data demonstrate the energy metabolism performed by viruses and bacteria in a snow algal bloom, as well as expand the overall knowledge of viral genomes in extreme environments.},
}

@article {pmid38646847,
year = {2024},
author = {Fontana, F and Longhi, G and Carli, E and Alessandri, G and Mancabelli, L and Lugli, GA and Tarracchini, C and Viappiani, A and Anzalone, R and Turroni, F and Milani, C and Ventura, M},
title = {Revealing the genetic traits of the foodborne microbial genus hafnia: Implications for the human gut microbiome.},
journal = {Environmental microbiology},
volume = {26},
number = {4},
pages = {e16626},
doi = {10.1111/1462-2920.16626},
pmid = {38646847},
issn = {1462-2920},
support = {//Cariparma/ ; //GenProbio Srl/ ; CUP D93C22000890001//Concession Decree No.1550 of 11 October 2022, Italian Ministry of University and Research/ ; PE00000003//Mission 4 Component 2 Investment 1.3 - Call for tender No. 341 of 15 March 2022, Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; //the National Recovery and Resilience Plan (NRRP)/ ; //ON Foods - Research and innovation network on food and nutrition Sustainability, Safety and Security -Working ON Foods/ ; },
abstract = {The bacterial genus Hafnia has recently attracted attention due to its complex metabolic features and host-interaction capabilities, which are associated with health benefits, primarily weight loss. However, significant gaps remain in our understanding of the genomic characteristics of this emerging microbial group. In this study, we utilized all available high-quality genomes of Hafnia alvei and Hafnia paralvei to uncover the broad distribution of Hafnia in human and honeybee guts, as well as in dairy products, by analysing 1068 metagenomic datasets. We then investigated the genetic traits related to Hafnia's production of vitamins and short-chain fatty acids (SCFAs) through a comparative genomics analysis that included all dominant bacterial species in the three environments under study. Our findings underscore the extensive metabolic capabilities of Hafnia, particularly in the production of vitamins such as thiamine (B1), nicotinate (B3), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and menaquinone (K2). Additionally, Hafnia demonstrated a conserved genetic makeup associated with SCFA production, including acetate, propanoate, and butanoate. These metabolic traits were further confirmed using RNAseq analyses of a newly isolated H. paralvei strain T10. Overall, our study illuminates the ecological distribution and genetic attributes of this bacterial genus, which is of increasing scientific and industrial relevance.},
}

@article {pmid38646629,
year = {2024},
author = {Nivetha, N and Shukla, PS and Nori, SS and Kumar, S and Suryanarayan, S},
title = {A red seaweed Kappaphycus alvarezii-based biostimulant (AgroGain[®]) improves the growth of Zea mays and impacts agricultural sustainability by beneficially priming rhizosphere soil microbial community.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1330237},
pmid = {38646629},
issn = {1664-302X},
abstract = {The overuse of chemical-based agricultural inputs has led to the degradation of soil with associated adverse effects on soil attributes and microbial population. This scenario leads to poor soil health and is reportedly on the rise globally. Additionally, chemical fertilizers pose serious risks to the ecosystem and human health. In this study, foliar sprays of biostimulant (AgroGain/LBS6) prepared from the cultivated, tropical red seaweed Kappaphycus alvarezii increased the phenotypic growth of Zea mays in terms of greater leaf area, total plant height, and shoot fresh and dry weights. In addition, LBS6 improved the accumulation of chlorophyll a and b, total carotenoids, total soluble sugars, amino acids, flavonoids, and phenolics in the treated plants. LBS6 applications also improved the total bacterial and fungal count in rhizospheric soil. The V3-V4 region of 16S rRNA gene from the soil metagenome was analyzed to study the abundance of bacterial communities which were increased in the rhizosphere of LBS6-treated plants. Treatments were found to enrich beneficial soil bacteria, i.e., Proteobacteria, especially the classes Alphaproteobacteria, Cyanobacteria, Firmicutes, Actinobacteriota, Verrucomicrobiota, Chloroflexi, and Acidobacteriota and several other phyla related to plant growth promotion. A metagenomic study of those soil samples from LBS6-sprayed plants was correlated with functional potential of soil microbiota. Enrichment of metabolisms such as nitrogen, sulfur, phosphorous, plant defense, amino acid, co-factors, and vitamins was observed in soils grown with LBS6-sprayed plants. These results were further confirmed by a significant increase in the activity of soil enzymes such as urease, acid phosphatase, FDAse, dehydrogenase, catalase, and biological index of fertility in the rhizosphere of LBS6-treated corn plant. These findings conclude that the foliar application of LBS6 on Z. mays improves and recruits beneficial microbes and alters soil ecology in a sustainable manner.},
}

@article {pmid38645890,
year = {2024},
author = {Zhou, J and Xu, H and Du, W and Peng, L},
title = {The First Case Report of Inactive Nontuberculous Mycobacterial Pulmonary Disease (NTM-PD) in a Pneumoconiosis Patient Caused by Mycobacterium europaeum in China.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {1515-1521},
pmid = {38645890},
issn = {1178-6973},
abstract = {We reported a 51-year-old male electric welder with stage I pneumoconiosis, who had no significant cough, sputum, fever, chest pain, or other discomfort. However, regular physical examination at our hospital revealed bilateral pulmonary nodules with cavity formation. Blood routine, liver or kidney function, and infection-related biomarkers, including interleukin-6 (IL-6), high-sensitivity C-reactive protein (hs-CRP), and procalcitonin (PCT), were normal. Sputum and alveolar lavage fluid (BALF) acid-fast bacilli (AFB) smears, BALF Mycobacterium tuberculosis (TB) PCR, and T-SPOT.TB were negative. The nucleic acid sequence of Mycobacterium europaeum was detected by BALF metagenomic next-generation sequencing (mNGS), which was confirmed by the subsequent positive culture for NTM. Considering stable conditions, no significant discomfort, and no significant changes in the lung lesion, the patient was diagnosed with inactive nontuberculous mycobacterial pulmonary disease (NTM-PD).},
}

@article {pmid38645888,
year = {2024},
author = {Song, RJ and Zhang, GL},
title = {A Rare Case Report of Disseminated Nocardia Farcinica Granulomatous Hepatitis and Clinical Management Experience.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {1523-1528},
pmid = {38645888},
issn = {1178-6973},
abstract = {BACKGROUND: Nocardiosis is primarily an opportunistic infection affecting immunocompromised individuals, with a predilection for the lungs, brain, or skin in those with compromised immune function. Granulomatous hepatitis caused by Nocardia is a rare clinical manifestation. This study aims to provide a systematic overview of the clinical features of Nocardiosis caused by Nocardia farcinica, enhancing our understanding of this disease.

METHODS: We report a case of a 75-year-old male with no underlying diseases presenting with a history of "recurrent fever for more than 4 months", along with fatigue, poor appetite, and pleural and abdominal effusion. Despite treatment at multiple hospitals, the patient showed little improvement. Chest CT revealed chronic inflammation, small nodules, bilateral pleural effusion, and pleural thickening. Abdominal CT indicated multiple low-density lesions in the liver, multiple small calcifications, and abdominal effusion.

RESULTS: Liver biopsy suggested inflammatory changes, with focal granuloma formation. Metagenomic next-generation sequencing (mNGS) of liver tissue indicated Nocardia farcinica, leading to the final diagnosis of disseminated Nocardia farcinica granulomatous hepatitis.

CONCLUSION: Nocardia infection is a rare disease primarily observed in immunocompromised patients but can also occur in those with normal immune function. The clinical and radiological features lack specificity; however, the utilization of mNGS technology enables rapid identification of the pathogenic microorganism. Nocardia farcinica is generally susceptible to sulfonamide drugs and amikacin, offering viable treatment options.},
}

@article {pmid38645300,
year = {2024},
author = {Daher, M and Iordanov, R and Al Mohajer, M and Sohail, MR and Staggers, KA and Hamdi, AM},
title = {Clinical utility of metagenomic next-generation sequencing in fever of undetermined origin.},
journal = {Therapeutic advances in infectious disease},
volume = {11},
number = {},
pages = {20499361241244969},
pmid = {38645300},
issn = {2049-9361},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a novel diagnostic tool increasingly used in the field of infectious diseases. Little guidance is available regarding its appropriate use in different patient populations and clinical syndromes. We aimed to review the clinical utility of mNGS in patients with a specific clinical syndrome and identify factors that may increase its utility.

METHODS: We retrospectively reviewed charts of 72 non-immunocompromised adults hospitalized with the clinical syndrome of 'fever of undetermined origin' and underwent mNGS testing. Standardized criteria from a previously published study were used to determine the clinical impact of mNGS testing. We applied logistic regression to identify factors associated with a positive clinical impact.

RESULTS: Of the 72 patients identified, 62.5% were males with a median age of 56. All patients had a fever at the time of evaluation. At least one organism was identified in 65.3% of cases; most commonly were Epstein-Barr virus (13.9%), cytomegalovirus (12.5%), and Rickettsia typhi (11.1%). Of those determined to have an infectious etiology of their febrile syndrome, 89.5% (n = 34/38) had a positive mNGS. Consistency between the organism(s) on mNGS and the clinically determined infectious etiology was 82.4%. mNGS had a positive clinical impact in 40.3% of cases, a negative impact in 2.8%, and no impact in 56.9% of cases. Besides age, we did not identify other factors associated with a higher likelihood of positive clinical impact.

CONCLUSION: In our review, mNGS had a positive clinical impact in a large proportion of adults with fever of undetermined origin, with minimal negative impact. However, mNGS results should be interpreted carefully given the high rate of detection of pathogens of unclear clinical significance. Randomized clinical trials are needed to assess the clinical utility of this novel diagnostic tool.},
}

@article {pmid38645218,
year = {2024},
author = {Moodley, S and Kroon, E and Naidoo, CC and Nyawo, GR and Wu, BG and Naidoo, S and Chiyaka, TL and Tshivhula, H and Singh, S and Li, Y and Warren, RM and Hoal, EG and Schurr, E and Clemente, J and Segal, LN and Möller, M and Theron, G},
title = {Latent tuberculosis infection is associated with an enrichment of short chain fatty acid producing bacteria in the stool of women living with HIV.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4182285/v1},
pmid = {38645218},
abstract = {Background: Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high TB burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI, including in PLHIV. Method : Within a parent study that recruited adult females with HIV from Cape Town, South Africa into predefined age categories (18-25, 35-60 years), we characterised the stool microbiota of those with [interferon- γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST-negative) LTBI (n=25 per group). 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet Multinomial Mixtures, DESeq2 and PICRUSt2. Results: No α- or β-diversity differences occurred by LTBI status; however, LTBI-positives were Faecalibacterium-, Blautia-, Gemmiger-, Bacteroides- enriched and Moryella-, Atopobium-, Corynebacterium-, Streptococcus -depleted. Inferred metagenome data showed LTBI-negative-enriched pathways included several involved in methylglyoxal degradation, L-arginine, putrescine, 4-aminobutanoate degradation and L-arginine and ornithine degradation. Stool from LTBI-positives demonstrated differential taxa abundance based on a quantitative response to antigen stimulation (Acidaminococcus- enrichment and Megamonas -, Alistipes -, and Paraprevotella -depletion associated with higher IGRA or TST responses, respectively). In LTBI-positives, older people had different β-diversities than younger people whereas, in LTBI-negatives, no differences occurred across age groups. Conclusion: Amongst female PLHIV, those with LTBI had, vs. those without LTBI, Faecalibacterium , Blautia , Gemmiger, Bacteriodes -enriched, which are producers of short chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.},
}

@article {pmid38645206,
year = {2024},
author = {Lu, D and Kalantar, KL and Chu, VT and Glascock, AL and Guerrero, ES and Bernick, N and Butcher, X and Ewing, K and Fahsbender, E and Holmes, O and Hoops, E and Jones, AE and Lim, R and McCanny, S and Reynoso, L and Rosario, K and Tang, J and Valenzuela, O and Mourani, PM and Pickering, AJ and Raphenya, AR and Alcock, BP and McArthur, AG and Langelier, CR},
title = {Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.12.589250},
pmid = {38645206},
abstract = {Antimicrobial resistant (AMR) pathogens represent urgent threats to human health, and their surveillance is of paramount importance. Metagenomic next generation sequencing (mNGS) has revolutionized such efforts, but remains challenging due to the lack of open-access bioinformatics tools capable of simultaneously analyzing both microbial and AMR gene sequences. To address this need, we developed the Chan Zuckerberg ID (CZ ID) AMR module, an open-access, cloud-based workflow designed to integrate detection of both microbes and AMR genes in mNGS and whole-genome sequencing (WGS) data. It leverages the Comprehensive Antibiotic Resistance Database and associated Resistance Gene Identifier software, and works synergistically with the CZ ID short-read mNGS module to enable broad detection of both microbes and AMR genes. We highlight diverse applications of the AMR module through analysis of both publicly available and newly generated mNGS and WGS data from four clinical cohort studies and an environmental surveillance project. Through genomic investigations of bacterial sepsis and pneumonia cases, hospital outbreaks, and wastewater surveillance data, we gain a deeper understanding of infectious agents and their resistomes, highlighting the value of integrating microbial identification and AMR profiling for both research and public health. We leverage additional functionalities of the CZ ID mNGS platform to couple resistome profiling with the assessment of phylogenetic relationships between nosocomial pathogens, and further demonstrate the potential to capture the longitudinal dynamics of pathogen and AMR genes in hospital acquired bacterial infections. In sum, the new AMR module advances the capabilities of the open-access CZ ID microbial bioinformatics platform by integrating pathogen detection and AMR profiling from mNGS and WGS data. Its development represents a critical step toward democratizing pathogen genomic analysis and supporting collaborative efforts to combat the growing threat of AMR.},
}

@article {pmid38645157,
year = {2024},
author = {Goh, CE and Bohn, B and Genkinger, JM and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Yuzefpolskaya, M and Colombo, PC and Rosenbaum, M and Knight, R and Desvarieux, M and Papapanou, PN and Jacobs, DR and Demmer, RT},
title = {Dietary nitrate intake and net nitrite-generating capacity of the oral microbiome interact to enhance cardiometabolic health: Results from the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS).},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.10.24305636},
pmid = {38645157},
abstract = {BACKGROUND: We investigated the association between dietary nitrate intake and early clinical cardiometabolic risk biomarkers, and explored whether the oral microbiome modifies the association between dietary nitrate intake and cardiometabolic biomarkers.

METHODS: Cross-sectional data from 668 (mean [SD] age 31 [9] years, 73% women) participants was analyzed. Dietary nitrate intakes and alternative healthy eating index (AHEI) scores were calculated from food frequency questionnaire responses and a validated US food database. Subgingival 16S rRNA microbial genes (Illumina, MiSeq) were sequenced, and PICRUSt2 estimated metagenomic content. The Microbiome Induced Nitric oxide Enrichment Score (MINES) was calculated as a microbial gene abundance ratio representing enhanced net capacity for NO generation. Cardiometabolic risk biomarkers included systolic and diastolic blood pressure, HbA1c, glucose, insulin, and insulin resistance (HOMA-IR), and were regressed on nitrate intake tertiles in adjusted multivariable linear models.

RESULTS: Mean nitrate intake was 190[171] mg/day. Higher nitrate intake was associated with lower insulin, and HOMA-IR but particularly among participants with low abundance of oral nitrite enriching bacteria. For example, among participants with a low MINES, mean insulin[95%CI] levels in high vs. low dietary nitrate consumers were 5.8[5.3,6.5] vs. 6.8[6.2,7.5] (p=0.004) while respective insulin levels were 6.0[5.4,6.6] vs. 5.9[5.3,6.5] (p=0.76) among partcipants with high MINES (interaction p=0.02).

CONCLUSION: Higher dietary nitrate intake was only associated with lower insulin and insulin resistance among individuals with reduced capacity for oral microbe-induced nitrite enrichment. These findings have implications for future precision medicine-oriented approaches that might consider assessing the oral microbiome prior to enrollment into dietary interventions or making dietary recommendations.

CLINICAL PERSPECTIVE: What is new?: In this population-based study we identified an interaction between dietary nitrate intake and oral nitrite enriching bacteria on cardiometabolic outcomes. Higher dietary nitrate intake was associated with lower insulin and insulin resistance only among participants with low abundance of oral nitrite enriching bacteria. This study suggests that cardiometabolic benefits of nitrate consumption might depend on the host microbiome's capacity to metabolize nitrates.What are the clinical implications?: Among people with low microbiome capacity for nitrate metabolism, higher levels of nitrate might be necessary to realize cardiometabolic benefits.Lack of microbiome assessments in prior studies could partially explain inconsistent findings from previous nitrate supplementation trials and observational studies.Future precision-medicine oriented trials studying the effects of dietary nitrate recommendations on cardiometabolic health, should consider assessing the oral microbiome.},
}

@article {pmid38645133,
year = {2024},
author = {Zelasko, S and Swaney, MH and Sandstrom, S and Davenport, TC and Seroogy, CM and Gern, JE and Kalan, LR and Currie, CR},
title = {Upper respiratory microbial communities of healthy populations are shaped by niche and age.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.14.589416},
pmid = {38645133},
abstract = {BACKGROUND: Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and functioning across healthy 24-month-old infant (n=229) and adult (n=100) populations.

RESULTS: We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.

CONCLUSIONS: In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functioning, with important implications for host health across the lifespan.},
}

@article {pmid38644786,
year = {2024},
author = {Xu, Z and Gao, X and Li, G and Nghiem, LD and Luo, W and Zhang, F},
title = {Microbial Sources and Sinks of Nitrous Oxide during Organic Waste Composting.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.3c10341},
pmid = {38644786},
issn = {1520-5851},
abstract = {Composting is widely used for organic waste management and is also a major source of nitrous oxide (N2O) emission. New insight into microbial sources and sinks is essential for process regulation to reduce N2O emission from composting. This study used genome-resolved metagenomics to decipher the genomic structures and physiological behaviors of individual bacteria for N2O sources and sinks during composting. Results showed that several nosZ-lacking denitrifiers in feedstocks drove N2O emission at the beginning of the composting. Such emission became negligible at the thermophilic stage, as high temperatures inhibited all denitrifiers for N2O production except for those containing nirK. The nosZ-lacking denitrifiers were notably enriched to increase N2O production at the cooling stage. Nevertheless, organic biodegradation limited energy availability for chemotaxis and flagellar assembly to restrain nirKS-containing denitrifiers for nitrate reduction toward N2O sources but insignificantly interrupt norBC- and nosZ-containing bacteria (particularly nosZ-containing nondenitrifiers) for N2O sinks by capturing N2O and nitric oxide (NO) for energy production, thereby reducing N2O emission at the mature stage. Furthermore, nosZII-type bacteria included all nosZ-containing nondenitrifiers and dominated N2O sinks. Thus, targeted strategies can be developed to restrict the physiological behaviors of nirKS-containing denitrifiers and expand the taxonomic distribution of nosZ for effective N2O mitigation in composting.},
}

@article {pmid38644605,
year = {2024},
author = {Castejon-Ramirez, S and Glasgow, HL and Ferrolino, JA and Hayden, RT and Maron, G and Hijano, DR},
title = {Plasma Metagenomic Sequencing in Immunocompromised Children: a Call for Caution in the Interpretation of Results.},
journal = {Journal of the Pediatric Infectious Diseases Society},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpids/piae038},
pmid = {38644605},
issn = {2048-7207},
}

@article {pmid38644496,
year = {2024},
author = {Gaston, JM and Alm, EJ and Zhang, AN},
title = {Fast and accurate variant identification tool for sequencing-based studies.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {90},
pmid = {38644496},
issn = {1741-7007},
support = {6934500//Massachusetts Institute of Technology/ ; },
abstract = {BACKGROUND: Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, and disease diagnosis. Genetic studies into microbiomes often require processing numerous sequencing datasets, necessitating variant identifiers with high speed, accuracy, and robustness.

RESULTS: We present QuickVariants, a bioinformatics tool that effectively summarizes variant information from read alignments and identifies variants. When tested on diverse bacterial sequencing data, QuickVariants demonstrates a ninefold higher median speed than bcftools, a widely used variant identifier, with higher accuracy in identifying both point mutations and indels. This accuracy extends to variant identification in virus samples, including SARS-CoV-2, particularly with significantly fewer false negative indels than bcftools. The high accuracy of QuickVariants is further demonstrated by its detection of a greater number of Omicron-specific indels (5 versus 0) and point mutations (61 versus 48-54) than bcftools in sewage metagenomes predominated by Omicron variants. Much of the reduced accuracy of bcftools was attributable to its misinterpretation of indels, often producing false negative indels and false positive point mutations at the same locations.

CONCLUSIONS: We introduce QuickVariants, a fast, accurate, and robust bioinformatics tool designed for identifying genetic variants for microbial studies. QuickVariants is available at https://github.com/caozhichongchong/QuickVariants .},
}

@article {pmid38644048,
year = {2024},
author = {Wielkopolan, B and Szabelska-Beręsewicz, A and Gawor, J and Obrępalska-Stęplowska, A},
title = {Cereal leaf beetle-associated bacteria enhance the survival of their host upon insecticide treatments and respond differently to insecticides with different modes of action.},
journal = {Environmental microbiology reports},
volume = {16},
number = {2},
pages = {e13247},
doi = {10.1111/1758-2229.13247},
pmid = {38644048},
issn = {1758-2229},
support = {UMO-2020/37/N/NZ9/02577//Polish National Science Centre/ ; },
abstract = {The cereal leaf beetle (CLB, Oulema melanopus) is one of the major cereal pests. The effect of insecticides belonging to different chemical classes, with different mechanisms of action and the active substances' concentrations on the CLB bacterial microbiome, was investigated. Targeted metagenomic analysis of the V3-V4 regions of the 16S ribosomal gene was used to determine the composition of the CLB bacterial microbiome. Each of the insecticides caused a decrease in the abundance of bacteria of the genus Pantoea, and an increase in the abundance of bacteria of the genus Stenotrophomonas, Acinetobacter, compared to untreated insects. After cypermethrin application, a decrease in the relative abundance of bacteria of the genus Pseudomonas was noted. The dominant bacterial genera in cypermethrin-treated larvae were Lactococcus, Pantoea, while in insects exposed to chlorpyrifos or flonicamid it was Pseudomonas. Insecticide-treated larvae were characterized, on average, by higher biodiversity and richness of bacterial genera, compared to untreated insects. The depletion of CLB-associated bacteria resulted in a decrease in larval survival, especially after cypermethrin and chlorpyrifos treatments. The use of a metagenome-based functional prediction approach revealed a higher predicted function of bacterial acetyl-CoA C-acetyltransferase in flonicamid and chlorpyrifos-treated larvae and tRNA dimethyltransferase in cypermethrin-treated insects than in untreated insects.},
}

@article {pmid38643884,
year = {2024},
author = {Liu, W and Xie, WY and Liu, HJ and Chen, C and Chen, SY and Jiang, GF and Zhao, FJ},
title = {Assessing intracellular and extracellular distribution of antibiotic resistance genes in the commercial organic fertilizers.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172558},
doi = {10.1016/j.scitotenv.2024.172558},
pmid = {38643884},
issn = {1879-1026},
abstract = {Compost-based organic fertilizers often contain high levels of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Previous studies focused on quantification of total ARGs and MGEs. For a more accurate risk assessment of the dissemination risk of antibiotic resistance, it is necessary to quantify the intracellular and extracellular distribution of ARGs and MGEs. In the present study, extracellular ARGs and MGEs (eARGs and eMGEs) and intracellular ARGs and MGEs (iARGs and iMGEs) were separately analyzed in 51 commercial composts derived from different raw materials by quantitative polymerase chain reaction (qPCR) and metagenomic sequencing. Results showed that eARGs and eMGEs accounted for 11-56 % and 4-45 % of the total absolute abundance of ARGs and MGEs, respectively. Comparable diversity, host composition and association with MGEs were observed between eARGs and iARGs. Contents of high-risk ARGs were similar between eARGs and iARGs, with high-risk ARGs in the two forms accounting for 6.7 % and 8.2 % of the total abundances, respectively. Twenty-four percent of the overall ARGs were present in plasmids, while 56.7 % of potentially mobile ARGs were found to be associated with plasmids. Variation partitioning analysis, null model and neutral community model indicated that the compositions of both eARGs and iARGs were largely driven by deterministic mechanisms. These results provide important insights into the cellular distribution of ARGs in manure composts that should be paid with specific attention in risk assessment and management.},
}

@article {pmid38643745,
year = {2024},
author = {Mang, Q and Gao, J and Li, Q and Sun, Y and Xu, G and Xu, P},
title = {Integrative analysis of metagenome and metabolome provides new insights into intestinal health protection in Coilia nasus larvae via probiotic intervention.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {50},
number = {},
pages = {101230},
doi = {10.1016/j.cbd.2024.101230},
pmid = {38643745},
issn = {1878-0407},
abstract = {With the development of large-scale intensive feeding, growth performance and animal welfare have attracted more and more attention. Exogenous probiotics can promote the growth performance of fish through improving intestinal microbiota; however, it remains unclear whether intestinal microbiota influence physiological biomarkers. Therefore, we performed metagenomic and metabolomic analysis to investigate the effects of a 90-day Lactiplantibacillus plantarum supplementation to a basal diet (1.0 × 10[8] CFU/g) on the growth performance, intestinal microbiota and their metabolites, and physiological biomarkers in Coilia nasus larvae. The results showed that the probiotic supplementation could significantly increase weight and body length. Moreover, it could also enhance digestive enzymes and tight junctions, and inhibit oxidative stress and inflammation. The metagenomic analysis showed that L. plantarum supplementation could significantly decrease the relative abundance of Proteobacteria and increase the relative abundance of Firmicutes. Additionally, pathogenic bacteria (Aeromonadaceae, Aeromonas, and Enterobacterales) were inhibited and beneficial bacteria (Bacillales) were promoted. The metabolome analysis showed that acetic acid and propanoic acid were significantly elevated, and were associated with Kitasatospora, Seonamhaeicola, and Thauera. A correlation analysis demonstrated that the digestive enzymes, tight junction, oxidative stress, and inflammation effects were significantly associated with the increased acetic acid and propanoic acid levels. These results indicated that L. plantarum supplementation could improve intestinal microbial community structure and function, which could raise acetic acid and propanoic acid levels to protect intestinal health and improve growth performance in C. nasus larvae.},
}

@article {pmid38643583,
year = {2024},
author = {Xu, R and Zhang, Y and Li, Y and Song, J and Liang, Y and Chen, F and Wei, X and Li, C and Liu, W and Rensing, C and Wang, Y and Chen, Y},
title = {Linking bacterial life strategies with the distribution pattern of antibiotic resistance genes in soil aggregates after straw addition.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134355},
doi = {10.1016/j.jhazmat.2024.134355},
pmid = {38643583},
issn = {1873-3336},
abstract = {Straw addition markedly affects the soil aggregates and microbial community structure. However, its influence on the profile of antibiotic resistance genes (ARGs), which are likely associated with changes in bacterial life strategies, remains unclear. To clarify this issue, a soil microcosm experiment was incubated under aerobic (WS) or anaerobic (AnWS) conditions after straw addition, and metagenomic sequencing was used to characterise ARGs and bacterial communities in soil aggregates. The results showed that straw addition shifted the bacterial life strategies from K- to r-strategists in all aggregates, and the aerobic and anaerobic conditions stimulated the growth of aerobic and anaerobic r-strategist bacteria, respectively. The WS decreased the relative abundances of dominant ARGs such as QnrS5, whereas the AnWS increased their abundance. After straw addition, the macroaggregates consistently exhibited a higher number of significantly altered bacteria and ARGs than the silt+clay fractions. Network analysis revealed that the WS increased the number of aerobic r-strategist bacterial nodes and fostered more interactions between r-and K-strategist bacteria, thus promoting ARGs prevalence, whereas AnWS exhibited an opposite trend. These findings provide a new perspective for understanding the fate of ARGs and their controlling factors in soil ecosystems after straw addition. ENVIRONMENTAL IMPLICATIONS: Straw soil amendment has been recommended to mitigate soil fertility degradation, improve soil structure, and ultimately increase crop yields. However, our findings highlight the importance of the elevated prevalence of ARGs associated with r-strategist bacteria in macroaggregates following the addition of organic matter, particularly fresh substrates. In addition, when assessing the environmental risk posed by ARGs in soil that receives crop straw, it is essential to account for the soil moisture content. This is because the species of r-strategist bacteria that thrive under aerobic and anaerobic conditions play a dominant role in the dissemination and accumulation of ARG.},
}

@article {pmid38643524,
year = {2024},
author = {Mishra, S and Zhang, X and Yang, X},
title = {Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition.},
journal = {Microbiological research},
volume = {284},
number = {},
pages = {127726},
doi = {10.1016/j.micres.2024.127726},
pmid = {38643524},
issn = {1618-0623},
abstract = {Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.},
}

@article {pmid38643472,
year = {2024},
author = {Kerekes, IK and Nagy, Á and Ősz, Á and Zalka, P},
title = {[Examination possibilities of microbial nucleic acid samples derived from the environment].},
journal = {Orvosi hetilap},
volume = {165},
number = {16},
pages = {613-619},
doi = {10.1556/650.2024.33025},
pmid = {38643472},
issn = {1788-6120},
}

@article {pmid38643272,
year = {2024},
author = {Hauptfeld, E and Pappas, N and van Iwaarden, S and Snoek, BL and Aldas-Vargas, A and Dutilh, BE and von Meijenfeldt, FAB},
title = {Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3373},
pmid = {38643272},
issn = {2041-1723},
abstract = {Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.},
}

@article {pmid38643166,
year = {2024},
author = {Luo, K and Peters, BA and Moon, JY and Xue, X and Wang, Z and Usyk, M and Hanna, DB and Landay, AL and Schneider, MF and Gustafson, D and Weber, KM and French, A and Sharma, A and Anastos, K and Wang, T and Brown, T and Clish, CB and Kaplan, RC and Knight, R and Burk, RD and Qi, Q},
title = {Metabolic and inflammatory perturbation of diabetes associated gut dysbiosis in people living with and without HIV infection.},
journal = {Genome medicine},
volume = {16},
number = {1},
pages = {59},
pmid = {38643166},
issn = {1756-994X},
support = {R01HL140976/HL/NHLBI NIH HHS/United States ; R01DK119268/DK/NIDDK NIH HHS/United States ; },
abstract = {BACKGROUND: Gut dysbiosis has been linked with both HIV infection and diabetes, but its interplay with metabolic and inflammatory responses in diabetes, particularly in the context of HIV infection, remains unclear.

METHODS: We first conducted a cross-sectional association analysis to characterize the gut microbial, circulating metabolite, and immune/inflammatory protein features associated with diabetes in up to 493 women (~ 146 with prevalent diabetes with 69.9% HIV +) of the Women's Interagency HIV Study. Prospective analyses were then conducted to determine associations of identified metabolites with incident diabetes over 12 years of follow-up in 694 participants (391 women from WIHS and 303 men from the Multicenter AIDS Cohort Study; 166 incident cases were recorded) with and without HIV infection. Mediation analyses were conducted to explore whether gut bacteria-diabetes associations are explained by altered metabolites and proteins.

RESULTS: Seven gut bacterial genera were identified to be associated with diabetes (FDR-q <  0.1), with positive associations for Shigella, Escherichia, Megasphaera, and Lactobacillus, and inverse associations for Adlercreutzia, Ruminococcus, and Intestinibacter. Importantly, the associations of most species, especially Adlercreutzia and Ruminococcus, were largely independent of antidiabetic medications use. Meanwhile, 18 proteins and 76 metabolites, including 3 microbially derived metabolites (trimethylamine N-oxide, phenylacetylglutamine (PAGln), imidazolepropionic acid (IMP)), 50 lipids (e.g., diradylglycerols (DGs) and triradylglycerols (TGs)) and 23 non-lipid metabolites, were associated with diabetes (FDR-q <  0.1), with the majority showing positive associations and more than half of them (59/76) associated with incident diabetes. In mediation analyses, several proteins, especially interleukin-18 receptor 1 and osteoprotegerin, IMP and PAGln partially mediate the observed bacterial genera-diabetes associations, particularly for those of Adlercreutzia and Escherichia. Many diabetes-associated metabolites and proteins were altered in HIV, but no effect modification on their associations with diabetes was observed by HIV.

CONCLUSION: Among individuals with and without HIV, multiple gut bacterial genera, blood metabolites, and proinflammatory proteins were associated with diabetes. The observed mediated effects by metabolites and proteins in genera-diabetes associations highlighted the potential involvement of inflammatory and metabolic perturbations in the link between gut dysbiosis and diabetes in the context of HIV infection.},
}

@article {pmid38643098,
year = {2024},
author = {Wang, Z and Wu, Y and Li, X and Ji, X and Liu, W},
title = {The gut microbiota facilitate their host tolerance to extreme temperatures.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {131},
pmid = {38643098},
issn = {1471-2180},
support = {31501175//National Natural Science Foundation of China/ ; RC342201//Talents in Anhui Agricultural University/ ; },
abstract = {BACKGROUND: Exposure to extreme cold or heat temperature is one leading cause of weather-associated mortality and morbidity in animals. Emerging studies demonstrate that the microbiota residing in guts act as an integral factor required to modulate host tolerance to cold or heat exposure, but common and unique patterns of animal-temperature associations between cold and heat have not been simultaneously examined. Therefore, we attempted to investigate the roles of gut microbiota in modulating tolerance to cold or heat exposure in mice.

RESULTS: The results showed that both cold and heat acutely change the body temperature of mice, but mice efficiently maintain their body temperature at conditions of chronic extreme temperatures. Mice adapt to extreme temperatures by adjusting body weight gain, food intake and energy harvest. Fascinatingly, 16 S rRNA sequencing shows that extreme temperatures result in a differential shift in the gut microbiota. Moreover, transplantation of the extreme-temperature microbiota is sufficient to enhance host tolerance to cold and heat, respectively. Metagenomic sequencing shows that the microbiota assists their hosts in resisting extreme temperatures through regulating the host insulin pathway.

CONCLUSIONS: Our findings highlight that the microbiota is a key factor orchestrating the overall energy homeostasis under extreme temperatures, providing an insight into the interaction and coevolution of hosts and gut microbiota.},
}

@article {pmid38642797,
year = {2024},
author = {Watanabe, M and Uematsu, M and Fujimoto, K and Hara, T and Yamamoto, M and Miyaoka, D and Yokota, C and Kamei, Y and Sugimoto, A and Kawasaki, N and Yabuno, T and Sato, N and Sato, S and Yamaguchi, K and Furukawa, Y and Tsuruta, D and Okada, F and Imoto, S and Uematsu, S},
title = {Targeted lysis of Staphylococcus hominis linked to axillary osmidrosis using bacteriophage-derived endolysin.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2024.03.039},
pmid = {38642797},
issn = {1523-1747},
}

@article {pmid38642768,
year = {2024},
author = {Li, Q and Yu, H and Peng, Y and Liu, R and Jing, Z and Wei, Y and Tu, S and Gao, H and Song, Y},
title = {Mitigated N2O emissions from submerged-plant-covered aquatic ecosystems on the Changjiang River Delta.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172592},
doi = {10.1016/j.scitotenv.2024.172592},
pmid = {38642768},
issn = {1879-1026},
abstract = {Submerged plants affect nitrogen cycling in aquatic ecosystems. However, whether and how submerged plants change nitrous oxide (N2O) production mechanism and emissions flux remains controversial. Current research primarily focuses on the feedback from N2O release to variation of substrate level and microbial communities. It is deficient in connecting the relative contribution of individual N2O production processes (i.e., the N2O partition). Here, we attempted to offer a comprehensive understanding of the N2O mitigation mechanism in aquatic ecosystems on the Changjiang River Delta according to stable isotopic techniques, metagenome-assembly genome analysis, and statistical analysis. We found that the submerged plant reduced 45 % of N2O emissions by slowing down the dissolved inorganic nitrogen conversion velocity to N2O in sediment (Vf-[DIN]sed). It was attributed to changing the N2O partition and suppressing the potential capacity of net N2O production (i.e., nor/nosZ). The dominated production processes showed a shift with increasing excess N2O. Meanwhile, distinct shift thresholds of planted and unplanted habitats reflected different mechanisms of stimulated N2O production. The hotspot zone of N2O production corresponded to high nor/nosZ and unsaturated oxygen (O2) in unplanted habitat. In contrast, planted habitat hotspot has lower nor/nosZ and supersaturated O2. O2 from photosynthesis critically impacted the activities of N2O producers and consumers. In summary, the presence of submerged plants is beneficial to mitigate N2O emissions from aquatic ecosystems.},
}

@article {pmid38642657,
year = {2024},
author = {Vacca, M and Celano, G and Serale, N and Costantino, G and Calabrese, FM and Calasso, M and De Angelis, M},
title = {Dynamic microbial and metabolic changes during Apulian Caciocavallo cheese-making and ripening produced according to a standardized protocol.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2023-24049},
pmid = {38642657},
issn = {1525-3198},
abstract = {The cheese microbiota plays a critical role in influencing its sensory and physicochemical properties. In this study, traditional Apulian Caciocavallo cheese coming from 4 different dairies in the same area and produced following standardized procedures have been examined, as well as the different bulk milks and natural whey starter cultures used. Moreover, considering the cheese wheels as the blocks of Caciocavallo cheeses as whole, these were characterized at different layers (i.e., core, under-rind, and rind) of the block using a multi-omics approach. In addition to physical-chemical characterization, culturomics, quantitative PCR, metagenomics, and metabolomics analysis, have been carried out post-salting and throughout ripening time (2 mo) to investigate the major shifts in the succession of the microbiota and flavor development. Culture-dependent and 16S rRNA metataxonomics results clearly clustered samples based on the microbiota biodiversity related to the production dairy plant as the result of the use of different NWS or intrinsic conditions of each production site. At the beginning of the ripening, cheeses were dominated by the Lactobacillus and, in 2 dairies (Art and SdC), Streptococcus genera associated with the NWS. The analysis allowed us to show that, although the diversity of identified genera did not change significantly between the rind, under-rind and core fractions of the same samples, there was an evolution in the relative abundance and absolute quantification, modifying and differentiating profiles during ripening. The qPCR mainly differentiated the temporal adaptation of those species originating from bulk milks and those provided by NWSs. The primary starter detected in NWS and cheese reassured the high relative concentration of 1-butanol, 2-butanol, 2-heptanol, 2-butanone, acetoin, delta-dodecalactone, hexanoic acid ethyl ester, octanoic acid ethyl ester, and VFFA during ripening, while cheeses displaying low abundances of Streptococcus and Lactococcus (dairy Del) have a lower total concentration of acetoin compared with Art and SdC. However, the sub-dominant strains and NSLAB present in cheeses are responsible for the production of secondary metabolites belonging to the chemical classes of ketones, alcohols, and organic acids, reaffirming the importance and relevance of autochthonous strains of each dairy plant although considering a delimited production area.},
}

@article {pmid38641693,
year = {2024},
author = {Chen, X and Yang, Y and Wang, J and Pan, C and Zhang, Z and Chen, S and Xie, S},
title = {Impacts of o-cresol spill on composition and function of river sediment and soil microbial communities.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38641693},
issn = {1614-7499},
abstract = {o-Cresol is a toxic substance with strong irritating and corrosive effects on skin and mucous membranes. To date, information on the effects of o-cresol on microbial communities in the natural environment is very limited. In the present study, 16S rRNA sequencing and metagenomic technique were carried out to elucidate the effects of the o-cresol spill on microbial communities in river sediments and nearby soils. o-Cresol spill induced the increase in the relative abundance of phyla Planctomycetes and Gemmatimonadetes, suggesting their resilience to o-cresol-induced stress. Uncultured Gemmatimonadetes genera and the MND1 genus exhibited enrichment, while the Pseudomonas genus dominated across all samples, indicating their potential pivotal roles in adapting to the o-cresol spill. Moreover, o-cresol spill impaired the metabolic functions of microbes but triggered their defense mechanisms. Under o-cresol pressure, microbial functions related to carbon fixation were upregulated and functions associated with sulfur metabolism were downregulated. In addition, the o-cresol spill led to an increase in functional genes related to the conversion of o-cresol to 3-methylcatechol. Several genes involved in the degradation of aromatic compounds were also identified, potentially contributing to the biodegradation of o-cresol. This study provides fresh insights into the repercussions of an abrupt o-cresol spill on microbial communities in natural environments, shedding light on their adaptability, defense mechanisms, and biodegradation potential.},
}

@article {pmid38641305,
year = {2024},
author = {Chen, Y and Zhang, C and Chen, Z and Yang, Y and Lin, Z and Deng, Z and Wang, X},
title = {Fe(II)-driven spatiotemporal assembly of heterotrophic and anammox bacteria enhances simultaneous nitrogen and phosphorus removal for low-strength municipal wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130713},
doi = {10.1016/j.biortech.2024.130713},
pmid = {38641305},
issn = {1873-2976},
abstract = {The mainstream anaerobic ammonium oxidation (anammox) faces considerable challenges with low-strength municipal wastewater. A Fe(Ⅱ)-amended partial denitrification coupled anammox (PD/A) process was conducted and achieved a long-term and efficient nitrogen and phosphorus removal, yielding effluent total nitrogen and phosphorus concentrations of 1.97 ± 1.03 mg/L and 0.23 ± 0.13 mg/L, respectively, which could well meet more stringent effluent discharge standard of some wastewater treatment plants in specific geographical locations, e.g., estuaries. Fe(Ⅱ)-driven vivianite formation provided key nucleuses for the optimization of the spatial distribution of heterotrophic and anammox bacteria with enhanced extracellular polymeric substances as key driving forces. Metagenomics analysis further revealed the increase of key genes, enhancing anammox bacteria homeostasis, which also bolstered the resistance to environmental perturbations. This study provided a comprehensive sight into the function of Fe(Ⅱ) in mainstream PD/A process, and explored a promising alternative for synergetic nitrogen and phosphorus removal for low-strength municipal wastewater treatment.},
}

@article {pmid38641105,
year = {2024},
author = {Lin, L and Xiong, J and Yue, T and Xu, W and Liu, L and Wang, F and Yang, S and Cao, W},
title = {Phosphorus starvation response genes and function coupling: A mechanism to regulate phosphorus availability in a subtropical estuary.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172575},
doi = {10.1016/j.scitotenv.2024.172575},
pmid = {38641105},
issn = {1879-1026},
abstract = {Phosphorus (P) plays an important role in regulating primary production in estuarine environments. However, knowledge of the P-functional gene composition of microbial communities and the mechanisms of microbial adaptation to changes in available P in estuaries remain limited. This study coupling 16 s rDNA and metagenomics sequencing was conducted to reveal the relationship between P cycling functional genes, microbial interactions, and P availability in the Jiulong River Estuary. The results showed that the relative abundance of P cycling functions genes was highest in winter, and lowest in summer. Spatially, the total relative abundance of P cycling functions genes was higher in the riverward than that in the seaward. P cycling functional microbial interactions and P cycling gene coupling were strongest in summer and in the seaward. Changes in both temperature and salinity had significant direct and indirect effects on P cycling function, and the influence of salinity on P cycling function was greater than that on the microbial community in the estuary. Salinity had significant direct negative effects on inorganic P-solubilization (IP), organic P-mineralization (OP), and P uptake and transport functions (PT). Whereas, salinity had a significant positive effect on P-starvation response regulation (PR) function. Thus, salinity and microbial communities regulate the soluble reactive phosphate concentrations in estuarine environments by strengthening internal coupling among P cycling functions, promoting PR function, and facilitating PT gene expression. PR is the most important predictors, PR, PT, and PR-PT together explained 38.56 % of the overall soluble reactive phosphorus (SRP) variation. Over 66 % of the explained SRP variations can be predicted by the PR, PT, and PR-PT functional genes. This finding improves the knowledge base of the microbial processes for P cycling and provides a foundation for eutrophication management strategies in the estuary.},
}

@article {pmid38640951,
year = {2024},
author = {Vezeau, N and Kahn, L},
title = {Current understanding and knowledge gaps regarding wildlife as reservoirs of antimicrobial resistance.},
journal = {American journal of veterinary research},
volume = {},
number = {},
pages = {1-9},
doi = {10.2460/ajvr.24.02.0040},
pmid = {38640951},
issn = {1943-5681},
abstract = {Antimicrobial resistance (AMR) is a serious health issue shared across all One Health domains. Wildlife species represent a key intersection of the animal and environmental domains. They are a relevant but understudied reservoir and route of spread for AMR throughout the environment. Most wildlife AMR research thus far has focused on avian species, terrestrial mammals, and a selection of aquatic and marine species. Pathogens often identified in terrestrial wildlife include enteric zoonotic organisms such as Eschericia coli and Salmonella spp, in addition to nonenterics such as Staphylococci. Resistances have been commonly identified to antimicrobials important in veterinary and human medicine, including β-lactams, tetracyclines, aminoglycosides, and macrolides. Our emerging understanding of the dynamics of AMR distribution across life on Earth provides further opportunities for us to assess the risk it poses to veterinary and human health. Future work will require prioritizing which wildlife most exacerbates and indicates AMR in domestic animals. However, decreasing prices and increasing ease for metagenomic sequencing allows for synergies with expanding wildlife viral disease surveillance. Improved understanding of how wildlife impacts veterinary and human healthcare may increase opportunities for related research funding and global equity in such research. The companion Currents in One Health article by Vezeau and Kahn, JAVMA, June 2024, addresses in further detail the routes of spread of AMR across different animal populations and actions that can be taken to mitigate AMR with special consideration for wildlife sources.},
}