@article {pmid40172215,
year = {2025},
author = {Brito Rodrigues, P and de Rezende Rodovalho, V and Sencio, V and Benech, N and Creskey, M and Silva Angulo, F and Delval, L and Robil, C and Gosset, P and Machelart, A and Haas, J and Descat, A and Goosens, JF and Beury, D and Maurier, F and Hot, D and Wolowczuk, I and Sokol, H and Zhang, X and Ramirez Vinolo, MA and Trottein, F},
title = {Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2486511},
doi = {10.1080/19490976.2025.2486511},
pmid = {40172215},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/virology/metabolism ; *Metagenomics ; *Metabolomics ; *Disease Models, Animal ; Cricetinae ; *SARS-CoV-2/genetics ; Aging ; Age Factors ; Dysbiosis/microbiology ; Male ; Bacteria/classification/genetics/metabolism/isolation & purification ; Mesocricetus ; Metabolome ; },
abstract = {Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium, Oscillospiraceae, Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.},
}

Animals
*Gastrointestinal Microbiome
*COVID-19/microbiology/virology/metabolism
*Metagenomics
*Metabolomics
*Disease Models, Animal
Cricetinae
*SARS-CoV-2/genetics
Aging
Age Factors
Dysbiosis/microbiology
Male
Bacteria/classification/genetics/metabolism/isolation & purification
Mesocricetus
Metabolome

@article {pmid40171165,
year = {2025},
author = {Shi, H and Li, J},
title = {MAGs-based genomic comparison of gut significantly enriched microbes in obese individuals pre- and post-bariatric surgery across diverse locations.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1485048},
pmid = {40171165},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; *Bariatric Surgery ; Metagenome ; Metagenomics/methods ; Genomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; Gastric Bypass ; Computational Biology/methods ; Adult ; },
abstract = {INTRODUCTION: Obesity, a pressing global health issue, is intricately associated with distinct gut microbiota profiles. Bariatric surgeries, such as Laparoscopic Sleeve Gastrectomy (LSG), Sleeve Gastrectomy (SG), and Roux-en-Y Gastric Bypass (RYGB), induce substantial weight loss and reshape gut microbiota composition and functionality, yet their comparative impacts remain underexplored.

METHODS: This study integrated four published metagenomic datasets, encompassing 500 samples, and employed a unified bioinformatics workflow for analysis. We assessed gut microbiota α-diversity, identified species biomarkers using three differential analysis approaches, and constructed high-quality Metagenome-Assembled Genomes (MAGs). Comparative genomic, functional profiling and KEGG pathway analyses were performed, alongside estimation of microbial growth rates via Peak-to-Trough Ratios (PTRs).

RESULTS: RYGB exhibited the most pronounced enhancement of gut microbiota α-diversity compared to LSG and SG. Cross-cohort analysis identified 39 species biomarkers: 27 enriched in the non-obesity group (NonOB_Enrich) and 12 in the obesity group (OB_Enrich). Among the MAGs, 177 were NonOB_Enrich and 14 were OB_Enrich. NonOB_Enrich MAGs displayed enriched carbohydrate degradation profiles (e.g., GH105, GH2, GH23, GH43, and GT0 families) and higher gene diversity in fatty acid biosynthesis and secondary metabolite pathways, alongside significant enrichment in amino acid metabolism (KEGG analysis). Post-surgery, Akkermansia muciniphila and Bacteroides uniformis showed elevated growth rates based on PTRs.

DISCUSSION: These findings underscore RYGB's superior impact on gut microbiota diversity and highlight distinct microbial functional adaptations linked to weight loss, offering insights for targeted therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Obesity/microbiology
*Bariatric Surgery
Metagenome
Metagenomics/methods
Genomics
Bacteria/classification/genetics/isolation & purification/metabolism
Gastric Bypass
Computational Biology/methods
Adult

@article {pmid40170844,
year = {2025},
author = {Zhou, Y and Han, W and Feng, Y and Wang, Y and Liu, X and Sun, T and Xu, J},
title = {Revealing gut microbiota biomarkers associated with melanoma immunotherapy response and key bacteria-fungi interaction relationships: evidence from metagenomics, machine learning, and SHAP methodology.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1539653},
pmid = {40170844},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Melanoma/therapy/immunology/microbiology ; *Metagenomics/methods ; *Immunotherapy/methods ; *Machine Learning ; Male ; *Bacteria/genetics/classification/immunology ; Female ; Fungi/immunology ; Middle Aged ; Skin Neoplasms/immunology/therapy/microbiology ; Biomarkers ; Aged ; Adult ; Treatment Outcome ; },
abstract = {INTRODUCTION: The gut microbiota is associated with the response to immunotherapy in cutaneous melanoma (CM). However, gut fungal biomarkers and bacterial-fungal interactions have yet to be determined.

METHODS: Metagenomic sequencing data of stool samples collected before immunotherapy from three independent groups of European ancestry CM patients were collected. After characterizing the relative abundances of bacteria and fungi, Linear Discriminant Analysis Effect Size (LEfSe) analysis, Random Forest (RF) model construction, and SHapley Additive exPlanations (SHAP) methodology were applied to identify biomarkers and key bacterial-fungal interactions associated with immunotherapy responders in CM.

RESULTS: Diversity analysis revealed significant differences in the bacterial and fungal composition between CM immunotherapy responders and non-responders. LEfSe analysis identified 45 bacterial and 4 fungal taxa as potential biomarkers. After constructing the RF model, the AUC of models built using bacterial and fungal data separately were 0.64 and 0.65, respectively. However, when bacterial and fungal data were combined, the AUC of the merged model increased to 0.71. In the merged model, the following taxa were identified as important biomarkers: Romboutsia, Endomicrobium, Aggregatilinea, Candidatus Moduliflexus, Colwellia, Akkermansia, Mucispirillum, and Rutstroemia, which were associated with responders, whereas Zancudomyces was associated with non-responders. Moreover, the positive correlation interaction between Akkermansia and Rutstroemia is considered a key bacterial-fungal interaction associated with CM immunotherapy response.

CONCLUSION: Our results provide valuable insights for the enrichment of responders to immunotherapy in CM patients. Moreover, this study highlights the critical role of bacterial-fungal interactions in CM immunotherapy.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Melanoma/therapy/immunology/microbiology
*Metagenomics/methods
*Immunotherapy/methods
*Machine Learning
Male
*Bacteria/genetics/classification/immunology
Female
Fungi/immunology
Middle Aged
Skin Neoplasms/immunology/therapy/microbiology
Biomarkers
Aged
Adult
Treatment Outcome

@article {pmid40169660,
year = {2025},
author = {Legrand, TPRA and Alexandre, PA and Wilson, A and Farr, RJ and Reverter, A and Denman, SE},
title = {Genome-centric metagenomics reveals uncharacterised microbiomes in Angus cattle.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {547},
pmid = {40169660},
issn = {2052-4463},
mesh = {Animals ; Cattle/microbiology ; *Metagenomics ; *Microbiota ; *Feces/microbiology ; Metagenome ; Saliva/microbiology ; Mouth/microbiology ; },
abstract = {Understanding the intricate nexus between cattle health and microbiome dynamics holds profound implications for enhancing animal productivity and welfare. However, our understanding of the role of these microbial communities is limited in beef cattle, especially in understudied body sites such as the oral and nasal microbiome. Here, using a genome-centric metagenomics approach, we recovered substantial metagenome-assembled genomes (MAGs) from the faecal, oral and nasal microbiome of Australian Angus cattle from different herds and life stages. The MAGs recovered from faecal samples were dominated by Bacillota and Bacteroidota, while the MAGs from saliva and nasal mucus samples were mainly associated with Pseudomonadota, Actinomycetota and Bacteroidota. Functional annotation of the MAGs revealed enriched pathways involved in the production of some amino acids, nucleic acids and short chain fatty acids (SCFA). The metabolic capacities of the MAGs were correlated with their taxonomy, notably at the phylum level. Overall, this study provides a comprehensive catalogue of MAGs to further our understanding of their role in the health and fitness of beef cattle.},
}

Animals
Cattle/microbiology
*Metagenomics
*Microbiota
*Feces/microbiology
Metagenome
Saliva/microbiology
Mouth/microbiology

@article {pmid40156868,
year = {2025},
author = {Yang, W and Luyten, Y and Reister, E and Mangelson, H and Sisson, Z and Auch, B and Liachko, I and Roberts, RJ and Ettwiller, L},
title = {Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.},
journal = {Nucleic acids research},
volume = {53},
number = {6},
pages = {},
pmid = {40156868},
issn = {1362-4962},
support = {//New England Biolabs, Inc./ ; R44AI172703/GF/NIH HHS/United States ; //Bill & Melinda Gates Foundation/ ; },
mesh = {*Methyltransferases/metabolism/genetics ; *Microbiota/genetics ; DNA Methylation ; Bacteriophages/genetics/enzymology ; High-Throughput Nucleotide Sequencing ; Bacteria/genetics/enzymology ; Substrate Specificity ; Bacterial Proteins/metabolism/genetics ; Sequence Analysis, DNA/methods ; DNA, Viral/genetics/metabolism ; },
abstract = {Methylation patterns in bacteria can be used to study restriction-modification or other defense systems with novel properties. While m4C and m6A methylation are well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 (rapid identification of methyltransferase specificity sequencing) on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on bacteriophage DNA and compared with host DNA, strengthening evidence for phage-host interactions. Applied to three different microbiomes, the method unveiled over 1900 motifs that were deposited in REBASE. The motifs include a novel eight-base recognition site (CATm5CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5C methyltransferase specificities, providing insights into bacterial biology and biotechnological applications.},
}

*Methyltransferases/metabolism/genetics
*Microbiota/genetics
DNA Methylation
Bacteriophages/genetics/enzymology
High-Throughput Nucleotide Sequencing
Bacteria/genetics/enzymology
Substrate Specificity
Bacterial Proteins/metabolism/genetics
Sequence Analysis, DNA/methods
DNA, Viral/genetics/metabolism

@article {pmid40062854,
year = {2025},
author = {Zhang, F and Luan, J and Suo, L and Wang, H and Zhao, Y and Sun, T and Ni, Y and Cao, H and Zou, X and Liu, B},
title = {Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study.},
journal = {Microbiology spectrum},
volume = {13},
number = {4},
pages = {e0263924},
pmid = {40062854},
issn = {2165-0497},
support = {2022YFA1304303//National Key R&D Program of China/ ; tsqn202103196//Taishan Scholars Program of Shandong Province/ ; 82370017//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Feces/microbiology ; Female ; *Metabolomics ; Middle Aged ; *Metagenomics ; Aged ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Community-Acquired Infections/microbiology/metabolism ; *Pneumonia/microbiology/metabolism ; *Fatty Acids, Volatile/metabolism/analysis ; Metabolome ; Adult ; Bile Acids and Salts/metabolism ; Metagenome ; },
abstract = {UNLABELLED: Emerging evidence suggests that altered gut microbiota is linked to community-acquired pneumonia (CAP), but the potential mechanisms by which gut microbiota and its metabolites contribute to the development of CAP remain unclear. Fecal samples from 32 CAP patients and 36 healthy controls were analyzed through metagenomic sequencing and metabolomic profiling. The gut microbiota composition in CAP patients showed significant differences and lower diversity compared to healthy controls. Genera involved in short-chain fatty acid (SCFA) production, such as Faecalibacterium, Ruminococcus, and Eubacterium, as well as species like Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, Prevotella copri, and Ruminococcus bromii, were significantly depleted in CAP patients. Bacterial co-occurrence network analysis revealed an over-representation of pro-inflammatory bacteria, which contributed to the core gut microbiome in CAP patients. Metabolomic analysis of fecal samples identified a distinct metabolic profile, with a notable increase in arachidonic acid, but a decrease in secondary bile acids, such as deoxycholic acid, lithocholic acid, and ursodeoxycholic acid, compared to healthy controls. Spearman correlation analysis between differential microbiota and bile acids showed that Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, and Prevotella copri were positively correlated with ursocholic acid, lithocholic acid, and ursodeoxycholic acid, respectively. Our results suggest that the reduction in secondary bile acids, insufficient production of SCFAs, and an overabundance of pro-inflammatory bacteria may contribute to metabolic inflammation in the body. These factors could play a key role in the pathogenesis of CAP, driven by gut microbiota alterations.

IMPORTANCE: This study presents a comprehensive metagenomic and metabolomic analysis of fecal samples from community-acquired pneumonia (CAP) patients, identifying key characteristics, such as decreased secondary bile acids, imbalanced short-chain fatty acid production, and increased pro-inflammatory bacteria. These findings provide valuable insights into the mechanisms linking gut microbiota alterations to CAP pathogenesis and suggest that targeting the gut microbiota could be a promising strategy for intervening in CAP.},
}

Humans
*Gastrointestinal Microbiome
Male
*Feces/microbiology
Female
*Metabolomics
Middle Aged
*Metagenomics
Aged
*Bacteria/classification/genetics/isolation & purification/metabolism
*Community-Acquired Infections/microbiology/metabolism
*Pneumonia/microbiology/metabolism
*Fatty Acids, Volatile/metabolism/analysis
Metabolome
Adult
Bile Acids and Salts/metabolism
Metagenome

@article {pmid40042334,
year = {2025},
author = {Venturini, AM and Gontijo, JB and Berrios, L and Rodrigues, JLM and Peay, KG and Tsai, SM},
title = {Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon.},
journal = {Microbiology spectrum},
volume = {13},
number = {4},
pages = {e0156124},
pmid = {40042334},
issn = {2165-0497},
support = {2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; DEB 1952687//National Science Foundation (NSF)/ ; 2015/13546-7//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2018/14974-0//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 140032/2015-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 133769/2015-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 314806/2021-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; DEB 1442214//National Science Foundation (NSF)/ ; //Canadian Institute for Advanced Research (CIFAR)/ ; 2109481//National Science Foundation (NSF)/ ; //Stanford Doerr School of Sustainability Discovery grant/ ; },
mesh = {*Soil Microbiology ; Brazil ; *Forests ; *Archaea/genetics/classification ; *Bacteria/genetics/classification/isolation & purification ; *Metagenome ; Soil/chemistry ; Phylogeny ; Genome, Archaeal ; Genomics ; Microbiota/genetics ; Genome, Bacterial ; Base Composition ; },
abstract = {Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.},
}

*Soil Microbiology
Brazil
*Forests
*Archaea/genetics/classification
*Bacteria/genetics/classification/isolation & purification
*Metagenome
Soil/chemistry
Phylogeny
Genome, Archaeal
Genomics
Microbiota/genetics
Genome, Bacterial
Base Composition

@article {pmid39760247,
year = {2025},
author = {Lee, CE and Messer, LF and Wattiez, R and Matallana-Surget, S},
title = {Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms.},
journal = {Proteomics},
volume = {25},
number = {7},
pages = {e202400208},
doi = {10.1002/pmic.202400208},
pmid = {39760247},
issn = {1615-9861},
support = {//Joint UKRI Natural Environment Research Council (NERC) and National Research Foundation (NRF) Singapore/ ; NE/V009621/1//UKRI NERC/NRF/ ; NRF-SEAP-2020-0001//UKRI NERC/NRF/ ; NE/S007342/1//NERC Scottish Universities Partnership for Environmental Research (SUPER) Doctoral Training Partnership (DTP)/ ; },
mesh = {*Biofilms/growth & development ; *Bacterial Proteins/metabolism/genetics ; Proteomics/methods ; Plastics/metabolism ; Proteome/metabolism/analysis ; Bacteria/genetics/metabolism/classification ; Microbiota/genetics/physiology ; Metagenome/genetics ; Polyethylene/metabolism ; Metagenomics/methods ; Multiomics ; },
abstract = {Marine plastispheres represent dynamic microhabitats where microorganisms colonise plastic debris and interact. Metaproteomics has provided novel insights into the metabolic processes within these communities; however, the early metabolic interactions driving the plastisphere formation remain unclear. This study utilised metaproteomic and metagenomic approaches to explore early plastisphere formation on low-density polyethylene (LDPE) over 3 (D3) and 7 (D7) days, focusing on microbial diversity, activity and biofilm development. In total, 2948 proteins were analysed, revealing dominant proteomes from Pseudomonas and Marinomonas, with near-complete metagenome-assembled genomes (MAGs). Pseudomonas dominated at D3, whilst at D7, Marinomonas, along with Acinetobacter, Vibrio and other genera became more prevalent. Pseudomonas and Marinomonas showed high expression of reactive oxygen species (ROS) suppression proteins, associated with oxidative stress regulation, whilst granule formation, and alternative carbon utilisation enzymes, also indicated nutrient limitations. Interestingly, 13 alkanes and other xenobiotic degradation enzymes were expressed by five genera. The expression of toxins, several type VI secretion system (TVISS) proteins, and biofilm formation proteins by Pseudomonas indicated their competitive advantage against other taxa. Upregulated metabolic pathways relating to substrate transport also suggested enhanced nutrient cross-feeding within the more diverse biofilm community. These insights enhance our understanding of plastisphere ecology and its potential for biotechnological applications.},
}

*Biofilms/growth & development
*Bacterial Proteins/metabolism/genetics
Proteomics/methods
Plastics/metabolism
Proteome/metabolism/analysis
Bacteria/genetics/metabolism/classification
Microbiota/genetics/physiology
Metagenome/genetics
Polyethylene/metabolism
Metagenomics/methods
Multiomics

@article {pmid40169555,
year = {2025},
author = {Li, H and Liu, P and Sun, T and Li, Y and Wu, J and Huang, Y and Yang, J and Yuan, M and Zhang, J and Yang, J and Wong, ML and Licinio, J and Zheng, P},
title = {Dynamic alterations of depressive-like behaviors, gut microbiome, and fecal metabolome in social defeat stress mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {115},
pmid = {40169555},
issn = {2158-3188},
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Stress, Psychological/metabolism/microbiology ; *Feces/microbiology/chemistry ; Male ; *Social Defeat ; *Metabolome ; *Disease Models, Animal ; *Depressive Disorder, Major/metabolism/microbiology ; *Behavior, Animal ; *Anhedonia ; Humans ; Mice, Inbred C57BL ; Female ; RNA, Ribosomal, 16S/genetics ; Depression/metabolism/microbiology ; },
abstract = {Gut microbiome is implicated in the onset and progression of major depressive disorder (MDD), but the dynamic alterations of depressive symptoms, gut microbiome, and fecal metabolome across different stages of stress exposure remain unclear. Here, we modified the chronic social defeat stress (CSDS) model to evaluate mice subjected to social defeat stress for 1, 4, 7, and 10 days. Behavioral tests, 16S rRNA, metagenomics, and fecal metabolomics were conducted to investigate the impact of stress exposure on behaviors, gut microbiota and fecal metabolites. We observed that depressive-like behaviors, such as anhedonia and social avoidance, worsened significantly as stress exposure increased. The microbial composition, function, and fecal metabolites exhibited distinct separations across the different social defeat stress groups. Mediation analysis identified key bacteria, such as Lachnospiraceae_UCG-001 and Bacteroidetes, and fecal metabolites like valeric acid and N-acetylaspartate. In our clinical depression cohort, we confirmed that fecal valeric acid levels, were significantly lower in depressive-like mice and MDD patients, correlating closely with stress exposure and anhedonia in mice. Further analysis of serum and brain metabolites in mice revealed sustained changes of N-acetylaspartate abundance in fecal, serum, and cortical samples following increasing stress exposure. Together, this study elucidated the characteristics of depressive-like behaviors, gut microbiome, and fecal metabolome across various social defeat stress exposure, and identified key bacteria and fecal metabolites potentially involved in modulating social defeat stress response and depressive-like behaviors, providing new insights into the pathogenesis and intervention of depression.},
}

Animals
*Gastrointestinal Microbiome
Mice
*Stress, Psychological/metabolism/microbiology
*Feces/microbiology/chemistry
Male
*Social Defeat
*Metabolome
*Disease Models, Animal
*Depressive Disorder, Major/metabolism/microbiology
*Behavior, Animal
*Anhedonia
Humans
Mice, Inbred C57BL
Female
RNA, Ribosomal, 16S/genetics
Depression/metabolism/microbiology

@article {pmid40169018,
year = {2025},
author = {Wallace, MA and Wille, M and Geoghegan, J and Imrie, RM and Holmes, EC and Harrison, XA and Longdon, B},
title = {Making sense of the virome in light of evolution and ecology.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2044},
pages = {20250389},
doi = {10.1098/rspb.2025.0389},
pmid = {40169018},
issn = {1471-2954},
support = {//Leverhulme Trust/ ; //National Health and Medical Research Council (NHMRC)/ ; //Royal Society/ ; /WT_/Wellcome Trust/United Kingdom ; //Webster Family Chair in Viral Pathogenesis/ ; //New Zealand Royal Society Rutherford Discovery Fellowship/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*Virome ; *Viruses/genetics ; Biological Evolution ; Metagenomics ; Ecology ; Ecosystem ; Phylogeny ; },
abstract = {Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.},
}

*Virome
*Viruses/genetics
Biological Evolution
Metagenomics
Ecology
Ecosystem
Phylogeny

@article {pmid40168325,
year = {2025},
author = {Yun, H and Seo, JH and Kim, YK and Yang, J},
title = {Examining the bacterial diversity including extracellular vesicles in air and soil: implications for human health.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0320916},
doi = {10.1371/journal.pone.0320916},
pmid = {40168325},
issn = {1932-6203},
mesh = {*Extracellular Vesicles/metabolism ; *Soil Microbiology ; Humans ; *Bacteria/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Air Microbiology ; Microbiota ; Biodiversity ; Metagenomics/methods ; },
abstract = {As the significance of human health continues to rise, the microbiome has shifted its focus from microbial composition to the functional roles it plays. In parallel, interest in ultrafine particles associated with clinically important impact has been increasing. Bacterial extracellular vesicles (BEVs), involved in systemic microbiome activity, are nano-sized spherical vesicles (20 - 100 nm in diameter) containing DNA, RNA, proteins, and lipids. They are known to be absorbed into the body potentially through air and soil, circulate in the blood, and directly impact diseases by affecting organs. Therefore, the aim of this study is to examine the biodiversity of bacteria and BEVs and predicted functional pathways. We sampled air and soil samples in Seoul, Korea and analyzed metagenomics based on 16S rRNA sequencing. At the phylum levels, Firmicutes in BEVs from soil and air were significantly higher than in bacteria, and Acidobacteria in both bacteria and BEVs from soil were significantly higher than from air (p < 0.05). The most dominant genera were Pseudomonas in bacteria from air and soil; and Escherichia-Shigella in BEVs from air and soil. In addition, Two-component system (ko02020) and ATP-binding cassette transporters (ko02010) were dominant functional pathways in both air and soil. The most functional pathways and orthologous groups were significantly different between air and soil (p < 0.05). In conclusion, human health can be affected differently depending on type of environment. Future study is necessary to have a better understanding of human health effects from environmental microbiota.},
}

*Extracellular Vesicles/metabolism
*Soil Microbiology
Humans
*Bacteria/genetics/classification/metabolism
*RNA, Ribosomal, 16S/genetics
Air Microbiology
Microbiota
Biodiversity
Metagenomics/methods

@article {pmid40167332,
year = {2025},
author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF},
title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14105},
doi = {10.1111/1755-0998.14105},
pmid = {40167332},
issn = {1755-0998},
support = {CEEC/0482/2020//Fundação para a Ciência e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Fundação para a Ciência e a Tecnologia/ ; LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Fundação para a Ciência e a Tecnologia/ ; UID/04292/2020//Fundação para a Ciência e a Tecnologia/ ; UID/BIA/00329/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; },
abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.},
}

@article {pmid40165946,
year = {2025},
author = {Guo, Z and Wang, X and Li, Y and Zhang, Y and Guo, P and Zhang, J and Zhang, Z and Ma, X},
title = {Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1563225},
pmid = {40165946},
issn = {1664-3224},
mesh = {Animals ; Mice ; *Pomegranate/chemistry ; *Zingiber officinale ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Enteritis/drug therapy/microbiology/veterinary ; *Aquaporins/metabolism/genetics ; Cytokines/metabolism ; Chronic Disease ; Disease Models, Animal ; Powders ; Plant Extracts/pharmacology/administration & dosage ; Aquaporin 3 ; Aquaporin 4 ; },
abstract = {To explore the efficacy and mechanism of Pomegranate peel Ginger ultrafine powder (PG) in treating chronic enteritis in mice. Sixty SPF-grade mice were randomly divided into a blank group, a model group, loperamide hydrochloride group (5 mg/kg), a high-dose PG group (100 mg/kg), a medium-dose group (50 mg/kg), and a low-dose group (25 mg/kg), with 10 mice in each group and an equal number of males and females. A chronic enteritis mouse model was established using a multifactorial method of low temperature + ice water + castor oil. The blank group was given an equal amount of physiological saline intragastrically, while the other groups were intervened with corresponding drugs for 7 consecutive days. After 7 days, samples were collected, and Enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of interleuckin 1β (IL-1β), IL-6, and Tumor necrosis factorα(TNF-α) in mouse serum. HE staining was used to examine the pathological changes in the small intestine. oxidative reagent kits were used to detect the content of total superoxide dismutase(T-SOD) and Malondialdehyde (MDA) in the small intestine. Western blot was used to detect the expression of Aquaporin 8(AQP8) proteins in the small intestine. Real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to detect the expression of AQP3, AQP4, AQP8, and Sodium/hydrogen exchanger 8 (NHE8) genes in the small intestine. metagenomics was used to detect the gut microbiota in mouse feces. Compared with the model group, all doses of PG groups reduced the levels of IL-1β, IL-6, and TNF-α in mouse serum (P<0.05), improved pathological changes in the small intestine, increased the content of T-SOD in the small intestine tissue, reduced the content of MDA, increased the expression of AQP4 and AQP8 mRNA, and decreased the expression of AQP3 and NHE8 mRNA (P<0.05), increased the expression of AQP8 protein. PG could improve the pathological changes of chronic enteritis in mice, enhance antioxidant capacity, and alleviate diarrhea caused by chronic enteritis by downregulating the expression of intestinal epithelial transport proteins and acute-phase proteins, and altering gut microbiota.},
}

Animals
Mice
*Pomegranate/chemistry
*Zingiber officinale
*Gastrointestinal Microbiome/drug effects
Male
Female
*Enteritis/drug therapy/microbiology/veterinary
*Aquaporins/metabolism/genetics
Cytokines/metabolism
Chronic Disease
Disease Models, Animal
Powders
Plant Extracts/pharmacology/administration & dosage
Aquaporin 3
Aquaporin 4

@article {pmid40165255,
year = {2025},
author = {Xie, B and Dong, C and Zhao, X and Qu, L and Lv, Y and Liu, H and Xu, J and Yu, Z and Shen, H and Shang, Y and Zhao, X and Zhang, J},
title = {Structural and functional alteration of the gut microbiomes in ICU staff: a cross-sectional analysis.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {141},
pmid = {40165255},
issn = {1466-609X},
support = {82402568//National Natural Science Foundation of China/ ; 82472223//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/physiology ; *Intensive Care Units/organization & administration/statistics & numerical data ; Male ; Female ; Prospective Studies ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Cohort Studies ; Feces/microbiology ; Health Personnel/statistics & numerical data ; },
abstract = {BACKGROUND: 16S rRNA sequencing has revealed structural alterations in the gut microbiomes of medical workers, particularly those working in intensive care unit (ICU). This study aims to further compare the taxonomic and functional characteristics of gut microbiomes between ICU staff and non-medical individuals using metagenomic sequencing.

METHODS: A prospective cross-sectional cohort study was conducted, fecal samples from 39 individuals in each group-ICU staff and non-medical subjects were analyzed using metagenomic sequencing. PERMANOVA (using the adonis function) was employed to analyze the genus-level profiles and assess the impact of individual parameters on the gut microbiome. Multiple databases were utilized to annotate and compare the functional differences in gut microbiomes between the two groups.

RESULTS: We observed that ICU staff exhibited a significant decrease in gut microbiome diversity, characterized by a marked decline in Actinobacteria and a substantial increase in Bacteroides and Bacteroidaceae. CAZy annotation revealed a notable increase in carbohydrate-active enzymes within the ICU staff cohort. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further indicated an elevated risk of endocrine and metabolic disorders, along with enhanced glycan biosynthesis and metabolism. Additionally, KEGG pathway enrichment analysis highlighted significant enrichment in cancer-related pathways. Analysis using the Virulence Factor Database (VFDB) showed a higher abundance of virulence factors associated with immune modulation, invasion, and antimicrobial activity/competitive advantage among ICU staff. Notably, no discernible difference in the presence of antibiotic resistance genes within the gut microbiomes was observed between the two groups. Importantly, all aforementioned differences demonstrated clear gender disparities.

CONCLUSIONS: Our findings indicated that ICU staff exhibited a reduction in gut microbiome diversity which was associated with an increase in virulence factors and carbohydrate-active enzymes, as well as with a heightened susceptibility to endocrine and metabolic diseases and cancers.},
}

Humans
Cross-Sectional Studies
*Gastrointestinal Microbiome/physiology
*Intensive Care Units/organization & administration/statistics & numerical data
Male
Female
Prospective Studies
Adult
Middle Aged
RNA, Ribosomal, 16S/analysis/genetics
Cohort Studies
Feces/microbiology
Health Personnel/statistics & numerical data

@article {pmid40164980,
year = {2025},
author = {Otani, S and Louise Jespersen, M and Brinch, C and Duus Møller, F and Pilgaard, B and Egholm Bruun Jensen, E and Leekitcharoenphon, P and Aaby Svendsen, C and Aarestrup, AH and Sonda, T and Sylvina, TJ and Leach, J and Piel, A and Stewart, F and Sapountzis, P and Kazyoba, PE and Kumburu, H and Aarestrup, FM},
title = {Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2484385},
doi = {10.1080/19490976.2025.2484385},
pmid = {40164980},
issn = {1949-0984},
mesh = {Animals ; *Diet ; *Hominidae/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Life Style ; Humans ; Adaptation, Physiological ; Pan troglodytes/microbiology ; Metagenome ; Phylogeny ; Africa ; },
abstract = {In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees. Even amongst shared bacterial communities, several core bacteria have co-diversified to fulfil unique dietary degradation functions within their host populations. These co-evolutionary trends extend to non-bacterial elements, such as mitochondrial DNA, antimicrobial resistance, and parasites. Our findings indicate that microbiome-host co-adaptations have led to both taxonomic and within taxa functional displacements to meet host physiological demands. The microbiome, in turn, transcends its taxonomic interchangeable role, reflecting the lifestyle, ecology and dietary history of its host.},
}

Animals
*Diet
*Hominidae/microbiology
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome
*Life Style
Humans
Adaptation, Physiological
Pan troglodytes/microbiology
Metagenome
Phylogeny
Africa

@article {pmid40164638,
year = {2025},
author = {Mills, S and Ijaz, UZ and Lens, PNL},
title = {Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {54},
pmid = {40164638},
issn = {2055-5008},
support = {15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; 15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; EP/P029329/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/V030515/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bioreactors/microbiology ; *Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification ; Microbiota ; High-Throughput Nucleotide Sequencing ; Microbial Consortia/genetics ; Methane/metabolism ; Metagenome ; Phylogeny ; },
abstract = {Different microbial communities are impacted disproportionately by environmental disturbances. The degree to which a community can remain unchanged under a disturbance is referred to as resistance[1]. However, the contributing ecological factors, which infer a community's resistance are unknown. In this study, the impact of historical environmental stability on ecological phenomena and microbial community resistance to shocks was investigated. Three separate methanogenic bioreactor consortia, which were subjected to varying degrees of historical environmental stability, and displayed different levels of resistance to an organic loading rate (OLR) shock were sampled. Their community composition was assessed using high throughput sequencing of 16S rRNA genes and assembly based metagenomics. The effect environmental instability on ecological phenomena such as microbial community assembly, microbial niche breadth and the rare biosphere were assessed in the context of each reactor's demonstrated resistance to an OLR shock. Additionally, metagenome assembled genomes were analysed for functional effects of prolonged stability/instability. The system which was subjected to more environmental instability experienced more temporal variation in community beta diversity and a proliferation of specialists, with more abundant two component regulatory systems. This community was more susceptible to deterministic community assembly and demonstrated a lower degree of resistance, indicating that microbial communities experiencing longer term environmental instability (e.g. variations in pH or temperature) are less able to resist a large disturbance.},
}

*RNA, Ribosomal, 16S/genetics
*Bioreactors/microbiology
*Metagenomics/methods
Bacteria/genetics/classification/isolation & purification
Microbiota
High-Throughput Nucleotide Sequencing
Microbial Consortia/genetics
Methane/metabolism
Metagenome
Phylogeny

@article {pmid39998261,
year = {2025},
author = {Woh, PY and Chen, Y and Kumpitsch, C and Mohammadzadeh, R and Schmidt, L and Moissl-Eichinger, C},
title = {Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment.},
journal = {Microbiology spectrum},
volume = {13},
number = {4},
pages = {e0218324},
doi = {10.1128/spectrum.02183-24},
pmid = {39998261},
issn = {2165-0497},
support = {F83, P32697, COE7//Austrian Science Fund (FWF)/ ; },
mesh = {Humans ; Middle Aged ; Female ; *Multiple Sclerosis/microbiology/drug therapy ; Adult ; *Gastrointestinal Microbiome/genetics ; Male ; Aged ; Methanobrevibacter/genetics/isolation & purification/metabolism ; Archaea/classification/genetics ; Metagenomics ; Methane/metabolism ; Metagenome ; },
abstract = {The role of the gut archaeal microbiome (archaeome) in health and disease remains poorly understood. Methanogenic archaea have been linked to multiple sclerosis (MS), but prior studies were limited by small cohorts and inconsistent methodologies. To address this, we re-evaluated the association between methanogenic archaea and MS using metagenomic data from the International Multiple Sclerosis Microbiome Study. We analyzed gut microbiome profiles from 115 MS patients and 115 healthy household controls across Buenos Aires (27.8%), Edinburgh (33.9%), New York (10.4%), and San Francisco (27.8%). Metagenomic sequences were taxonomically classified using kraken2/bracken and a curated profiling database to detect archaea, specifically Methanobrevibacter species. Most MS patients were female (80/115), aged 25-72 years (median: 44.5), and 70% were undergoing treatment, including dimethyl fumarate (n = 21), fingolimod (n = 20), glatiramer acetate (n = 14), interferon (n = 18), natalizumab (n = 6), or ocrelizumab/rituximab (n = 1). We found no significant differences in overall archaeome profiles between MS patients and controls. However, treated MS patients exhibited higher abundances of Methanobrevibacter smithii and M. sp900766745 compared to untreated patients. Notably, M. sp900766745 abundance correlated with lower disease severity scores in treated patients. Our results suggest that gut methanogens are not directly associated with MS onset or progression but may reflect microbiome health during treatment. These findings highlight potential roles for M. smithii and M. sp900766745 in modulating treatment outcomes, warranting further investigation into their relevance to gut microbiome function and MS management.IMPORTANCEMultiple sclerosis (MS) is a chronic neuroinflammatory disease affecting the central nervous system, with approximately 2.8 million people diagnosed worldwide, mainly young adults aged 20-30 years. While recent studies have focused on bacterial changes in the MS microbiome, the role of gut archaea has been less explored. Previous research suggested a potential link between methanogenic archaea and MS disease status, but these findings remained inconclusive. Our study addresses this gap by investigating the gut archaeal composition in MS patients and examining how it changes in response to treatment. By focusing on methanogens, we aim to uncover novel insights into their role in MS, potentially revealing new biomarkers or therapeutic targets. This research is crucial for enhancing our understanding of the gut microbiome's impact on MS and improving patient management.},
}

Humans
Middle Aged
Female
*Multiple Sclerosis/microbiology/drug therapy
Adult
*Gastrointestinal Microbiome/genetics
Male
Aged
Methanobrevibacter/genetics/isolation & purification/metabolism
Archaea/classification/genetics
Metagenomics
Methane/metabolism
Metagenome

@article {pmid39998243,
year = {2025},
author = {Brochu, HN and Zhang, Q and Song, K and Wang, L and Deare, EA and Williams, JD and Icenhour, CR and Iyer, LK},
title = {Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples.},
journal = {Microbiology spectrum},
volume = {13},
number = {4},
pages = {e0258224},
doi = {10.1128/spectrum.02582-24},
pmid = {39998243},
issn = {2165-0497},
mesh = {Humans ; *Vaginosis, Bacterial/microbiology/diagnosis ; Female ; *Vagina/microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Adult ; Polymerase Chain Reaction/methods ; Actinobacteria ; },
abstract = {Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions. Modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab test that targets Atopobium (Fannyhessea) vaginae, Megasphaera-1, and Bacterial Vaginosis Associated Bacterium (BVAB)-2. Remnant clinician-collected NuSwab vaginal swabs underwent DNA extraction and 16S V3-V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab test. Community state types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). 16S V3-V4 rRNA gene sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3-V4 ASVs, identifying 83 unique genera. NuSwab microbe quantification was strongly concordant with quantification by sequencing (P < 0.01). Samples in CST-I (18 of 18, 100%), CST-II (three of three, 100%), CST-III (15 of 17, 88%), and CST-V (one of one, 100%) were largely categorized as BV-negative via the NuSwab panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings highlight robust sequencing-based quantification of Labcorp NuSwab BV microbes, accurate discrimination of vaginal microbiome CSTs dominated by distinct Lactobacilli, and expanded the identification of BV-associated bacterial and metabolic biomarkers.IMPORTANCEBacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either panels of select microbes or on physical and microscopic evaluations by technicians. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can faithfully reproduce targeted PCR diagnostic results and can improve our knowledge of healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.},
}

Humans
*Vaginosis, Bacterial/microbiology/diagnosis
Female
*Vagina/microbiology
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
DNA, Bacterial/genetics
Adult
Polymerase Chain Reaction/methods
Actinobacteria

@article {pmid40164860,
year = {2025},
author = {Adawiah, A and Meryandini, A and Ridwan, R and Fidriyanto, R and Sarwono, KA and Wiryawan, KG},
title = {The rumen microbiome and metabolome profile of Ongole crossbreed cattle fed probiotics and protected amino acids.},
journal = {Tropical animal health and production},
volume = {57},
number = {3},
pages = {148},
pmid = {40164860},
issn = {1573-7438},
mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Amino Acids/metabolism ; *Animal Feed/analysis ; Male ; *Metabolome ; *Diet/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration & dosage/pharmacology ; Cross-Over Studies ; Dietary Supplements/analysis ; Bacteria/classification/metabolism/genetics ; },
abstract = {This study aimed to investigate the microbial population dynamics and metabolite profiles of Ongole crossbreed cattle (OCC) fed a combination of feed additives using metagenomic and metabolomic analyses. A crossover design was employed, involving four 3-year-old fistulated OCC bulls, each receiving four distinct dietary treatments per experimental period, followed by a washout phase with a basal diet. The treatments consisted of a basal diet (G1) as control, and the addition of feed additives as follows: G2: probiotics (Lactiplantibacillus plantarum); G3: premix; G4: G2 + G3 + amino acids lysine and methionine; and G5: G2 + G3 + amino acids protected with tannin. Rumen fluid was collected for the analysis of microbiome dynamics and metabolite profiles. The bacterial communities in diets G1, G2, G3, and G5 exhibited similar compositions, dominated by Bacteroidota, particularly the genus Prevotella. The G5 diet successfully suppressed the population of archaea, notably Methanosarcinales and Methanobacteriales, which are associated with methane production. A total of 28 significant metabolites (VIP > 1) was identified in rumen fluid, including lipid prenols, phenolic compounds, indoles and derivatives, saturated and unsaturated hydrocarbons, fatty acyls, benzene derivatives, and organooxygen compounds. The volatile compounds profile of rumen fluid showed a marked increase in prenol lipid compounds, especially in the G5 diet. Additionally, Methanosarcinales and Methanobacteriales were negatively correlated with prenol lipid levels. The inclusion of probiotics and protected amino acids alters the microbiome community structure and metabolites, positively affecting ruminant productivity.},
}

Animals
*Rumen/microbiology/metabolism
Cattle
*Amino Acids/metabolism
*Animal Feed/analysis
Male
*Metabolome
*Diet/veterinary
*Gastrointestinal Microbiome/drug effects
*Probiotics/administration & dosage/pharmacology
Cross-Over Studies
Dietary Supplements/analysis
Bacteria/classification/metabolism/genetics

@article {pmid40158160,
year = {2025},
author = {Zhu, M and Wang, Q and Yang, Y and Liu, X and Zhang, J and Li, G and Liu, W and Xiang, X and Chen, J},
title = {Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {50},
pmid = {40158160},
issn = {1475-2891},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Child ; Male ; Cross-Sectional Studies ; *Metabolome/physiology ; Female ; Child, Preschool ; *Feces/microbiology ; China ; *Diet/methods ; Metabolomics/methods ; Nutritional Status ; Multiomics ; },
abstract = {The gut microbiome can modulate nutrient metabolism to produce many metabolites interacting with the host. However, the intricate interactions among dietary intake, the gut microbiome and metabolites, and host metabolites need to be further explored although some studies have been devoted to it. Here, in a cross-sectional studies, 88 children aged 2-12 years were enrolled from northwestern China. The dietary intake data were collected via a designed food frequency questionnaire to calculate plant-based diet indices (PDIs). Stool and plasma samples were collected for metagenomic and broad-targeted metabolomic analysis. Spearman's rank correlation was used to describe the associations between nutrients/PDIs and the gut microbiota and metabolites. PDI was significantly positively associated with Bilophila wadsworthia, Bacteroides thetaiotaomicron, and Alistipes indistinctus, etc., but was obviously negatively correlated with Roseburia intestinalis, Faecalibacterium prausnitzii, etc. However, these species showed no significant associations with either healthy PDI (hPDI) or unhealthy PDI (uPDI). Interestingly, hPDI was significantly positively related to species, including Ruminococcus bicirculans, and was significantly negatively associated with uPDI, and vice versa. The above correlation trends were also observed between PDIs and predicted gut microbial functional pathways, microbial metabolites and the host metabolome. Notably, the significantly related pathways were focused mainly on substances and energy metabolism. PDI was significantly positively associated with the fecal contents of P-aminobenzoate, chenodeoxycholic acid, 4,6-dihydroxyquinoline, quinoline-4,8-diol, etc., but was significantly negatively associated with those of TMAO, FFA, creatine phosphate, etc. In plasma, PDI was significantly positively associated with sarcosine, ornithine, L-histidine, etc., but was distinctly negatively correlated with FFAs, carnitine C2:0, etc. Strikingly, the healthy plant-based diet index (hPDI) is correlated with increased levels of metabolites related to tryptophan metabolism, whereas the unhealthy PDI (uPDI) is linked to increased levels of metabolites associated with tyrosine and sphingolipid metabolism, which are pathways commonly associated with Western diets. Our studies provide reliable data support and a comprehensive understanding of the effects of dietary intake on the gut microbiome and microbial and host metabolites and lay a foundation for further studies of the diet-gut microbiota-microbial metabolites and host metabolism.},
}

*Gastrointestinal Microbiome/physiology
Humans
Child
Male
Cross-Sectional Studies
*Metabolome/physiology
Female
Child, Preschool
*Feces/microbiology
China
*Diet/methods
Metabolomics/methods
Nutritional Status
Multiomics

@article {pmid40158141,
year = {2025},
author = {Jiang, Y and Aton, M and Zhu, Q and Lu, YY},
title = {Modeling microbiome-trait associations with taxonomy-adaptive neural networks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {87},
pmid = {40158141},
issn = {2049-2618},
support = {RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; },
mesh = {Humans ; *Neural Networks, Computer ; *Microbiota ; Metagenomics/methods ; Bacteria/classification/genetics ; Computer Simulation ; },
abstract = {The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun metagenomic sequencing technologies have produced vast amounts of microbiome data, analyzing such data is highly challenging due to its sparsity, noisiness, and high feature dimensionality. Here, we develop MIOSTONE, an accurate and interpretable neural network model for microbiome-disease association that simulates a real taxonomy by encoding the relationships among microbial features. The taxonomy-encoding architecture provides a natural bridge from variations in microbial taxa abundance to variations in traits, encompassing increasingly coarse scales from species to domains. MIOSTONE has the ability to determine whether taxa within the corresponding taxonomic group provide a better explanation in a data-driven manner. MIOSTONE serves as an effective predictive model, as it not only accurately predicts microbiome-trait associations across extensive simulated and real datasets but also offers interpretability for scientific discovery. Both attributes are crucial for facilitating in silico investigations into the biological mechanisms underlying such associations among microbial taxa. Video Abstract.},
}

Humans
*Neural Networks, Computer
*Microbiota
Metagenomics/methods
Bacteria/classification/genetics
Computer Simulation

@article {pmid40157532,
year = {2025},
author = {Pienaar, RD and Herrero, S and Cerqueira de Araujo, A and Krupa, F and Abd-Alla, AMM and Herniou, EA},
title = {High-throughput screening reveals high diversity and widespread distribution of viruses in black soldier flies (Hermetia illucens).},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108322},
doi = {10.1016/j.jip.2025.108322},
pmid = {40157532},
issn = {1096-0805},
abstract = {Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (Hermetia illucens, BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. A high-throughput pipeline allowed the simultaneous investigation of 203 next generation sequencing datasets. This revealed the presence of seven viruses belonging to the families Dicistroviridae, Iflaviridae, Rhabdoviridae, Solinviviridae, Inseviridae, Lebotiviridae, and an unclassified Bunyavirales. Here we describe five viruses, which were detected in BSF from multiple origins, outlining the diversity of naturally occurring viruses associated with BSF colonies. As this viral community may also include BSF pathogens, we developed molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.},
}

@article {pmid40090450,
year = {2025},
author = {Wu, H and Chen, S and Deng, Y and Shen, J and Xu, Y and Wen, T and Yuan, J and Shen, Q and Xue, C},
title = {Dynamics of antibiotic resistance genes and the bacterial community after stress from a single Dazomet fumigation.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {372},
number = {},
pages = {126048},
doi = {10.1016/j.envpol.2025.126048},
pmid = {40090450},
issn = {1873-6424},
mesh = {*Fumigation ; *Soil Microbiology ; *Bacteria/genetics/drug effects ; Thiadiazines/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; RNA, Ribosomal, 16S/genetics ; Soil Pollutants/toxicity ; Microbiota/drug effects/genetics ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; },
abstract = {Although chemical fumigants are widely applied in agriculture to control soil-borne diseases, their influence on soil antibiotic resistance genes (ARGs) remains poorly understood. This study employed metagenomic sequencing to investigate the dynamic response and recovery processes of soil bacterial communities and ARGs after the end of fumigation with Dazomet. The results revealed that the effects of Dazomet were both phased and recoverable. Initially, no significant shifts in bacterial community diversity were observed; however, by day 10 of recovery (Dazomet10), diversity had decreased by 3.1 %. By contrast, ARG levels surged by 17.3 % and 10.9 % on days 10 and 20 (Dazomet20), respectively, before reverting to the baseline by day 50 (Dazomet50). These patterns were corroborated by qPCR data, which showed a 90.8 % reduction in 16S rRNA gene abundance, alongside a 4.17- to 4.38-fold increase in the relative abundance of ARGs at Dazomet10 and Dazomet20. Approximately 63 % of the variation in ARGs was attributed to bacterial community composition and mobile genetic elements (MGEs). Combined with community analysis and host-tracking analysis, it was found that Streptomyces and Nocardioides were identified as key ARGs hosts. Overall, the microbial communities and resistome required at least 50 days after the end of fumigation to recover to their pre-fumigation state. This study sheds light on the dynamic interactions between bacterial communities and ARGs during recovery from Dazomet fumigation and underscores the critical need for the rational use of fumigants in agricultural practices.},
}

*Fumigation
*Soil Microbiology
*Bacteria/genetics/drug effects
Thiadiazines/pharmacology
Drug Resistance, Microbial/genetics
Genes, Bacterial
RNA, Ribosomal, 16S/genetics
Soil Pollutants/toxicity
Microbiota/drug effects/genetics
Soil/chemistry
Anti-Bacterial Agents/pharmacology
Drug Resistance, Bacterial/genetics

@article {pmid40086705,
year = {2025},
author = {Ma, G and Chai, Y and Tye, KD and Xie, H and Meng, L and Tang, X and Luo, H and Xiao, X},
title = {Predictive analysis of the impact of probiotic administration during pregnancy on the functional pathways of the gut microbiome in healthy infants based on 16S rRNA gene sequencing.},
journal = {Gene},
volume = {952},
number = {},
pages = {149414},
doi = {10.1016/j.gene.2025.149414},
pmid = {40086705},
issn = {1879-0038},
mesh = {Humans ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Infant, Newborn ; Infant ; *Feces/microbiology ; Adult ; Bacteria/classification/genetics ; },
abstract = {Maternal probiotic supplementation altered the microbial composition in infants' gut, yet its effect on the functional pathways of the microbiota remains unclear. This study aimed to explore the potential impact of maternal probiotic intake on the predicted functional pathways of the gut microbiome in healthy infants. A total of 24 pregnant women were randomly allocated to either the control group or the probiotic group. The women in the probiotic group began receiving probiotics at the 32nd week of pregnancy and continued until delivery. Meconium and fecal samples were collected from infants at birth, as well as on the 3rd day, 14th day, and 6th month after birth. The functional characteristics of the microbial community were inferred using 16S rRNA gene analysis, processed with PICRUSt software, and cross-referenced with the KEGG database. The probiotic group had lower levels of Actinobacteria and Bacteroidetes, while Bifidobacterium growth was notably increased in the infant gut microbiota. At day 0 postpartum, the control group exhibited higher levels of Prevotellaceae compared to the probiotic group (P < 0.05). However, no significant differences were found by day 3. At day 14, the control group exhibited higher levels of Bacteroidaceae and Bacteroides, while Bacteroides_thetaiotaomicron was more abundant in the probiotic group (P < 0.05). By 6 months, the control group showed a higher abundance of Firmicutes (P < 0.05). On day 0 postpartum, maternal probiotic consumption increased the Environmental information processing pathway at KEGG Level 1, and increased Energy metabolism, Metabolism of cofactors and vitamins, and Cell growth and death pathways at KEGG Level 2. It also increased Histidine metabolism, One carbon pool by folate, and Folate biosynthesis at KEGG Level 3. No changes were observed in the infant gut microbiota's functional metabolic pathways at 3 days postpartum. At 14 days postpartum, probiotics reduced Lipid metabolism pathways at KEGG Level 2 and the Citrate cycle at KEGG Level 3. At 6 months postpartum, probiotics decreased Carbohydrate metabolism pathways at KEGG Level 2. Our findings suggest that probiotic supplementation during pregnancy affects the functional metabolism of the gut microbiota in healthy infants. This, in turn, may influence the development of the infant's immune system, metabolism, and overall health by modifying the gut microbial environment.},
}

Humans
*Probiotics/administration & dosage
*Gastrointestinal Microbiome/drug effects/genetics
Female
Pregnancy
*RNA, Ribosomal, 16S/genetics
Infant, Newborn
Infant
*Feces/microbiology
Adult
Bacteria/classification/genetics

@article {pmid40074067,
year = {2025},
author = {Pragasam, AK and Maurya, S and Jain, K and Pal, S and Raja, C and Yadav, R and Kumar, S and Purohit, A and Pradhan, D and Kajal, K and Talukdar, D and Singh, AN and Verma, J and Jana, P and Rawat, S and Kshetrapal, P and Krishna, A and Kumar, S and Bansal, VK and Das, B and Srikanth, CV and Garg, PK},
title = {Invasive Salmonella Typhimurium colonizes gallbladder and contributes to gallbladder carcinogenesis through activation of host epigenetic modulator KDM6B.},
journal = {Cancer letters},
volume = {618},
number = {},
pages = {217621},
doi = {10.1016/j.canlet.2025.217621},
pmid = {40074067},
issn = {1872-7980},
mesh = {Animals ; *Salmonella typhimurium/pathogenicity/genetics ; *Gallbladder Neoplasms/microbiology/pathology/genetics ; Humans ; Mice ; *Salmonella Infections/microbiology/pathology/genetics ; *Epigenesis, Genetic ; Gallbladder/microbiology/pathology ; Histone Demethylases/genetics/metabolism ; Gastrointestinal Microbiome ; Female ; Carcinogenesis/genetics ; Male ; Cell Line, Tumor ; },
abstract = {Gallbladder stones alone do not explain the risk of gallbladder cancer (GBC) as the sole etiological factor. Chronic microbial infection, particularly Salmonella, has been implicated in GB carcinogenesis, but its causative role and the underlying mechanisms are largely unknown. We studied gut and gallbladder tissue microbiome through targeted metagenomics to identify pathogenic bacteria in GBC. Virulence and pathogenicity of identified Salmonella Typhimurium from GBC tissue were studied after culture by whole genome sequencing, phylogenetic analysis, mutational profiling, and pangenome analysis. Mechanistic studies for GBC carcinogenesis were carried out in a mouse model of gallstones and chronic Salmonella infection, a cellular model using GBC (NOZ) cell lines, and a xenograft tumor model. We found an increased abundance of Salmonella in the gut microbiome of patients with GBC and culturable S. Typhimurium from the gallbladder cancer tissue. Comparative genomics of S. Typhimurium isolated from the GBC tissue showed a high invasive index. S. Typhimurium isolates harbored horizontally acquired virulence functions in their accessory genome. Chronic S. Typhimurium infection caused chronic inflammation, pre-malignant changes, and tumor-promoting mechanisms in the mouse model with gallbladder stones with activation of the epigenetic modulator KDM6B both in the mouse model and human GBC. Inhibition of KDM6B reduced engrafted tumor size in SCID mice. Of the differentially regulated genes in human GBC tissue, ADAMTSL5, CX3CR1, and SPSB4 were also significantly dysregulated in NOZ cells infected with Salmonella. Chronic Salmonella infection contributes to gallbladder carcinogenesis through a host epigenetic mechanism involving KDM6B.},
}

Animals
*Salmonella typhimurium/pathogenicity/genetics
*Gallbladder Neoplasms/microbiology/pathology/genetics
Humans
Mice
*Salmonella Infections/microbiology/pathology/genetics
*Epigenesis, Genetic
Gallbladder/microbiology/pathology
Histone Demethylases/genetics/metabolism
Gastrointestinal Microbiome
Female
Carcinogenesis/genetics
Male
Cell Line, Tumor

@article {pmid40064231,
year = {2025},
author = {Jia, Y and Huang, D and Lan, X and Sun, X and Lin, W and Sun, W and Wang, Y},
title = {Community structure and metabolic potentials of keystone taxa and their associated bacteriophages within rice root endophytic microbiome in response to metal(loid)s contamination.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {372},
number = {},
pages = {126028},
doi = {10.1016/j.envpol.2025.126028},
pmid = {40064231},
issn = {1873-6424},
mesh = {*Oryza/microbiology ; *Plant Roots/microbiology ; *Endophytes/physiology ; *Metals, Heavy ; *Microbiota ; *Soil Pollutants/metabolism ; *Bacteriophages/physiology ; Bacteria/genetics/classification/metabolism/isolation & purification ; Soil Microbiology ; },
abstract = {Heavy metal (HM) contamination of agricultural products is of global environmental concern as it directly threatened the food safety. Plant-associated microbiome, particularly endophytic microbiome, hold the potential for mitigating HM stress as well as promoting plant growth. The metabolic potentials of the endophytes, especially those under the HM stresses, have not been well addressed. Rice, a major staple food worldwide, is more vulnerable to HM contamination compared to other crops and therefore requires special attentions. Therefore, this study selected rice as the target plants. Geochemical analysis and amplicon sequencing were combined to characterize the rice root endophytic bacterial communities and identify keystone taxa in two HM-contaminated rice fields. Metagenomic analysis was employed to investigate the metabolic potentials of these keystone taxa. Burkholderiales and Rhizobiales were identified as predominant keystone taxa. The metagenome-assembled genome (MAG)s associated with these keystone populations suggested that they possessed diverse genetic potentials related to metal resistance and transformation (e.g., As resistance and cycling, V reduction, Cr efflux and reduction), and plant growth promotion (nitrogen fixation, phosphate solubilization, oxidative stress resistance, indole-3-acetic acid, and siderophore production). Moreover, bacteriophages encoding auxiliary metabolism genes (AMGs) associated with the HM resistance as well as nitrogen and phosphate acquisition were identified, suggesting that these phages may contribute to these crucial biogeochemical processes within rice roots. The current findings revealed the beneficial roles of rice endophytic keystone taxa and their associated bacteriophages within HM-contaminated rice root endophytic microbiome, which may provide valuable insights on future applications of employing root microbiome for safety management of agriculture productions.},
}

*Oryza/microbiology
*Plant Roots/microbiology
*Endophytes/physiology
*Metals, Heavy
*Microbiota
*Soil Pollutants/metabolism
*Bacteriophages/physiology
Bacteria/genetics/classification/metabolism/isolation & purification
Soil Microbiology

@article {pmid40054424,
year = {2025},
author = {Ding, C and Sun, J},
title = {The potential contribution of microbial communities to carbon fixation and nitrogen cycle in the Eastern Indian Ocean.},
journal = {Marine environmental research},
volume = {207},
number = {},
pages = {107056},
doi = {10.1016/j.marenvres.2025.107056},
pmid = {40054424},
issn = {1879-0291},
mesh = {Indian Ocean ; *Carbon Cycle ; *Nitrogen Cycle ; *Microbiota ; *Seawater/microbiology/chemistry ; *Nitrogen Fixation ; RNA, Ribosomal, 16S/genetics ; Nitrogen/metabolism/analysis ; Bacteria/metabolism/genetics/classification ; },
abstract = {This study investigated the diversity and metabolic potential of microbial communities in the Eastern Indian Ocean (EIO) through 16S rDNA gene sequencing and metagenomics analyses. Water samples were collected from the surface waters (5 m depth) and 150 m depth layer in the EIO between March 20th and June 6th, 2019. This study reveals microbial-driven biogeochemical dynamics in the oligotrophic Eastern Indian Ocean, where vertically stratified communities (Cyanobacteria/Proteobacteria-dominated surface vs. diversified Proteobacteria at 150 m) and latitudinal diversity gradients reflect nutrient limitations. Metagenomics identified four carbon fixation strategies: the Calvin cycle dominated epipelagic CO2 assimilation, while the 3-hydroxypropionate bicycle showed elevated surface activity, alongside reductive citrate and Wood-Ljungdahl pathways involving novel Actinobacteria. Nitrogen cycling exhibited spatial heterogeneity: nifH-dominated nitrogen fixation in the surface waters, prevalent narGHI nitrate reduction, and divergent nirS/nirK/nosZ distributions tied to nutrient gradients. Proteobacteria and Actinobacteria were key nitrogen fixers, with novel Actinobacteriota diazotrophs expanding known diversity. Elevated nosZ abundance in the Bay of Bengal underscored regional nitrous oxide consumption hotspots. These findings underscore microbial mediation of carbon-nitrogen fluxes in oligotrophic systems, providing genomic insights into ecosystem responses to climate-driven ocean changes.},
}

Indian Ocean
*Carbon Cycle
*Nitrogen Cycle
*Microbiota
*Seawater/microbiology/chemistry
*Nitrogen Fixation
RNA, Ribosomal, 16S/genetics
Nitrogen/metabolism/analysis
Bacteria/metabolism/genetics/classification

@article {pmid38847202,
year = {2025},
author = {Sharma, P and Singh, S and Singh, AV and Das, K and Bhaskar, Y and Goel, I and Singh, H and Das, R},
title = {Alteration of gastric microbiota in Helicobacter pylori - infected individuals suffering from gastroesophageal reflux disease, duodenal ulcer, and gastritis.},
journal = {Indian journal of pathology & microbiology},
volume = {68},
number = {1},
pages = {61-68},
pmid = {38847202},
issn = {0974-5130},
mesh = {Humans ; *Helicobacter Infections/microbiology ; *Duodenal Ulcer/microbiology ; *Gastritis/microbiology ; *Gastroesophageal Reflux/microbiology ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Adult ; Middle Aged ; *Helicobacter pylori/genetics/pathogenicity/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; Aged ; },
abstract = {BACKGROUND/AIM: Helicobacter pylori (H. pylori) colonization affects the gastric microbiome, causing gastrointestinal (GI) diseases. Modern sequencing technology provides insights into GI microbe interaction with H. pylori and their metabolic pathways in causing GI diseases. We aim to compare the gastric microbiota alteration due to H. pylori infection in patients suffering from GI diseases.

MATERIALS AND METHODS: Genomic DNA were isolated from gastric antrum tissue from 37 H . pylori -infected patients diagnosed with GERD, duodenal ulcers, and gastritis. We conducted the genomic library preparation and sequencing of the amplified product using 16S rRNA NGS analysis. Using microbiome analyst tool diversity analysis, random forest analysis and ANOVA were conducted to find out the comparison of microbial abundance. We have also conducted functional pathway prediction analysis using PICRUSt.

RESULTS: Metagenomic analysis shows high bacterial diversity in H. pylori -positive gastritis patients. Streptococcus infantis and Neisseria subflava were significantly higher in duodenal ulcer (DU) and gastritis groups. Acinetobacter lwoffii and Helicobacter pullorum were significantly high in the gastritis group only. The functional metabolic pathway analyses revealed that gastroesophageal reflux disease (GERD) samples were significantly enriched with the energy metabolism and xenobiotic biodegradation and metabolism pathways, whereas fructose-1,6-bisphosphatase III was found less in gastritis and DU groups.

CONCLUSION: There is a difference in microbiota composition in different disease outcomes. We found positive association between microbial diversity and H. pylori in gastritis group only, whereas negative association was found in DU and GERD groups. The functional metabolic pathway analysis revealed significant differences in various disease outcomes.},
}

Humans
*Helicobacter Infections/microbiology
*Duodenal Ulcer/microbiology
*Gastritis/microbiology
*Gastroesophageal Reflux/microbiology
Male
Female
*Gastrointestinal Microbiome/genetics
Adult
Middle Aged
*Helicobacter pylori/genetics/pathogenicity/isolation & purification
*RNA, Ribosomal, 16S/genetics
Metagenomics/methods
Bacteria/classification/genetics/isolation & purification
Young Adult
Aged

@article {pmid40156577,
year = {2025},
author = {Kop, LFM and Koch, H and Martins, PD and Suarez, C and Karačić, S and Persson, F and Wilén, BM and Hagelia, P and Jetten, MSM and Lücker, S},
title = {High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf032},
pmid = {40156577},
issn = {1574-6941},
abstract = {Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7±15% but a wide range between 1.2-61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome (MAG) analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.},
}

@article {pmid40050500,
year = {2025},
author = {Dave, M and Tattar, R},
title = {Antimicrobial resistance genes in the oral microbiome.},
journal = {Evidence-based dentistry},
volume = {26},
number = {1},
pages = {42-43},
pmid = {40050500},
issn = {1476-5446},
mesh = {*Mouth/microbiology ; Humans ; *Microbiota/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Polymerase Chain Reaction ; Biofilms/drug effects ; },
abstract = {A COMMENTARY ON: Sukumar S, Rahmanyar Z, El Jurf H Q et al. Mapping the oral resistome: a systematic review. J Med Microbiol 2024; https://doi.org/10.1099/jmm.0.001866 .

DESIGN: This systematic review, without meta-analysis, aimed to map the oral resistome by analysing clinical studies that detected bacterial antimicrobial resistance genes (ARGs) in the oral cavity using molecular techniques.

DATA SOURCES: The researchers used Medline, Embase, Web of Science, CINAHL and Scopus databases from January 2015 to August 2023.

STUDY SELECTION: This systematic review included cross-sectional or longitudinal clinical studies that detected ARGs using molecular techniques; specifically polymerase chain reaction (PCR) or next-generation sequencing (NGS) metagenomics for samples from the oral cavity (saliva, gingival biofilm, pulp, or oral mucosa). Studies were excluded if they were in vitro or animal studies, literature reviews and not focused on ARG detection.

DATA EXTRACTION AND SYNTHESIS: Five reviewers independently screened titles and abstracts based on inclusion criteria. Full-text reports were then independently assessed for eligibility by three reviewers. Extracted data encompassed publication details, sample size, country, molecular methods used, number of ARGs detected, participants' health status, antibiotic exposure, and sample location within the oral cavity.

RESULTS: Out of 580 initially identified studies, 15 met the inclusion criteria. These studies, published between 2015 and 2023 from 12 different countries, employed either PCR (n = 10) or NGS metagenomics (n = 5) to detect ARGs from a pool of 1486 participants (1 study did not report on the number of participants). PCR-based studies identified an average of 7 ARGs (range 1-20), while NGS studies identified an average of 34 ARGs (range 7-70). In total, 159 unique ARGs conferring resistance to 22 antibiotic classes were identified across six regions of the oral cavity. The supragingival biofilm and saliva exhibited the highest richness of ARGs, defined by the number of unique ARGs detected. Genes conferring resistance to 19 antibiotic classes were present in the supragingival biofilm. Notably, 49 ARGs, including tetracycline and macrolide resistance genes, were found across all sampled locations, indicating a widespread distribution within the oral cavity. Thirteen studies reported on bacterial species associated with ARGs. NGS studies identified a mean of 65 ARG-carrying bacterial species, compared to a mean of 4 species in PCR studies. Specifically, 25 ARG-carrying species were identified in PCR studies, while NGS studies identified 177 species. Four studies reported ARGs associated with streptococcal species implicated in distant-site infections such as infective endocarditis. ESKAPE pathogens (group of highly virulent multidrug-resistant bacteria) were detected with ARGs in various oral sites using both PCR and NGS methods. Comparisons between healthy and diseased states revealed that a healthy oral microbiome harbours a more diverse resistome at the antibiotic class level. The supragingival resistome demonstrated the richest composition in both health and disease, with tetracycline ARGs predominating in the supragingival and saliva resistomes in cases of dental caries.

CONCLUSIONS: The analysis of the oral resistome from these 15 studies identified three ARGs present in all sites of the oral cavity, suggesting the presence of a core resistome. NGS studies provided greater insights compared to PCR studies; however, the overall research base is limited. Further comprehensive studies are necessary to fully map the oral resistome.},
}

*Mouth/microbiology
Humans
*Microbiota/drug effects/genetics
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Genes, Bacterial
Polymerase Chain Reaction
Biofilms/drug effects

@article {pmid40150979,
year = {2025},
author = {Yildirim, EA and Laptev, GY and Ilina, LA and Ponomareva, ES and Brazhnik, EA and Smetannikova, TS and Novikova, NI and Turina, DG and Filippova, VA and Dubrovin, AV and Dubrovina, AS and Kalitkina, KA and Klyuchnikova, IA and Zaikin, VA and Griffin, DK and Romanov, MN},
title = {Metagenomic Composition and Predicted Metabolic Pathway Analyses of the Endometrial and Rectal Microbiota in Dairy Cows Following the Introduction of a Complex Feed Additive.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {17},
number = {1},
pages = {25725},
doi = {10.31083/FBE25725},
pmid = {40150979},
issn = {1945-0508},
support = {24-16-00131//Russian Science Foundation/ ; },
mesh = {Animals ; Cattle/microbiology ; Female ; *Animal Feed ; *Rectum/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; Metabolic Networks and Pathways ; Metagenomics ; Dairying ; },
abstract = {BACKGROUND: The microbiome composition in dairy cows (Bos taurus) directly impacts on health and reproductive performance. This study aimed to determine the metagenomic composition and predicted microbial community functions in the endometrium and rectal chyme of cows fed a complex feed additive (CFA). The latter included the Bacillus mucilaginosus 159 strain, a short-chain fatty acid, plus essential oils.

METHODS: Clinically healthy cows were divided into two groups (n = 15 in each): (I) a control group fed the standard diet, and (II) an experimental group. CFA was introduced into the diet of Group II during the entire transit period at a dose of 50 g per animal per day; moreover, all animals received Pen-Strep 400 antibiotics to prevent endometritis and other pathologies. The microbial community composition from the endometrium and rectal chyme biotopes was assessed using targeted next-generation sequencing.

RESULTS: Significant changes were observed in the composition and predicted metabolic pathways due to the CFA administration, with the endometrial microbiota being more responsive to CFA than the intestinal chyme microbiome. Remarkably, the Actinobacteriota representatives disappeared in the endometrium of Group II animals compared to controls, whose content ranged from 0.34 to 3.3%. The use of CFA also resulted in a less pronounced effect in four predicted metabolic pathways for microbial degradation of catechol in the endometrium compared to controls (p < 0.05).

CONCLUSIONS: Our findings support the concept of a relationship between the gut microbiome and the reproductive system microflora of cows, as we observed changes in the composition and predicted metabolic pathways of the endometrial microbiota after orally administering CFA. This emphasizes the need for an integrated approach combining the correction of microecological disorders in the intestines and the reproductive system simultaneously.},
}

Animals
Cattle/microbiology
Female
*Animal Feed
*Rectum/microbiology
*Endometrium/microbiology/metabolism
*Microbiota
Metabolic Networks and Pathways
Metagenomics
Dairying

@article {pmid40149936,
year = {2025},
author = {Zhan, J and Cheng, J and Chang, W and Su, Y and Yue, X and Wu, C},
title = {Absolute Quantitative Metagenomic Analysis Provides More Accurate Insights for the Anti-Colitis Effect of Berberine via Modulation of Gut Microbiota.},
journal = {Biomolecules},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/biom15030400},
pmid = {40149936},
issn = {2218-273X},
mesh = {*Berberine/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Metagenomics/methods ; Colitis, Ulcerative/microbiology/drug therapy ; Mice ; Bacteria/drug effects/genetics/classification ; Male ; Butyric Acid/pharmacology ; Disease Models, Animal ; },
abstract = {Current gut microbiota studies often rely on relative quantitative sequencing. However, under certain circumstances, while the relative quantitative abundance of these bacteria may remain stable, the absolute quantities of specific bacteria can vary considerably. Since the function of bacteria is directly linked to their total numbers, absolute quantification is crucial. This study aims to identify the optimal method for microbiome analysis by comparing relative and absolute quantitative sequencing. Using ulcerative colitis, which is closely associated with gut microbiota, as a disease model and berberine (which affects microbiota) versus sodium butyrate (which does not) as drugs, relative and absolute quantitative methods were used to evaluate the varying effects of the different drugs on the regulation of gut microbiota in UC-affected animals. The regulatory effects of BBR on gut microbiota were further synthesized as identified in earlier studies using an individual-based meta-analysis, and we compared these findings with our absolute sequencing results. The results from absolute sequencing were more consistent with the actual microbial community, suggesting that relative abundance measurements might not accurately reflect the true abundance of microbial species. Moreover, meta-analysis results were only partially consistent with absolute quantitative sequencing and sometimes directly opposed, suggesting that relative quantitative sequencing analyses are prone to misinterpretation and incorrect correlation of results. This study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.},
}

*Berberine/pharmacology
*Gastrointestinal Microbiome/drug effects/genetics
Animals
*Metagenomics/methods
Colitis, Ulcerative/microbiology/drug therapy
Mice
Bacteria/drug effects/genetics/classification
Male
Butyric Acid/pharmacology
Disease Models, Animal

@article {pmid40149437,
year = {2025},
author = {Alharbi, SM and Al-Sulami, N and Al-Amrah, H and Anwar, Y and Gadah, OA and Bahamdain, LA and Al-Matary, M and Alamri, AM and Bahieldin, A},
title = {Metagenomic Characterization of the Maerua crassifolia Soil Rhizosphere: Uncovering Microbial Networks for Nutrient Acquisition and Plant Resilience in Arid Ecosystems.},
journal = {Genes},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/genes16030285},
pmid = {40149437},
issn = {2073-4425},
mesh = {*Rhizosphere ; *Soil Microbiology ; Mycorrhizae/genetics/classification ; Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics/methods ; Metagenome ; Ecosystem ; Microbiota/genetics ; Plant Roots/microbiology ; Fungi/genetics/classification ; },
abstract = {Background/Objectives:Maerua crassifolia, a threatened medicinal species endemic to drylands, exhibits a pronounced drought sensitivity. Despite the critical role of microorganisms, particularly bacteria and fungi, the microbial consortia in M. crassifolia's rhizosphere remain underexplored. Methods: Metagenomic whole genome shotgun sequencing (WGS) was employed to elucidate the taxonomic composition of bacterial and fungal communities inhabiting the soil rhizosphere of M. crassifolia. Results: The data revealed a marked predominance of bacterial genomes relative to fungal communities, as evidenced by non-redundant gene analysis. Notably, arbuscular mycorrhizal fungi (AMF), specifically Rhizophagus clarus, Rhizophagus irregularis and Funneliformis geosporum, are key rhizosphere colonizers. This study confirmed the presence of phosphate-solubilizing bacteria (PSB), such as Sphingomonas spp., Cyanobacteria and Pseudomonadota, underscoring the critical role of these microorganisms in the phosphorus cycle. Additionally, the study uncovered the presence of previously uncharacterized species within the phylum Actinobacteria, as well as unidentified taxa from the Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla, which may represent novel microbial taxa with potential plant growth-promoting properties. Conclusions: Findings suggest a complex, symbiotic network where AMF facilitate phosphorus uptake through plant-root interactions. In a tripartite symbiosis, PSB enhance inorganic phosphorus solubilization, increasing bioavailability, which AMF assimilate and deliver to plant roots, optimizing nutrition. This bacterial-fungal interplay is essential for plant resilience in arid environments. Future investigations should prioritize the isolation and characterization of underexplored microbial taxa residing in the rhizosphere of M. crassifolia, with particular emphasis on members of the Actinobacteria, Betaproteobacteria, Gemmatimonadota and Chloroflexota phyla to uncover their roles in nutrient acquisition and sustainability.},
}

*Rhizosphere
*Soil Microbiology
Mycorrhizae/genetics/classification
Bacteria/genetics/classification/metabolism/isolation & purification
Metagenomics/methods
Metagenome
Ecosystem
Microbiota/genetics
Plant Roots/microbiology
Fungi/genetics/classification

@article {pmid40122128,
year = {2025},
author = {Zhang, D and Wang, Q and Li, D and Chen, S and Chen, J and Zhu, X and Bai, F},
title = {Gut microbiome composition and metabolic activity in metabolic-associated fatty liver disease.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2482158},
doi = {10.1080/21505594.2025.2482158},
pmid = {40122128},
issn = {2150-5608},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Female ; Adult ; China ; Bacteria/classification/genetics/metabolism/isolation & purification ; Eubacterium/metabolism/genetics ; Fatty Liver/microbiology/metabolism ; Metagenomics ; Metabolomics ; Case-Control Studies ; Metabolome ; Metagenome ; },
abstract = {Metabolic Associated Fatty Liver Disease (MAFLD) impacts approximately 25% of the global population. Between April 2023 and July 2023, 60 patients with MAFLD, along with 60 age, ethnicity, and sex-matched healthy controls (HCs), were enrolled from the Inner Mongolia Autonomous Region, China. Analysis of gut microbiota composition and plasma metabolic profiles was conducted using metagenome sequencing and LC-MS. LEfSe analysis identified five pivotal species: Eubacterium rectale, Dialister invisus, Pseudoruminococcus massiliensis, GGB3278 SGB4328, and Ruminococcaceae bacteria. In subgroup analysis, Eubacterium rectale tended to increase by more than 2 times and more than double in the non-obese MAFLD group, and MAFLD with moderate hepatic steatosis (HS), respectively. Plasma samples identified 172 metabolites mainly composed of fatty acid metabolites such as propionic acid and butyric acid analogues. Ruminococcaceae bacteria have a strong positive correlation with β-alanine, uric acid, and L-valine. Pseudoruminococcus massiliensis has a strong positive correlation with β-alanine. Combinations of phenomics and metabolomics yielded the highest accuracy (AUC = 0.97) in the MAFLD diagnosis. Combinations of phenomics and metagenomics yielded the highest accuracy (AUC = 0.94) in the prediction of the MAFLD HS progress. Increases in Eubacterium rectale and decreases in Dialister invisus seem to be indicative of MAFLD patients. Eubacterium rectale may predict HS degree of MAFLD and play an important role in the development of non-obese MAFLD. Eubacterium rectale can generate more propionic acid and butyric acid analogues to absorb energy and increase lipid synthesis and ultimately cause MAFLD.},
}

Humans
*Gastrointestinal Microbiome
Male
Middle Aged
Female
Adult
China
Bacteria/classification/genetics/metabolism/isolation & purification
Eubacterium/metabolism/genetics
Fatty Liver/microbiology/metabolism
Metagenomics
Metabolomics
Case-Control Studies
Metabolome
Metagenome

@article {pmid40146796,
year = {2025},
author = {Li, J and Zhu, Y and Chang, Q and Gong, Y and Wan, J and Xu, S},
title = {Comparative Analysis of Microbiological Profiles and Antibiotic Resistance Genes in Subjects with Colorectal Cancer and Healthy Individuals.},
journal = {Polish journal of microbiology},
volume = {74},
number = {1},
pages = {71-81},
doi = {10.33073/pjm-2025-006},
pmid = {40146796},
issn = {2544-4646},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Male ; Middle Aged ; Female ; *Bacteria/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Aged ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Adult ; },
abstract = {Alteration of the gut microbiota (GM) is associated with various diseases, including colorectal cancer (CRC). With the development of next-generation sequencing techniques, metagenomic sequencing, along with metabolic function and antibiotic-resistant gene analyses, has been used to investigate differences in GM between CRC patients and healthy controls. Fecal samples were obtained from seven CRC patients and six healthy subjects, and the sequencing data were analyzed for similarity, a-diversity, principal component analysis (PCA), and linear discriminant analyses (LDA). Regarding Actinobacteria, 3 orders, 5 families, 9 genera, and 19 species were identified with no differences between the CRC and control groups, while the levels of Bifidobacterium bifidum and Bifidobacterium dentium were higher, and the level of Bifidobacterium breve was lower in the CRC group compared to the healthy controls (p = 0.053). Otherwise, 2 genera (Leuco-nostoc and Salmonella) and 7 species of bacteria (Parabacteroides merdae, Alistipes shahii, Alistipes finegoldii, Clostridium nexile, Salmonella enterica, unclassified Salmonella, Enterobacter cloacae) were found to be significantly differently distributed between CRC patients and healthy controls. PCA-LDA successfully classified these 2 groups with satisfactory accuracy (84.52% for metabolic function and 77.38% for resistant genes). These findings underscore the potential of GM as a diagnostic tool for CRC, offering a promising avenue for non-invasive screening and risk assessment. The identification of specific microbial signatures, particularly those linked to metabolic functions and resistance traits, could open new doors for understanding the role of the microbiome in CRC progression and treatment resistance.},
}

Humans
*Colorectal Neoplasms/microbiology
Male
Middle Aged
Female
*Bacteria/genetics/classification/isolation & purification
*Gastrointestinal Microbiome
Feces/microbiology
Aged
Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Adult

@article {pmid40144403,
year = {2025},
author = {Li, Z and Zou, D and Liu, R and Pan, J and Huang, J and Ma, J and Huang, L and He, J and Fu, L and Zheng, X and Wang, M and Fang, J and Dong, H and Li, M and Huang, L and Dai, X},
title = {A hunting ground for predatory bacteria at the Zhenbei seamount in the South China Sea.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf042},
pmid = {40144403},
issn = {2730-6151},
abstract = {Seamounts are critical marine biodiversity hot spots, while the metabolic activity of their microbial community remains largely unknown. In this study, we investigated the diversity and activity of free-living and particle-attached microorganisms in the surface, middle, and bottom layers of seawater at the Zhenbei seamount in the South China Sea using omics approaches, including 16S ribosomal RNA (rRNA)/16S rDNA ratio analysis. Over 20 phyla were detected, with Proteobacteria, Actinobacteriota, Cyanobacteria, Bacteroidota, Thaumarchaeota, and Planctomycetota being predominant. Surprisingly, Bdellovibrionota and Myxococcota, the two well-known predatory bacteria, exhibited exceptionally higher rRNA/rDNA ratios than the other phyla, with rRNA abundances being 10- or even 200-fold higher than their rDNA abundances. These metabolically active predatory bacteria are mainly uncultured species. A total of 23 Myxococcota metagenome-assembled genomes (MAGs) and 12 Bdellovibrionota MAGs were assembled. The most highly overexpressed genes frequently detected in these MAGs were those that encode flagellum and pilus proteins as well as T4-like virus tail tube protein, indicating that these predator bacteria were likely active in hunting. Our results suggest that seamounts may serve as hunting grounds for predatory bacteria, which may be involved in controlling the flows of elements and energy in the seamount microbial communities and, thus, in shaping the seamount ecosystems.},
}

@article {pmid40142589,
year = {2025},
author = {Chen, X and Gao, L and Kou, Y and Wang, X and Li, X and He, H and Wang, M},
title = {Composition, Distribution and Mobility Potential of the Antibiotic Resistome in Sediments from the East China Sea Revealed by Metagenomic Analysis.},
journal = {Microorganisms},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/microorganisms13030697},
pmid = {40142589},
issn = {2076-2607},
support = {41806131//National Natural Science Foundation of China/ ; 42120104006//National Natural Science Foundation of China/ ; ZR2024QD036//Natural Science Foundation of Shandong Province/ ; },
abstract = {Marine sediments are recognized as crucial reservoirs of antibiotic resistance genes (ARGs). However, the antibiotic resistome in sediments of the East China Sea, an area heavily impacted by human activities, has not been thoroughly studied. Here, we conducted a systematic investigation into the antibiotic resistome in these sediments using metagenomic analysis. Overall, we detected eighty ARG subtypes and nineteen ARG types. Beta-lactams were the dominant ARG type, and Gammaproteobacteria was the main ARG host in this study. Mobile genetic elements (MGEs) were not major drivers of ARG profiles. Although the ARG host communities significantly differed between the spring and autumn (p < 0.05), the antibiotic resistome remained stable across the two seasons. The assembly of ARGs and their hosts was governed by stochastic processes, and a high ratio of stochastic processes implied its crucial role in the assembly and stabilization of the antibiotic resistome. Co-occurrence network analysis revealed an important role of Deltaproteobacteria in the stabilization of ARG profiles across seasons. Environmental parameters (e.g., temperature and density) played certain roles in the stabilization of the antibiotic resistome between spring and autumn. Moreover, nine human pathogen bacteria (HPB) were detected in this study. We also found that the health risks caused by ARGs were relatively higher in the spring. Our results will provide a strong foundation for the development of targeted management strategies to mitigate the further dissemination and spread of ARGs in marine sediments.},
}

@article {pmid40141768,
year = {2025},
author = {Ghobashy, MOI and Al-Otaibi, AS and Alharbi, BM and Alshehri, D and Ghabban, H and Albalawi, DA and Alenzi, AM and Alatawy, M and Alatawi, FA and Algammal, AM and Mir, R and Mahrous, YM},
title = {Metagenomic Characterization of Microbiome Taxa Associated with Coral Reef Communities in North Area of Tabuk Region, Saudia Arabia.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/life15030423},
pmid = {40141768},
issn = {2075-1729},
support = {Research no.0144-1444-S//Deanship of Research and Graduate Studies at University of Tabuk/ ; },
abstract = {The coral microbiome is highly related to the overall health and the survival and proliferation of coral reefs. The Red Sea's unique physiochemical characteristics, such a significant north-south temperature and salinity gradient, make it a very intriguing research system. However, the Red Sea is rather isolated, with a very diversified ecosystem rich in coral communities, and the makeup of the coral-associated microbiome remains little understood. Therefore, comprehending the makeup and dispersion of the endogenous microbiome associated with coral is crucial for understanding how the coral microbiome coexists and interacts, as well as its contribution to temperature tolerance and resistance against possible pathogens. Here, we investigate metagenomic sequencing targeting 16S rRNA using DNAs from the sediment samples to identify the coral microbiome and to understand the dynamics of microbial taxa and genes in the surface mucous layer (SML) microbiome of the coral communities in three distinct areas close to and far from coral communities in the Red Sea. These findings highlight the genomic array of the microbiome in three areas around and beneath the coral communities and revealed distinct bacterial communities in each group, where Pseudoalteromonas agarivorans (30%), Vibrio owensii (11%), and Pseudoalteromonas sp. Xi13 (10%) were the most predominant species in samples closer to coral (a coral-associated microbiome), with the domination of Pseudoalteromonas_agarivorans and Vibrio_owensii in Alshreah samples distant from coral, while Pseudoalteromonas_sp._Xi13 was more abundant in closer samples. Moreover, Proteobacteria such as Pseudoalteromonas, Pseudomonas and Cyanobacteria were the most prevalent phyla of the coral microbiome. Further, Saweehal showed the highest diversity far from corals (52.8%) and in Alshreah (7.35%) compared to Marwan (1.75%). The microbial community was less diversified in the samples from Alshreah Far (5.99%) and Marwan Far (1.75%), which had comparatively lower values for all indices. Also, Vibrio species were the most prevalent microorganisms in the coral mucus, and the prevalence of these bacteria is significantly higher than those found in the surrounding saltwater. These findings reveal that there is a notable difference in microbial diversity across the various settings and locales, revealing that geographic variables and coral closeness affect the diversity of microbial communities. There were significant differences in microbial community composition regarding the proximity to coral. In addition, there were strong positive correlations between genera Pseudoalteromonas and Vibrio in close-to-coral environments, suggesting that these bacteria may play a synergistic role in Immunizing coral, raising its tolerance towards environmental stress and overall coral health.},
}

@article {pmid40140988,
year = {2025},
author = {Yan, Q and Huang, L and Li, S and Zhang, Y and Guo, R and Zhang, P and Lei, Z and Lv, Q and Chen, F and Li, Z and Meng, J and Li, J and Wang, G and Chen, C and Ullah, H and Cheng, L and Fan, S and You, W and Zhang, Y and Ma, J and Sha, S and Sun, W},
title = {The Chinese gut virus catalogue reveals gut virome diversity and disease-related viral signatures.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {30},
pmid = {40140988},
issn = {1756-994X},
mesh = {Humans ; *Virome/genetics ; *Viruses/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; China ; Female ; Feces/virology ; Male ; Metagenomics/methods ; Genome, Viral ; Asian People/genetics ; East Asian People ; },
abstract = {BACKGROUND: The gut viral community has been increasingly recognized for its role in human physiology and health; however, our understanding of its genetic makeup, functional potential, and disease associations remains incomplete.

METHODS: In this study, we collected 11,286 bulk or viral metagenomes from fecal samples across large-scale Chinese populations to establish a Chinese Gut Virus Catalogue (cnGVC) using a de novo virus identification approach. We then examined the diversity and compositional patterns of the gut virome in relation to common diseases by analyzing 6311 bulk metagenomes representing 28 disease or unhealthy states.

RESULTS: The cnGVC contains 93,462 nonredundant viral genomes, with over 70% of these being novel viruses not included in existing gut viral databases. This resource enabled us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we profiled the gut virome in large-scale populations, assessed sex- and age-related variations, and identified 4238 universal viral signatures of diseases. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.698) and high-risk patients from controls (AUC = 0.761), and its predictive ability was also validated in external cohorts.

CONCLUSIONS: Our resources and findings significantly expand the current understanding of the human gut virome and provide a comprehensive view of the associations between gut viruses and common diseases. This will pave the way for novel strategies in the treatment and prevention of these diseases.},
}

Humans
*Virome/genetics
*Viruses/genetics/classification
*Gastrointestinal Microbiome/genetics
*Metagenome
China
Female
Feces/virology
Male
Metagenomics/methods
Genome, Viral
Asian People/genetics
East Asian People

@article {pmid40140473,
year = {2025},
author = {Brown, AA and Widdowson, M and Brandt, S and Mohammadzadeh, P and Rosenberg, JB and Jepsen, JRM and Ebdrup, BH and Hernández-Lorca, M and Bønnelykke, K and Chawes, B and Stokholm, J and Thorsen, J and Ibrahimi, P and Li, X and Sørensen, SJ and Rasmussen, MA},
title = {Associations of the gut microbiome and inflammatory markers with mental health symptoms: a cross-sectional study on Danish adolescents.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {10378},
pmid = {40140473},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Adolescent ; Cross-Sectional Studies ; Female ; Denmark/epidemiology ; *Inflammation/metabolism ; *Attention Deficit Disorder with Hyperactivity/metabolism/microbiology ; *Biomarkers ; *Depression/metabolism ; Anxiety/microbiology ; Mental Health ; Stress, Psychological/metabolism ; Feces/microbiology ; },
abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder that often persists into adulthood and is accompanied by comorbid mental health problems. This cross-sectional cohort study analyzed 411 18-year-olds from the Danish COPSAC2000 birth cohort to investigate the relationship between the gut microbiome, fasting and postprandial systemic inflammation, ADHD symptoms, and symptoms of anxiety, stress, and depression. ADHD was assessed using the Adult ADHD Self-Report Scale (ASRS), while depression, stress, and anxiety were evaluated with the Depression, Anxiety, and Stress Scale 21 (DASS-21). Fecal metagenomic data and inflammation levels, measured as glycosylated protein A (GlycA), were analyzed following a standardized meal challenge. In males, higher ADHD symptom scores correlated significantly with increased abundance of a tryptophan biosynthesis pathway (MetaCyc Metabolic Pathways Database) and elevated fasting and postprandial GlycA levels (p < 0.05). While the severity of depression, anxiety, and stress symptoms showed weak associations with GlycA and the gut microbiome, our findings indicate a significant link between ADHD symptoms and postprandial inflammation, warranting further investigation into underlying mechanisms.},
}

Humans
*Gastrointestinal Microbiome
Male
Adolescent
Cross-Sectional Studies
Female
Denmark/epidemiology
*Inflammation/metabolism
*Attention Deficit Disorder with Hyperactivity/metabolism/microbiology
*Biomarkers
*Depression/metabolism
Anxiety/microbiology
Mental Health
Stress, Psychological/metabolism
Feces/microbiology

@article {pmid40139249,
year = {2025},
author = {Taylor, JT and Lee, V and Dearlove, T and Jolly, M and Wierenga, JR and Dubrulle, J and Hodgkinson-Bean, J and Hunter, S and Gartrell, B and Morgan, K and McInnes, K and French, N and Holmes, EC and Geoghegan, JL},
title = {A Metagenomic Investigation into Apteryx rowi Dermatosis Identifies Multiple Novel Viruses and a Highly Abundant Nematode.},
journal = {Journal of wildlife diseases},
volume = {},
number = {},
pages = {},
doi = {10.7589/JWD-D-24-00115},
pmid = {40139249},
issn = {1943-3700},
abstract = {Sporadic cases of dermatosis have been reported in wild Ōkārito Rowi (Apteryx rowi), a species of brown kiwi, for over a decade. The disease exhibits distinctive features, including lesions, lichenification, and feather loss. Swab samples and full-thickness skin biopsies were collected during a survey of affected kiwi in 2023 for a metatranscriptome-based, total infectome investigation to identify any possible microbial agents associated with the disease. Our approach identified novel viruses as well as a species of nematode in high relative abundance. We found a highly abundant hepacivirus within the Flaviviridae, but only in some mild cases of dermatitis across all sample types, and in both active and chronic infections. In addition, we found a significant shift in the taxonomic composition of the nonviral microbiome within severe chronic dermatitis cases, particularly an increased abundance of transcripts from a Eucoleus sp. parasitic. Although determining the primary cause of disease in critically endangered wildlife such as Rowi remains challenging, our detection of novel and highly abundant microorganisms opens new lines of inquiry to investigate their potential association with dermatosis in this nationally iconic species.},
}

@article {pmid40138008,
year = {2025},
author = {Davasaz Tabrizi, E and Sevil, M and Arican, E},
title = {Bioinformatic strategies in metagenomics of chronic prostatitis.},
journal = {World journal of urology},
volume = {43},
number = {1},
pages = {188},
pmid = {40138008},
issn = {1433-8726},
mesh = {Male ; *Prostatitis/microbiology ; Humans ; Adult ; *Metagenomics ; *Computational Biology ; Chronic Disease ; Young Adult ; Middle Aged ; Microbiota/genetics ; },
abstract = {PURPOSE: Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a prevalent urological condition in young men, significantly affecting quality of life due to persistent discomfort and neuropsychological symptoms. Despite its high prevalence, the etiology of CP/CPPS remains poorly understood. This study investigated urinary microbiota differences between CP/CPPS patients and healthy controls to identify microbial contributors, antibiotic resistance genes (ARGs), and virulence factors of dominant bacteria, as well as to explore potential therapeutic targets.

METHODS: Urine samples were collected from 58 CP/CPPS patients and 25 controls. Symptom severity was assessed by a specialist urologist using the NIH Chronic Prostatitis Symptom Index and UPOINT classification. Bacterial-specific 16 S rRNA sequencing was performed using nanopore technology, with bioinformatics analyses conducted via ONT guppy 5.0.11, NCBI and SLV 16 S bacterial taxonomic databases, UPGMA hierarchical clustering, and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC). Pairwise comparisons were analyzed using the Mann-Whitney U test.

RESULTS: Distinct microbial diversity patterns were observed between patients and controls. Bacillus species were significantly enriched in CP/CPPS patients, while Enterococcus species predominated in controls. Younger patients exhibited unique microbiome profiles compared to older groups. Bioinformatics analyses identified ARGs and virulence factors associated with Bacillus species, implicating them in localized inflammation. Antibiotics like pleuromutilin or vancomycin were identified as potential therapeutic options, though experimental validation was beyond the study's scope.

CONCLUSION: These findings highlight microbial imbalances and provide a foundation for microbiome-targeted therapeutic strategies for CP/CPPS management in the future. Additionally, the identification of bacterial virulence factors and ARG provides insights into the potential mechanisms driving persistent symptoms. Future research with larger cohorts and experimental validation of the suggested therapeutic options may contribute to more effective treatment for CP/CPPS.},
}

Male
*Prostatitis/microbiology
Humans
Adult
*Metagenomics
*Computational Biology
Chronic Disease
Young Adult
Middle Aged
Microbiota/genetics

@article {pmid40137713,
year = {2025},
author = {Shaw, CA and Soltero-Rivera, M and Profeta, R and Weimer, BC},
title = {Case Report: Shift from Aggressive Periodontitis to Feline Chronic Gingivostomatitis Is Linked to Increased Microbial Diversity.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/pathogens14030228},
pmid = {40137713},
issn = {2076-0817},
support = {UL1 TR001860/NH/NIH HHS/United States ; },
mesh = {Animals ; Cats ; *Microbiota/genetics ; *Cat Diseases/microbiology/diagnosis ; *Aggressive Periodontitis/microbiology ; Stomatitis/microbiology/veterinary ; Bacteria/genetics/classification/isolation & purification ; Disease Progression ; Mouth/microbiology ; Metagenomics ; Male ; },
abstract = {Aggressive Periodontitis (AP) and Feline Chronic Gingivostomatitis (FCGS) are two oral inflammatory diseases in cats with unknown etiology. Both conditions present with severe inflammation of the oral cavity and in FCGS it is found with additional deterioration of the non-keratinized mucosa. The oral microbiome is increasingly implicated in disease progression, but little is known about shifts in the microbial community during the AP and FCGS progression. To that end, we used deep metagenomic sequencing with total RNA on three longitudinal samples of the oral microbiome in a cat first diagnosed with AP that progressed to FCGS. This deep sequencing approach revealed that increased diversity at both the genus and species levels marked the shift from AP to FCGS, including increases in Porphyromonas and Treponema species, and decreased Streptobacillus species. The metatranscriptomes were then probed for expression of antimicrobial resistance genes and virulence factors. Disease-related genes that include cheY, and ompP5 were expressed in early AP and FCGS, while others like galU were only expressed in one or the other disease state. Both genus and species-level shifts were observed along the longitudinal microbiome samples with a noted increase in species diversity in the FCGS-associated microbiome. Corroborating that functional shifts accompany taxonomic changes, the AMR and virulence factor expression similarly changed between the sampling points. Together, these taxonomic and functional shifts indicate that AP and FCGS are potentially linked and may be marked by changes in the oral microbiome, which supports the development of microbial-based clinical diagnostics and therapeutics.},
}

Animals
Cats
*Microbiota/genetics
*Cat Diseases/microbiology/diagnosis
*Aggressive Periodontitis/microbiology
Stomatitis/microbiology/veterinary
Bacteria/genetics/classification/isolation & purification
Disease Progression
Mouth/microbiology
Metagenomics
Male

@article {pmid40133298,
year = {2025},
author = {Bhanu, P and Buchke, S and Hemandhar-Kumar, N and Varsha, P and Kiran, SKR and Vikneswaran, G and Alva, A and Basavaraj, GS and Kumar, J},
title = {Comparative metagenomic analysis of the oral microbiome in COVID-19 patients and healthy individuals.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {10303},
pmid = {40133298},
issn = {2045-2322},
support = {20210001//Bangalore Bioinnovation Centre/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology ; *Mouth/microbiology/virology ; *Microbiota/genetics ; *Metagenomics/methods ; *SARS-CoV-2/genetics/isolation & purification ; Male ; Female ; Adult ; Middle Aged ; Metagenome ; Aged ; },
abstract = {COVID-19, caused by SARS-CoV-2, affects multiple body systems, including the oral cavity, where it may disrupt the oral microbiome in ways that contribute to disease pathology. Understanding the long-term interaction between SARS-CoV-2 and the oral microbiome is crucial, as it may reveal microbial markers valuable for diagnosing or monitoring persistent health issues in COVID-19 survivors. Metagenomic sequencing revealed significant microbial shifts in the oral microbiome of COVID-19 patients, showing reduced microbial diversity and increased prevalence of opportunistic pathogens compared to healthy individuals. Alpha diversity measures indicated lower microbial diversity and evenness, while beta diversity analyses demonstrated distinct microbial community compositions. Core microbiome analysis identified unique taxa in COVID-19 patients that may contribute to disease pathology, while differential abundance analysis highlighted specific taxa shifts, including an increase in potential pathogens. Our findings advance the understanding of microbial changes in the oral microbiome associated with COVID-19 and suggest potential targets for microbiome-based interventions. While these results indicate associations with possible health impacts, further research is needed to determine causative links and long-term implications for COVID-19 survivors. This foundational research highlights the potential for microbiome science to inform diagnostic tools, such as microbial markers for disease progression, and therapeutic approaches, including targeted probiotics, which could ultimately support better patient outcomes and public health strategies.},
}

Humans
*COVID-19/microbiology/virology
*Mouth/microbiology/virology
*Microbiota/genetics
*Metagenomics/methods
*SARS-CoV-2/genetics/isolation & purification
Male
Female
Adult
Middle Aged
Metagenome
Aged

@article {pmid40101714,
year = {2025},
author = {Lynn, HM and Gordon, JI},
title = {Sequential co-assembly reduces computational resources and errors in metagenome-assembled genomes.},
journal = {Cell reports methods},
volume = {5},
number = {3},
pages = {101005},
doi = {10.1016/j.crmeth.2025.101005},
pmid = {40101714},
issn = {2667-2375},
mesh = {Animals ; Humans ; *Metagenome/genetics ; Mice ; *Gastrointestinal Microbiome/genetics ; Bangladesh ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Metagenomics/methods ; },
abstract = {Generating metagenome-assembled genomes from DNA shotgun sequencing datasets can demand considerable computational resources. Here, we describe a sequential co-assembly method that reduces the assembly of duplicate reads through successive application of single-node computing tools for read assembly and mapping. Using a simulated mouse microbiome DNA shotgun sequencing dataset, we demonstrated that this approach shortens assembly time, uses less memory than traditional co-assembly, and produces significantly fewer assembly errors. Applying sequential co-assembly to shotgun sequencing reads from (1) a longitudinal study of gut microbiomes from undernourished Bangladeshi children and (2) a 2.3-terabyte dataset generated from gnotobiotic mice colonized with pooled microbiomes from these children that was too large to be handled by a traditional co-assembly approach also demonstrated significant reductions in assembly time and memory requirements. These results suggest that this approach should be useful in resource-constrained settings, including in low- and middle-income countries.},
}

Animals
Humans
*Metagenome/genetics
Mice
*Gastrointestinal Microbiome/genetics
Bangladesh
Sequence Analysis, DNA/methods
Computational Biology/methods
Metagenomics/methods

@article {pmid40077957,
year = {2025},
author = {Ma, Z and Wen, X and Zhang, Y and Ai, Z and Zhao, X and Dong, N and Dou, X and Shan, A},
title = {Thymol Alleviates Colitis by Modulating Intestinal Barrier Damage, Gut Microbiota, and Amino Acid Metabolic Pathways.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {12},
pages = {7211-7227},
doi = {10.1021/acs.jafc.4c10406},
pmid = {40077957},
issn = {1520-5118},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Colitis/chemically induced/metabolism/drug therapy/microbiology ; *Amino Acids/metabolism ; Humans ; *Mice, Inbred C57BL ; *Intestinal Mucosa/metabolism/drug effects ; *Thymol/pharmacology/administration & dosage/metabolism ; Male ; Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; Metabolic Networks and Pathways/drug effects ; Dextran Sulfate/adverse effects ; Colon/metabolism/microbiology/drug effects ; Cytokines/metabolism/genetics ; },
abstract = {Thymol (THY) is a phenolic monoterpene compound that has garnered attention due to its various biological properties, including antioxidant, anti-inflammatory, and immune-regulatory effects. The purpose of this study was to determine the therapeutic and protective effects of THY in colitic mice, with a particular focus on the mechanisms involving gut microbiota. The results showed that early intervention with THY (40 and 80 mg/kg) not only alleviated the clinical symptoms and colonic damage in mice with dextran sodium sulfate (DSS)-induced colitis but also suppressed the colonic production of inflammatory cytokines (IL-1β, IL-6, and IL-18) and enhanced the expression of mucins (MUC1 and MUC2) and trefoil factor family 3 (TFF3), thereby improving the integrity of the intestinal epithelial barrier. In addition, THY altered the composition of the gut microbiota in colitis mice by increasing the abundance of Bacteroides and reducing the abundance of Proteobacteria. Fecal microbial transplantation (FMT) results demonstrated that FM from THY donor mice significantly improved symptoms of inflammatory bowel disease (IBD), confirming the crucial role of the gut microbiota. Metagenomic and untargeted metabolomic studies found that the characteristic microbiota of THY is Prevotellaceae, and THY significantly upregulated the amino acid metabolic pathways related to arginine and proline metabolism, arginine biosynthesis, and glycerophospholipid metabolism. In summary, THY holds significant potential as a functional additive to enhance host intestinal activity.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Colitis/chemically induced/metabolism/drug therapy/microbiology
*Amino Acids/metabolism
Humans
*Mice, Inbred C57BL
*Intestinal Mucosa/metabolism/drug effects
*Thymol/pharmacology/administration & dosage/metabolism
Male
Bacteria/classification/genetics/metabolism/isolation & purification/drug effects
Metabolic Networks and Pathways/drug effects
Dextran Sulfate/adverse effects
Colon/metabolism/microbiology/drug effects
Cytokines/metabolism/genetics

@article {pmid40015021,
year = {2025},
author = {Velásquez-Reyes, D and García-Alamilla, P and Kirchmayr, MR and Lugo-Cervantes, E and Gschaedler, A},
title = {Contribution of post-harvest processing in cocoa bean: Chemometric and metagenomic analysis in fermentation step.},
journal = {Food chemistry},
volume = {477},
number = {},
pages = {143458},
doi = {10.1016/j.foodchem.2025.143458},
pmid = {40015021},
issn = {1873-7072},
mesh = {*Cacao/microbiology/chemistry/metabolism ; *Fermentation ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; *Metagenomics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Microbiota ; Mexico ; Gas Chromatography-Mass Spectrometry ; Food Handling ; Odorants/analysis ; Taste ; },
abstract = {Cocoa fermentation is a heterogeneous process, exhibiting a high degree of diversity of flavor, aroma, and microbial communities. A study was conducted to examine cocoa fermentations in five municipalities of a region in Mexico, with the objective of associating post-harvest practices, geographic area, and chemical and microbiological profiles. Through the application of high-performance DNA sequencing, the microbial diversity was identified, and the non-volatile and volatile compounds were identified and quantified by UHPLC-RID/PDA and HS-SPME/GC-MS, respectively. Using PCA, PLS regression and Pearson correlation, post-harvest practices, geographical factors, microbial communities, and volatile and non-volatile compounds were made. The absence of control in cocoa fermentation was associated to Aspergillus, Escherichia, and Bacillus, and reduced the production of essential acids for aroma. This study provides data on the diversity of post-harvest practices and their impact on cocoa quality.},
}

*Cacao/microbiology/chemistry/metabolism
*Fermentation
*Volatile Organic Compounds/metabolism/chemistry/analysis
*Metagenomics
*Bacteria/genetics/classification/metabolism/isolation & purification
Microbiota
Mexico
Gas Chromatography-Mass Spectrometry
Food Handling
Odorants/analysis
Taste

@article {pmid40011766,
year = {2025},
author = {Proctor, DM and Sansom, SE and Deming, C and Conlan, S and Blaustein, RA and Atkins, TK and , and Dangana, T and Fukuda, C and Thotapalli, L and Kong, HH and Lin, MY and Hayden, MK and Segre, JA},
title = {Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes.},
journal = {Nature},
volume = {639},
number = {8056},
pages = {1016-1023},
pmid = {40011766},
issn = {1476-4687},
mesh = {Humans ; *Nursing Homes ; *Skin/microbiology ; *Candida auris/genetics ; Klebsiella pneumoniae/isolation & purification/genetics/drug effects ; Metagenomics ; Female ; Male ; Enterococcus faecium/genetics/isolation & purification/drug effects ; Staphylococcus aureus/genetics/drug effects/isolation & purification ; Pseudomonas aeruginosa/genetics/isolation & purification/drug effects ; Acinetobacter baumannii/genetics/drug effects/isolation & purification ; Microbiota ; Bacterial Proteins/genetics/metabolism ; Candidiasis/microbiology/epidemiology ; beta-Lactamases ; },
abstract = {Antimicrobial resistance is a public health threat associated with increased morbidity, mortality and financial burden in nursing homes and other healthcare settings[1]. Residents of nursing homes are at increased risk of pathogen colonization and infection owing to antimicrobial-resistant bacteria and fungi. Nursing homes act as reservoirs, amplifiers and disseminators of antimicrobial resistance in healthcare networks and across geographical regions[2]. Here we investigate the genomic epidemiology of the emerging, multidrug-resistant human fungal pathogen Candida auris in a ventilator-capable nursing home. Coupling strain-resolved metagenomics with isolate sequencing, we report skin colonization and clonal spread of C. auris on the skin of nursing home residents and throughout a metropolitan region. We also report that most Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Entobacter species (ESKAPE) pathogens and other high-priority pathogens (including Escherichia coli, Providencia stuartii, Proteus mirabilis and Morganella morganii) are shared in a nursing home. Integrating microbiome and clinical microbiology data, we detect carbapenemase genes at multiple skin sites on residents identified as carriers of these genes. We analyse publicly available shotgun metagenomic samples (stool and skin) collected from residents with varying medical conditions living in seven other nursing homes and provide additional evidence of previously unappreciated bacterial strain sharing. Taken together, our data suggest that skin is a reservoir for colonization by C. auris and ESKAPE pathogens and their associated antimicrobial-resistance genes.},
}

Humans
*Nursing Homes
*Skin/microbiology
*Candida auris/genetics
Klebsiella pneumoniae/isolation & purification/genetics/drug effects
Metagenomics
Female
Male
Enterococcus faecium/genetics/isolation & purification/drug effects
Staphylococcus aureus/genetics/drug effects/isolation & purification
Pseudomonas aeruginosa/genetics/isolation & purification/drug effects
Acinetobacter baumannii/genetics/drug effects/isolation & purification
Microbiota
Bacterial Proteins/genetics/metabolism
Candidiasis/microbiology/epidemiology
beta-Lactamases

@article {pmid39983731,
year = {2025},
author = {Saha, S and Kalathera, J and Sumi, TS and Mane, V and Zimmermann, S and Waschina, S and Pande, S},
title = {Mass lysis of predatory bacteria drives the enrichment of antibiotic resistance in soil microbial communities.},
journal = {Current biology : CB},
volume = {35},
number = {6},
pages = {1258-1268.e6},
doi = {10.1016/j.cub.2025.01.068},
pmid = {39983731},
issn = {1879-0445},
mesh = {*Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial ; Microbial Interactions ; Drug Resistance, Microbial ; },
abstract = {Numerous studies have investigated the effects of antibiotics on the evolution and maintenance of antimicrobial resistance (AMR). However, the impact of microbial interactions in antibiotic-free environments on resistance within complex communities remains unclear. We investigated whether the predatory bacterium M. xanthus, which can produce antimicrobials and employ various contact-dependent and -independent prey-killing mechanisms, influences the abundance of antibiotic-resistant bacteria in its local environment simply through its presence, regardless of active predation. We observed an association between the presence of M. xanthus in soil and the frequency of antibiotic-resistant bacteria. Additionally, culture-based and metagenomic analysis showed that coculturing M. xanthus with soil-derived communities in liquid cultures enriched AMR among non-myxobacterial isolates. This is because the lysis of M. xanthus, triggered during the starvation phase of the coculture experiments, releases diffusible growth-inhibitory compounds that enrich pre-existing resistant bacteria. Furthermore, our results show that death during multicellular fruiting body formation-a starvation-induced stress response in M. xanthus that results in over 90% cell death-also releases growth-inhibitory molecules that enrich resistant bacteria. Hence, the higher abundance of resistant bacteria in soil communities, where M. xanthus can be detected, was because of the diffusible growth-inhibitory substances that were released due to the death of M. xanthus cells during fruiting body formation. Together, our findings demonstrate how the death of M. xanthus, an important aspect of its life cycle, can impact antibiotic resistomes in natural soil communities without the anthropogenic influx of antibiotics.},
}

*Soil Microbiology
*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects
Bacteria/drug effects/genetics
Drug Resistance, Bacterial
Microbial Interactions
Drug Resistance, Microbial

@article {pmid39966520,
year = {2025},
author = {Diener, C and Holscher, HD and Filek, K and Corbin, KD and Moissl-Eichinger, C and Gibbons, SM},
title = {Metagenomic estimation of dietary intake from human stool.},
journal = {Nature metabolism},
volume = {7},
number = {3},
pages = {617-630},
pmid = {39966520},
issn = {2522-5812},
support = {R01 DK133468/DK/NIDDK NIH HHS/United States ; R01DK133468//U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)/ ; Cluster of Excellence COE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; },
mesh = {Humans ; *Feces/microbiology ; *Metagenomics/methods ; *Diet ; Adult ; Gastrointestinal Microbiome/genetics ; Infant ; Metagenome ; Male ; Female ; Metabolic Syndrome/microbiology ; Eating ; },
abstract = {Dietary intake is tightly coupled to gut microbiota composition, human metabolism and the incidence of virtually all major chronic diseases. Dietary and nutrient intake are usually assessed using self-reporting methods, including dietary questionnaires and food records, which suffer from reporting biases and require strong compliance from study participants. Here, we present Metagenomic Estimation of Dietary Intake (MEDI): a method for quantifying food-derived DNA in human faecal metagenomes. We show that DNA-containing food components can be reliably detected in stool-derived metagenomic data, even when present at low abundances (more than ten reads). We show how MEDI dietary intake profiles can be converted into detailed metabolic representations of nutrient intake. MEDI identifies the onset of solid food consumption in infants, shows significant agreement with food frequency questionnaire responses in an adult population and shows agreement with food and nutrient intake in two controlled-feeding studies. Finally, we identify specific dietary features associated with metabolic syndrome in a large clinical cohort without dietary records, providing a proof-of-concept for detailed tracking of individual-specific, health-relevant dietary patterns without the need for questionnaires.},
}

Humans
*Feces/microbiology
*Metagenomics/methods
*Diet
Adult
Gastrointestinal Microbiome/genetics
Infant
Metagenome
Male
Female
Metabolic Syndrome/microbiology
Eating

@article {pmid40136549,
year = {2025},
author = {Pizzi, S and Conti, A and Di Canito, A and Casagrande Pierantoni, D and Foschino, R and Setati, ME and Vigentini, I},
title = {Endophytic Diversity in Vitis vinifera with Different Vineyard Managements and Vitis sylvestris Populations from Northern Italy: A Comparative Study of Culture-Dependent and Amplicon Sequencing Methods.},
journal = {Biology},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/biology14030293},
pmid = {40136549},
issn = {2079-7737},
support = {150549//Italy/South Africa Joint Research Programme (ISARP) 2023-2025/ ; },
abstract = {This study aimed to investigate the endophytic microbial populations associated with wild and domesticated grapevines using both culture-based and culture-independent methods. Through culture-based methods, 148 endophytes were identified. The dominant fungal species included Aureobasidium pullulans, Alternaria alternata, and Cladosporium allicinum, while predominant bacterial species were Ralstonia pikettii, Nocardia niigatensis, and Sphingomonas echinoides. Culture-independent methods employed metagenomic techniques to explore microbial biodiversity, focusing on targeted amplification of bacterial 16S rRNA as well as fungal ITS and 26S rRNA gene regions. The main bacterial species identified included Halomonas sp., Sphingomonas sp. and Massilia sp., whereas the fungal population was dominated by Cladosporium sp., Malassezia sp. and Mucor sp. The findings revealed that vineyard management practices did not lead to statistically significant variations in microbial communities. The consistent presence of these genera across all samples suggests that they are stable components of the grapevine endophytic microbiota, remaining relatively unaffected by external environmental factors.},
}

@article {pmid40135504,
year = {2025},
author = {Pelto, J and Auranen, K and Kujala, JV and Lahti, L},
title = {Elementary methods provide more replicable results in microbial differential abundance analysis.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf130},
pmid = {40135504},
issn = {1477-4054},
support = {952914//European Union's Horizon 2020 research and innovation programme/ ; },
mesh = {*Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Humans ; Reproducibility of Results ; Computational Biology/methods ; Bacteria/genetics/classification ; },
abstract = {Differential abundance analysis (DAA) is a key component of microbiome studies. Although dozens of methods exist, there is currently no consensus on the preferred methods. While the correctness of results in DAA is an ambiguous concept and cannot be fully evaluated without setting the ground truth and employing simulated data, we argue that a well-performing method should be effective in producing highly reproducible results. We compared the performance of 14 DAA methods by employing datasets from 53 taxonomic profiling studies based on 16S rRNA gene or shotgun metagenomic sequencing. For each method, we examined how the results replicated between random partitions of each dataset and between datasets from separate studies. While certain methods showed good consistency, some widely used methods were observed to produce a substantial number of conflicting findings. Overall, when considering consistency together with sensitivity, the best performance was attained by analyzing relative abundances with a nonparametric method (Wilcoxon test or ordinal regression model) or linear regression/t-test. Moreover, a comparable performance was obtained by analyzing presence/absence of taxa with logistic regression.},
}

*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Humans
Reproducibility of Results
Computational Biology/methods
Bacteria/genetics/classification

@article {pmid40132013,
year = {2025},
author = {Halo, BA and Aljabri, YAS and Yaish, MW},
title = {Drought-induced microbial dynamics in cowpea rhizosphere: Exploring bacterial diversity and bioinoculant prospects.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0320197},
doi = {10.1371/journal.pone.0320197},
pmid = {40132013},
issn = {1932-6203},
mesh = {*Rhizosphere ; *Vigna/microbiology/genetics ; *Droughts ; *Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Biodiversity ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Microbiota ; Plant Roots/microbiology ; },
abstract = {Rhizospheric bacterial communities in plants contribute to drought resilience by promoting plant-soil interactions, yet their biodiversity and ecological impacts are not fully characterized. In cowpeas, these interactions may be crucial in enhancing tolerance to drought conditions. In this study, cowpea plants were subjected to drought treatment, the soil attached to the roots was collected, environmental DNA (e-DNA) was extracted, and the bacterial communities were identified as amplicon sequence variants (ASVs) by metagenomics analysis of the 16S rRNA gene. Microbial communities under drought and control conditions were analyzed using taxonomy and diversity metrics. The sequencing results revealed 5,571 ASVs, and taxonomic analysis identified 1,752 bacterial species. Alpha and beta diversity analyses showed less conserved microbial community structures and compositions among the samples isolated from the rhizosphere under drought conditions compared to untreated samples, implying the enhancement effect of drought on species' biodiversity and richness. The differential accumulation analysis of the bacterial community identified 75 species that accumulated significantly (P ≤ 0.05) in response to drought, including 13 species exclusively present, seven absent, and 46 forming a high-abundance cluster within the hierarchical heatmap. These species were also grouped into specific clades in the phylogenetic tree, suggesting common genetic ancestry and potentially shared traits associated with drought tolerance. The differentially accumulated bacterial list included previously characterized species from drought and saline habitats. These findings suggest that drought stress significantly alters the composition and abundance of epiphytic bacterial communities, potentially impacting the rhizosphere's ecological balance and interactions with cowpeas. The results highlight microbial adaptations that enhance plant resilience through improved stress mitigation, providing meaningful understandings for advancing sustainable agriculture and developing microbial-based strategies to boost crop productivity in drought-prone regions.},
}

*Rhizosphere
*Vigna/microbiology/genetics
*Droughts
*Soil Microbiology
*Bacteria/genetics/classification/isolation & purification
*Biodiversity
*RNA, Ribosomal, 16S/genetics
*Phylogeny
Microbiota
Plant Roots/microbiology

@article {pmid40129931,
year = {2025},
author = {Lee, G and Rosa, BA and Fernandez-Baca, MV and Martin, J and Ore, RA and Ortiz, P and Cabada, MM and Mitreva, M},
title = {Distinct gut microbiome features characterize Fasciola hepatica infection and predict triclabendazole treatment outcomes in Peruvian patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1555171},
doi = {10.3389/fcimb.2025.1555171},
pmid = {40129931},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; Peru ; Animals ; *Fasciola hepatica/drug effects/genetics ; *Fascioliasis/drug therapy/microbiology ; *Triclabendazole/therapeutic use ; Treatment Outcome ; *Anthelmintics/pharmacology/therapeutic use ; Female ; Male ; Adult ; Middle Aged ; Bacteria/classification/genetics/drug effects/isolation & purification ; Metagenomics ; Young Adult ; Feces/microbiology/parasitology ; },
abstract = {BACKGROUND: Fasciola hepatica, a globally distributed helminth, causes fasciolosis, a disease with significant health and economic impacts. Variability in triclabendazole (TCBZ) efficacy and emerging resistance are remaining challenges. Evidence suggests that the gut microbiome influences host-helminth interactions and is associated with anthelmintic effects, but its association with human F. hepatica infection and TCBZ efficacy is not well understood.

METHODS: In this study, we investigated the relationship between Fasciola hepatica infection and the gut microbiome through metagenomic shotgun sequencing of 30 infected and 60 age- and sex-matched uninfected individuals from Peru. Additionally, we performed a longitudinal analysis to evaluate microbiome dynamics in relation to TCBZ treatment response.

RESULTS AND DISCUSSION: Infection was associated with specific microbial taxonomic and functional features, including higher abundance of Negativibacillus sp900547015, Blautia A sp000285855, and Prevotella sp002299635 species, and enrichment of microbial pathways linked to survival under stress and depletion of pathways for microbial growth. Unexpectedly, we identified that responders to TCBZ treatment (who cleared infection) harbored many microbiome features significantly different relative to non-responders, both before and after treatment. Specifically, the microbiomes of responders had a higher abundance Firmicutes A and Bacteroides species as well as phospholipid synthesis and glucuronidation pathways, while non-responders had higher abundance of Actinobacteria species including several from the Parolsenella and Bifidobacterium genera, and Bifidobacterium shunt and amino acid biosynthesis pathways.

CONCLUSIONS: Our findings underscore the impact of helminth infection on gut microbiome and suggest a potential role of gut microbiota in modulating TCBZ efficacy, offering novel insights into F. hepatica-microbiome interactions and paving the way for microbiome-informed treatment approaches.},
}

*Gastrointestinal Microbiome/drug effects/genetics
Humans
Peru
Animals
*Fasciola hepatica/drug effects/genetics
*Fascioliasis/drug therapy/microbiology
*Triclabendazole/therapeutic use
Treatment Outcome
*Anthelmintics/pharmacology/therapeutic use
Female
Male
Adult
Middle Aged
Bacteria/classification/genetics/drug effects/isolation & purification
Metagenomics
Young Adult
Feces/microbiology/parasitology

@article {pmid40129261,
year = {2025},
author = {Boden, JS and Som, SM and Brazelton, WJ and Anderson, RE and Stüeken, EE},
title = {Evaluating Serpentinization as a Source of Phosphite to Microbial Communities in Hydrothermal Vents.},
journal = {Geobiology},
volume = {23},
number = {2},
pages = {e70016},
doi = {10.1111/gbi.70016},
pmid = {40129261},
issn = {1472-4669},
support = {NE/V010824/1//Natural Environment Research Council/ ; 80NSSC19K1427//NASA Planetary Science Division ISFM Program/ ; OCE-1536405//National Science Foundation/ ; 80NSSC18K0829//NASA Astrobiology Program/ ; 80NSSC19K1427//NASA Astrobiology Program/ ; },
mesh = {*Hydrothermal Vents/microbiology ; *Phosphites/chemistry/metabolism ; Microbiota ; Bacteria/genetics/metabolism/classification ; Phosphorus/metabolism/analysis ; },
abstract = {Previous studies have documented the presence of phosphite, a reduced and highly soluble form of phosphorus, in serpentinites, which has led to the hypothesis that serpentinizing hydrothermal vents could have been an important source of bioavailable phosphorus for early microbial communities in the Archean. Here, we test this hypothesis by evaluating the genomic hallmarks of phosphorus usage in microbial communities living in modern hydrothermal vents with and without influence from serpentinization. These genomic analyses are combined with results from a geochemical model that calculates phosphorus speciation during serpentinization as a function of temperature, water:rock ratio, and lithology at thermodynamic equilibrium. We find little to no genomic evidence of phosphite use in serpentinizing environments at the Voltri Massif or the Von Damm hydrothermal field at the Mid Cayman Rise, but relatively more in the Lost City hydrothermal field, Coast Range Ophiolite Microbial Observatory, The Cedars, and chimney samples from Old City hydrothermal field and Prony Bay hydrothermal field, as well as in the non-serpentinizing hydrothermal vents at Axial Seamount. Geochemical modeling shows that phosphite production is favored at ca 275°C-325°C and low water:rock ratios, which may explain previous observations of phosphite in serpentinite rocks; however, most of the initial phosphate is trapped in apatite during serpentinization, suppressing the absolute phosphite yield. As a result, phosphite from serpentinizing vents could have supported microbial growth around olivine minerals in chimney walls and suspended aggregates, but it is unlikely to have fueled substantial primary productivity in diffusely venting fluids during life's origin and evolution in the Archean unless substrates equivalent to dunites (composed of > 90 wt% olivine) were more common.},
}

*Hydrothermal Vents/microbiology
*Phosphites/chemistry/metabolism
Microbiota
Bacteria/genetics/metabolism/classification
Phosphorus/metabolism/analysis

@article {pmid40128855,
year = {2025},
author = {DeVeaux, AL and Hall-Moore, C and Shaikh, N and Wallace, M and Burnham, CD and Schnadower, D and Kuppermann, N and Mahajan, P and Ramilo, O and Tarr, PI and Dantas, G and Schwartz, DJ},
title = {Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {82},
pmid = {40128855},
issn = {2049-2618},
support = {R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; R01AI155893//National Institute of Allergy and Infectious Diseases/ ; T32GM139774/GM/NIGMS NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; P30DK052574/DK/NIDDK NIH HHS/United States ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; R01HD062477//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; U03MC00007/HRSA/HRSA HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; Male ; *Metagenomics/methods ; Infant, Newborn ; *Fever/microbiology ; *Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Urinary Tract Infections/microbiology ; Case-Control Studies ; Bacterial Infections/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Extraintestinal bacterial infections (EBIs), e.g., urinary tract infection, bacteremia, and meningitis, occur in approximately 10% of febrile infants younger than 60 days. Although many EBI-causing species commonly reside in the infant gut, proof that the digestive system is a pre-infection habitat remains unestablished.

RESULTS: We studied a cohort of febrile term infants < 60 days old who presented to one of thirteen US emergency departments in the Pediatric Emergency Care Applied Research Network from 2016 to 2019. Forty EBI cases and 74 febrile controls matched for age, sex, and race without documented EBIs were selected for analysis. Shotgun sequencing was performed of the gut microbiome and of strains cultured from the gut and extraintestinal site(s) of EBI cases, including blood, urine, and/or cerebrospinal fluid. Using a combination of EBI isolate genomics and fecal metagenomics, we detected an intestinal strain presumptively isogenic to the EBI pathogen (> 99.999% average nucleotide identity) in 63% of infants with EBIs. Although there was no difference in gut microbiome diversity between cases and controls, we observed significantly increased Escherichia coli relative abundance in the gut microbiome of infants with EBIs caused by E. coli. Infants with E. coli infections who were colonized by the putatively isogenic pathogen strain had significantly higher E. coli phylogroup B2 abundance in their gut, and their microbiome was more likely to contain virulence factor loci associated with adherence, exotoxin production, and nutritional/metabolic function.

CONCLUSIONS: The intestine plausibly serves as a reservoir for EBI pathogens in a subset of febrile term infants, prompting consideration of new opportunities for surveillance and EBI prevention among colonized, pre-symptomatic infants. Video Abstract.},
}

Humans
*Gastrointestinal Microbiome/genetics
Infant
Female
Male
*Metagenomics/methods
Infant, Newborn
*Fever/microbiology
*Feces/microbiology
Bacteria/classification/genetics/isolation & purification
Urinary Tract Infections/microbiology
Case-Control Studies
Bacterial Infections/microbiology
Metagenome

@article {pmid40128848,
year = {2025},
author = {Byrne, SR and DeMott, MS and Yuan, Y and Ghanegolmohammadi, F and Kaiser, S and Fox, JG and Alm, EJ and Dedon, PC},
title = {Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {81},
pmid = {40128848},
issn = {2049-2618},
support = {T32-ES007020//NIEHS Training Grant in Environmental Toxicology/ ; R01-OD028099-01//NIH Transformative Award/ ; R01-OD028099-01//NIH Transformative Award/ ; P30-ES002109//NIEHS Core Center Grant/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Feces/microbiology ; *Bacteria/genetics/classification/metabolism ; Mice ; Animals ; Epigenesis, Genetic ; Epigenome ; Female ; Male ; Phosphates/metabolism ; },
abstract = {BACKGROUND: Epigenetic regulation of gene expression and host defense is well established in microbial communities, with dozens of DNA modifications comprising the epigenomes of prokaryotes and bacteriophage. Phosphorothioation (PT) of DNA, in which a chemically reactive sulfur atom replaces a non-bridging oxygen in the sugar-phosphate backbone, is catalyzed by dnd and ssp gene families widespread in bacteria and archaea. However, little is known about the role of PTs or other microbial epigenetic modifications in the human microbiome. Here we optimized and applied fecal DNA extraction, mass spectrometric, and metagenomics technologies to characterize the landscape and temporal dynamics of gut microbes possessing PT modifications.

RESULTS: Exploiting the nuclease-resistance of PTs, mass spectrometric analysis of limit digests of PT-containing DNA reveals PT dinucleotides as part of genomic consensus sequences, with 16 possible dinucleotide combinations. Analysis of mouse fecal DNA revealed a highly uniform spectrum of 11 PT dinucleotides in all littermates, with PTs estimated to occur in 5-10% of gut microbes. Though at similar levels, PT dinucleotides in fecal DNA from 11 healthy humans possessed signature combinations and levels of individual PTs. Comparison with a widely distributed microbial epigenetic mark, m[6]dA, suggested temporal dynamics consistent with expectations for gut microbial communities based on Taylor's Power Law. Application of PT-seq for site-specific metagenomic analysis of PT-containing bacteria in one fecal donor revealed the larger consensus sequences for the PT dinucleotides in Bacteroidota, Bacillota (formerly Firmicutes), Actinomycetota (formerly Actinobacteria), and Pseudomonadota (formerly Proteobacteria), which differed from unbiased metagenomics and suggested that the abundance of PT-containing bacteria did not simply mirror the spectrum of gut bacteria. PT-seq further revealed low abundance PT sites not detected as dinucleotides by mass spectrometry, attesting to the complementarity of the technologies. Video Abstract CONCLUSIONS: The results of our studies provide a benchmark for understanding the behavior of an abundant and chemically reactive epigenetic mark in the human gut microbiome, with implications for inflammatory conditions of the gut.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Feces/microbiology
*Bacteria/genetics/classification/metabolism
Mice
Animals
Epigenesis, Genetic
Epigenome
Female
Male
Phosphates/metabolism

@article {pmid40128575,
year = {2025},
author = {Yun, H and Seo, JH and Kim, YG and Yang, J},
title = {Impact of scented candle use on indoor air quality and airborne microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {10181},
pmid = {40128575},
issn = {2045-2322},
support = {RS-2023-00244833//National Research Foundation of Korea/ ; },
mesh = {*Air Pollution, Indoor/analysis ; *Microbiota ; *Particulate Matter/analysis ; *Air Microbiology ; Humans ; Bacteria/classification/isolation & purification ; Environmental Monitoring/methods ; Extracellular Vesicles ; },
abstract = {Indoor air quality has become a growing concern worldwide due to its significant impact on human health, particularly in residential environments where people spend most of their time. Many studies have examined particulate matter (PM) in indoor air and indoor bioaerosols. However, there is a significant lack of research on airborne micro-sized bacteria (m-AB) and nano-sized bacterial extracellular vesicles (n-ABE), particularly those produced by common household activities, such as burning scented candles. This study investigates changes in PM concentrations and indoor microbiome composition resulting from candle use. Air samples were collected from three locations in residential homes: at the candle-lit spot (CL), 3 m away (3m_CL), and 6 m away (6m_CL). PM10 concentrations peaked at 1.52 times the baseline at the source after 5 min of burning, while PM2.5 and PM1 remained elevated at 3m_CL and 6m_CL over time. Before burning, dominant m-AB genera included Phyllobacterium and Pseudomonas, while post-burning, Phyllobacterium myrsinacearum in n-ABE significantly increased, marking its first detection in indoor air. This suggests that existing airborne bacteria may undergo growth or apoptosis due to combustion byproducts. These findings highlight the importance of improving ventilation in indoor spaces to minimize health risks from prolonged exposure to airborne particles and bacterial vesicles.},
}

*Air Pollution, Indoor/analysis
*Microbiota
*Particulate Matter/analysis
*Air Microbiology
Humans
Bacteria/classification/isolation & purification
Environmental Monitoring/methods
Extracellular Vesicles

@article {pmid40128181,
year = {2025},
author = {Yan, W and Shi, X and Zhao, Y and Liu, X and Jia, X and Gao, L and Yuan, J and Liao, A and Yasui, H and Wang, X and Wang, X and Zhang, R and Wang, H},
title = {Microbiota-reprogrammed phosphatidylcholine inactivates cytotoxic CD8 T cells through UFMylation via exosomal SerpinB9 in multiple myeloma.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2863},
pmid = {40128181},
issn = {2041-1723},
support = {2022-YGJC-61;2022-MS-219//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; },
mesh = {Female ; Animals ; Mice ; Humans ; Cell Line ; *T-Lymphocytes, Cytotoxic/immunology ; *Gastrointestinal Microbiome ; *Phosphatidylcholines/immunology/metabolism ; *Multiple Myeloma/genetics/immunology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Exosomes/immunology/metabolism ; *Serpins/genetics/immunology/metabolism ; *Membrane Proteins/genetics/immunology/metabolism ; },
abstract = {Gut microbiome influences tumorigenesis and tumor progression through regulating the tumor microenvironment (TME) and modifying blood metabolites. However, the mechanisms by which gut microbiome and blood metabolites regulate the TME in multiple myeloma (MM) remain unclear. By employing16S rRNA gene sequencing coupled with metagenomics and ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry, we find that Lachnospiraceae are high and phosphatidylcholine (PC) are low in MM patients. We further show that Lachnospiraceae inhibits PC production from MM cells and enhances cytotoxic CD8 T cell function. Mechanistically, PC promotes Sb9 mRNA maturation in MM cells by LIN28A/B via lysophosphatidic acid, thus enhances exosamal Sb9 production. Exosamal Sb9 then reduces GZMB expression by suppressing tumor protein p53 (TP53) UFMylation via the competitive binding of TP53 with the ubiquitin-fold modifier conjugating enzyme 1 in CD8 T cells. We thus show that Lachnospiraceae and PC may be potential therapeutic targets for MM treatment.},
}

Female
Animals
Mice
Humans
Cell Line
*T-Lymphocytes, Cytotoxic/immunology
*Gastrointestinal Microbiome
*Phosphatidylcholines/immunology/metabolism
*Multiple Myeloma/genetics/immunology/metabolism/pathology
RNA, Ribosomal, 16S/genetics
Metagenomics
*Exosomes/immunology/metabolism
*Serpins/genetics/immunology/metabolism
*Membrane Proteins/genetics/immunology/metabolism

@article {pmid39950811,
year = {2025},
author = {Kwon, J and Tanner, W and Kong, Y and Wade, M and Bitler, C and Chiavegato, MB and Pettigrew, MM},
title = {Prospective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems.},
journal = {mSphere},
volume = {10},
number = {3},
pages = {e0073824},
doi = {10.1128/msphere.00738-24},
pmid = {39950811},
issn = {2379-5042},
support = {20-006612//Greenacres Foundation/ ; },
mesh = {Animals ; Cattle ; *Animal Feed/analysis ; *Edible Grain/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Bacteria/classification/drug effects/genetics/isolation & purification ; *Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; Gastrointestinal Tract/microbiology ; Diet/veterinary ; Poaceae/microbiology ; Prospective Studies ; Animal Husbandry/methods ; Drug Resistance, Bacterial/genetics ; Male ; Female ; },
abstract = {Most antimicrobials sold in the United States are used in food animals. Farm management practices contribute to antibacterial resistance (AR). Controversially, grass-fed diets have been recommended over grain-fed diets to reduce AR in beef cattle. Ionophore feed additives (non-therapeutic antibiotics that enhance feed efficiency) may contribute to AR development. We used shotgun metagenomic sequencing of fecal swabs to prospectively compare the cattle gastrointestinal resistome and microbiota in two different production systems over five periods from pre-weaning to pre-harvest. Cattle were grass-fed and pasture-raised (system A, n = 33) or grain-fed with ionophore additives in feedlots (system B, n = 34). System A cattle averaged 639 lb and 22.8 months of age, and system B cattle averaged 1,173 lb and 12.4 months of age preharvest. In total, 367 antibiotic resistance genes (ARGs) and 329 bacterial species were identified. The resistome of system A cattle had higher alpha diversity than system B cattle over their lifespan (P = 0.008). Beta-diversity estimates indicated overlap in the pre-weaning resistome and microbiota in both systems, which diverged post-weaning, with increases in several medically important ARGs when system B cattle transitioned to a grain diet. Analysis of compositions of microbiomes with bias correction indicated that levels of tetracycline, macrolide, aminoglycoside, beta-lactam, and bacitracin ARGs were significantly higher in system B cattle pre-harvest. Resistome changes were highly correlated with bacterial community changes (Procrustes, M[2] = 0.958; P = 0.001). Potentially modifiable farm management strategies, including diet and ionophores, may influence abundance and diversity of ARGs in fecal samples from cattle.IMPORTANCEAntibiotic resistance is a One Health threat. More antibiotics are used in agriculture than in human medicine. We compared the relative abundance of antibiotic resistance genes (ARGs) and bacterial species in cattle raised in two different cattle production systems (grass- and grain-fed). Fecal swab samples were collected at five time points spanning pre-weaning and prior to harvest. The antibiotic resistance gene and bacterial communities were relatively similar in the pre-weaning period when cattle in both systems were milking and on pasture. Resistance genes and bacterial communities diverged post-weaning when system B cattle were given a grain diet with feed additives for growth promotion containing non-medically important antibiotics (i.e., ionophores). The levels of medically important ARGs (e.g., macrolides) increased in system B grain-fed cattle post-weaning and were higher than in system A just prior to slaughter. These data provide additional evidence that farm management strategies impact the level of antibiotic resistance.},
}

Animals
Cattle
*Animal Feed/analysis
*Edible Grain/microbiology
*Gastrointestinal Microbiome/drug effects/genetics
*Bacteria/classification/drug effects/genetics/isolation & purification
*Feces/microbiology
*Anti-Bacterial Agents/pharmacology
Gastrointestinal Tract/microbiology
Diet/veterinary
Poaceae/microbiology
Prospective Studies
Animal Husbandry/methods
Drug Resistance, Bacterial/genetics
Male
Female

@article {pmid39945541,
year = {2025},
author = {Lapid, R and Motro, Y and Craddock, H and Salah, I and King, R and Winner, K and Kahila Bar-Gal, G and Moran-Gilad, J},
title = {Abundance of clinically relevant antimicrobial resistance genes in the golden jackal (Canis aureus) gut.},
journal = {mSphere},
volume = {10},
number = {3},
pages = {e0081924},
doi = {10.1128/msphere.00819-24},
pmid = {39945541},
issn = {2379-5042},
mesh = {Animals ; *Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Gastrointestinal Microbiome/genetics ; beta-Lactamases/genetics ; Metagenomics ; Genes, Bacterial/genetics ; Israel ; Bacteria/genetics/drug effects/classification/isolation & purification ; },
abstract = {UNLABELLED: The spread of antimicrobial resistance (AMR) is a critical One Health issue. Wildlife could act as reservoirs or vehicles of AMR bacteria (ARBs) and AMR genes (ARGs) but are relatively understudied. We sought to investigate clinically relevant ARGs in golden jackals (Canis aureus) thriving near human settlements in Israel. Fecal samples were collected from 111 jackals across four regions over a 10-month period. Various animal and spatio-temporal metadata were collected. Samples were analyzed by quantitative PCR (qPCR) for beta-lactamases (blaTEM, blaCTX-M15, and blaSHV), qnrS and int1. A subset of samples was subject to shotgun metagenomic sequencing followed by resistome and microbiome analyses. qPCR detected a high prevalence of ARGs, including beta-lactamases (blaTEM-1, 96.4%; blaCTX-M-15, 51.4%, blaSHV, 15.3%), fluoroquinolone resistance (qnrS, 87.4%), and class 1 integrons (Int1, 94.6%). The blaTEM-1 gene was found to be more prevalent in adult jackals compared to younger ones. Metagenomic analysis of a subset of samples revealed a diverse gut microbiome harboring a rich resistome with tetracycline resistance genes being the most prevalent. Metagenome-assembled genome analysis further identified several ARGs associated with clinically relevant bacteria. These findings highlight the potential role of golden jackals as reservoirs for AMR and emphasize the need for ongoing surveillance to better understand AMR transmission dynamics at the wildlife-human interface.

IMPORTANCE: The research highlights the potential role of the golden jackals as reservoirs for antimicrobial resistance (AMR). The high prevalence of clinically relevant AMR genes in these jackals emphasizes the need for ongoing surveillance and monitoring to better understand AMR transmission dynamics at the wildlife-human interface.},
}

Animals
*Feces/microbiology
*Drug Resistance, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
Gastrointestinal Microbiome/genetics
beta-Lactamases/genetics
Metagenomics
Genes, Bacterial/genetics
Israel
Bacteria/genetics/drug effects/classification/isolation & purification

@article {pmid40124740,
year = {2025},
author = {Brucato, N and Lisant, V and Kinipi, C and Kik, A and Besnard, G and Leavesley, M and Ricaut, FX},
title = {Influence of betel nut chewing on oral microbiome in Papua New Guinea.},
journal = {Evolution, medicine, and public health},
volume = {13},
number = {1},
pages = {36-44},
doi = {10.1093/emph/eoae030},
pmid = {40124740},
issn = {2050-6201},
abstract = {BACKGROUND AND OBJECTIVES: For thousands of years, betel nut has been used as a psychoactive agent in Asian and Oceanian populations. Betel nut chewing was associated with the alteration of human oral microbiome and with diseases such as oral cancer and periodontitis, but only in populations of Asian cultural background. We studied the influence of betel nut chewing on the oral microbiome in Papua New Guinea, where half of the population uses betel nut and the prevalence of these diseases is one of the highest in the world.

METHODOLOGY: We characterized the oral microbiomes of 100 Papua New Guineans. We defined two cohorts of betel chewers (n = 50) and non-chewers (n = 50) based on a genetic approach to identify the presence of betel nut in saliva. We statistically compared the alpha and beta microbial diversities between the two cohorts. We performed linear discriminant analyses to identify bacterial species more prevalent in each cohort.

RESULTS: We found that oral microbial diversity is significantly different between betel chewers and non-chewers. The dysbiosis observed in betel chewers, led to an increase of pathogenic bacterial species including Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, known to be in the aetiology of periodontal diseases.

CONCLUSIONS AND IMPLICATIONS: Our study strongly supports the alteration of human oral microbiome by betel nut use, potentially leading to periodontal diseases. It also shows the need to consider local specificities (e.g. different habits, betel nut types, and oral microbial diversities) to better characterize the impact of betel nut chewing on health.},
}

@article {pmid40122890,
year = {2025},
author = {Nori, SRC and Walsh, CJ and McAuliffe, FM and Moore, RL and Van Sinderen, D and Feehily, C and Cotter, PD},
title = {Strain-level variation among vaginal Lactobacillus crispatus and Lactobacillus iners as identified by comparative metagenomics.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {49},
pmid = {40122890},
issn = {2055-5008},
support = {H2020-MSCA-COFUND-2019-945385//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)/ ; 18/CRT/6214//Science Foundation Ireland (SFI)/ ; },
mesh = {Female ; *Vagina/microbiology ; Humans ; *Lactobacillus/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Lactobacillus crispatus/genetics/isolation & purification ; Pregnancy ; Microbiota ; Ireland ; Host Microbial Interactions ; Metagenome ; Genome, Bacterial ; Gardnerella vaginalis/genetics/isolation & purification/classification ; },
abstract = {The vaginal microbiome, a relatively simple, low diversity ecosystem crucial for female health, is often dominated by Lactobacillus spp. Detailed strain-level data, facilitated by shotgun sequencing, can provide a greater understanding of the mechanisms of colonization and host-microbe interactions. We analysed 354 vaginal metagenomes from pregnant women in Ireland to investigate metagenomic community state types and strain-level variation, focusing on cell surface interfaces. Our analysis revealed multiple subspecies, with Lactobacillus crispatus and Lactobacillus iners being the most dominant. We found genes, including putative mucin-binding genes, distinct to L. crispatus subspecies. Using 337 metagenome-assembled genomes, we observed a higher number of strain-specific genes in L. crispatus related to cell wall biogenesis, carbohydrate and amino acid metabolism, many under positive selection. A cell surface glycan gene cluster was predominantly found in L. crispatus but absent in L. iners and Gardnerella vaginalis. These findings highlight strain-specific factors associated with colonisation and host-microbe interactions.},
}

Female
*Vagina/microbiology
Humans
*Lactobacillus/genetics/classification/isolation & purification
*Metagenomics/methods
*Lactobacillus crispatus/genetics/isolation & purification
Pregnancy
Microbiota
Ireland
Host Microbial Interactions
Metagenome
Genome, Bacterial
Gardnerella vaginalis/genetics/isolation & purification/classification

@article {pmid40037293,
year = {2025},
author = {Delherbe, NA and Gomez, O and Plominsky, AM and Oliver, A and Manzanera, M and Kalyuzhnaya, MG},
title = {Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf026},
pmid = {40037293},
issn = {1751-7370},
support = {DE-SC0024289//U.S. Department of Energy/ ; },
mesh = {*Methane/metabolism ; *Soil Microbiology ; California ; *Microbiota ; Metagenomics ; Ecosystem ; Desert Climate ; Metagenome ; Bacteria/genetics/classification/isolation & purification/metabolism ; Plants/microbiology ; Phylogeny ; Atmosphere ; },
abstract = {Drylands cover one-third of the Earth's surface and are one of the largest terrestrial sinks for methane. Understanding the structure-function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors-water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 and 12.73 μmol m2 h-1, peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum, two Methylobacter, and uncultivated Methylococcaceae). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum. Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.},
}

*Methane/metabolism
*Soil Microbiology
California
*Microbiota
Metagenomics
Ecosystem
Desert Climate
Metagenome
Bacteria/genetics/classification/isolation & purification/metabolism
Plants/microbiology
Phylogeny
Atmosphere

@article {pmid39961017,
year = {2025},
author = {Colman, DR and Templeton, AS and Spear, JR and Boyd, ES},
title = {Microbial ecology of serpentinite-hosted ecosystems.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf029},
pmid = {39961017},
issn = {1751-7370},
support = {80NSSC21K0489//NASA Exobiology and Evolutionary Biology program/ ; },
mesh = {*Ecosystem ; *Microbiota ; Hydrothermal Vents/microbiology ; Bacteria/genetics/classification/metabolism ; Metagenomics ; Seawater/microbiology ; Geologic Sediments/microbiology ; },
abstract = {Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.},
}

*Ecosystem
*Microbiota
Hydrothermal Vents/microbiology
Bacteria/genetics/classification/metabolism
Metagenomics
Seawater/microbiology
Geologic Sediments/microbiology

@article {pmid40121033,
year = {2025},
author = {Wong, MK and Boukhaled, GM and Armstrong, E and Liu, R and Heirali, AA and Yee, NR and Tsang, J and Spiliopoulou, P and Schneeberger, PHH and Wang, BX and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B},
title = {Microbial Ecosystem Therapeutics 4 (MET4) elicits treatment-specific IgG responses associated with changes in gut microbiota in immune checkpoint inhibitor recipients with advanced solid tumors.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {3},
pages = {},
doi = {10.1136/jitc-2024-010681},
pmid = {40121033},
issn = {2051-1426},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Neoplasms/immunology/drug therapy/therapy ; *Immunoglobulin G/blood/immunology ; Male ; Female ; Middle Aged ; Aged ; },
abstract = {BACKGROUND: Gut microbiome modulation has shown promise in its potential to treat cancer in combination with immunotherapy. Mechanistically, the pathways and routes by which gut microbiota may influence systemic and antitumor immunity remain uncertain. Here, we used blood and stool samples from Microbial Ecosystem Therapeutic 4 (MET4)-IO, an early-phase trial testing the safety and engraftment of the MET4 bacterial consortium in immune checkpoint inhibitor recipients, to assess how MET4 may affect systemic immunity.

METHODS: Circulating antibody responses induced by MET4 were assessed using an antimicrobial antibody flow cytometry assay on pretreatment and post-treatment plasma. Antibody responses were associated with taxonomic changes in stool identified by metagenomic sequencing. Mass cytometry was performed on peripheral blood mononuclear cells to identify shifts in circulating immune subsets associated with antibody responses.

RESULTS: Increases in circulating anti-MET4 immunoglobulin G (IgG) responses were measured by flow cytometry post-consortium treatment in MET4 recipients, but not untreated control participants, with five individuals displaying notably higher antibody responses. Stronger IgG responses were associated with greater increases in multiple taxa, including MET4 microbe Collinsella aerofaciens, which was previously linked with immune checkpoint response. However, these taxa were not enriched in the IgG-bound fraction post-MET4 treatment. Greater increases in circulating B cells and FoxP3[+] CD4[+] T cells post-MET4 treatment were observed in the blood of high IgG responders, while CD14[+] and CD16[+] monocyte populations were decreased in these individuals.

CONCLUSION: These results demonstrate the induction of treatment-specific circulating humoral immunity by a bacterial consortium and suggest potential mechanisms by which gut microbes may contribute to antitumor immunity.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Neoplasms/immunology/drug therapy/therapy
*Immunoglobulin G/blood/immunology
Male
Female
Middle Aged
Aged

@article {pmid40086306,
year = {2025},
author = {Russo, A and D'Alessandro, A and Di Paola, M and Cerasuolo, B and Renzi, S and Meriggi, N and Conti, L and Costa, J and Pogni, R and Martellini, T and Cincinelli, A and Ugolini, A and Cavalieri, D},
title = {On the role of bacterial gut microbiota from supralittoral amphipod Talitrus saltator (Montagu, 1808) in bioplastic degradation.},
journal = {The Science of the total environment},
volume = {972},
number = {},
pages = {179109},
doi = {10.1016/j.scitotenv.2025.179109},
pmid = {40086306},
issn = {1879-1026},
mesh = {Animals ; *Amphipoda/physiology ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical ; Plastics ; Bacteria ; Biodegradation, Environmental ; },
abstract = {Despite the promise of a reduced environmental impact, bioplastics are subjected to dispersion and accumulation similarly to traditional plastics, especially in marine and coastal environments. The environmental impact of bioplastics is attracting increasing attention due to the growing market demand. The ability of the supralittoral amphipod Talitrus saltator to ingest and survive on pristine starch-based bioplastic has already been assessed. However, the involvement of the gut microbiota of this key coastal species in making bioplastics a dietary supplement, remains unknown. In this study, we investigated the modification of T. saltator gut microbiota following bioplastic ingestion and the effect of this change on the modification of their chemical composition. Groups of adult amphipods were fed with: 1 - two different kinds of starch-based bioplastic; 2 - a 50 %/50 % chitosan-starch mixture; and 3 - paper and dry-fish-food. Freshly collected, unfed individuals were used as control group. Faecal pellets from the amphipods were collected and characterized using ATR-FTIR spectroscopy. DNA was extracted from gut samples for metagenomic analysis. Spectroscopic investigation suggested a partial digestion of polysaccharide components in the experimental polymeric materials. The analysis of the gut microbiota revealed that bioplastic feeding induced modification of sandhopper's gut microbial communities, shifting the abundance of specific microbial genera already present in the gut, towards bacterial genera associated with plastic/bioplastic degradation, especially in groups fed with starch-based bioplastics. Overall, our results highlight the involvement of T. saltator's gut microbiota in bioplastic modification, providing new insights into the potential role of microbial consortia associated to sandhoppers in bioplastic management.},
}

Animals
*Amphipoda/physiology
*Gastrointestinal Microbiome/drug effects
*Water Pollutants, Chemical
Plastics
Bacteria
Biodegradation, Environmental

@article {pmid39983413,
year = {2025},
author = {Li, Q and Li, H and Tian, L and Wang, Y and Ouyang, Z and Li, L and Mao, Y},
title = {Genomic insights and metabolic pathways of an enriched bacterial community capable of degrading polyethylene.},
journal = {Environment international},
volume = {197},
number = {},
pages = {109334},
doi = {10.1016/j.envint.2025.109334},
pmid = {39983413},
issn = {1873-6750},
mesh = {*Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; *Polyethylene/metabolism ; *Metabolic Networks and Pathways ; Sewage/microbiology ; Metagenome ; Microbiota ; Genomics ; },
abstract = {In the face of mounting global plastic pollution, especially concerning microplastics, biodegradation must be a sustainable solution. The key factor driving this technology is to explore efficient plastic-biodegraders from different habitats, among which activated sludge (AS) may be an important option since it holds diverse microorganisms occupying various ecological niches. Here we intend to enrich the plastic-degrading microorganisms from AS by using polyethylene (PE) plastic as the carbon and energy source. After a 28-day incubation, the weight loss of PE films reached 3% and the hydrophobicity decreased, indicating physical biodegradation. Moreover, Fourier-transform infrared spectroscopy (FTIR) results showed the formation of several new oxygen-containing functional groups on PE. Microbial analysis extracted 26 metagenome-assembled genomes (MAGs) from the enriched microbial communities. Among them MAG10, MAG21 and MAG26 displayed the increased abundance upon PE addition and harbored abundant genes related to carbohydrate transport and metabolism, suggesting their potential to degrade PE. Additionally, functional analysis revealed 14 plastic degradation-related genes, including oxidase, laccase, and lipase, indicating the significant potential in plastic degradation. Furthermore, a pathway for synergistic biodegradation of PE was proposed based on the potential PE degradation genes retrieved from MAGs. This work offers a promising and sustainable solution to plastic pollution by enriching the potential biodegraders from AS.},
}

*Biodegradation, Environmental
*Bacteria/metabolism/genetics
*Polyethylene/metabolism
*Metabolic Networks and Pathways
Sewage/microbiology
Metagenome
Microbiota
Genomics

@article {pmid39985228,
year = {2025},
author = {Song, MJ and Freund, F and Tribble, CM and Toffelmier, E and Miller, C and Bradley Shaffer, H and Li, FW and Rothfels, CJ},
title = {The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal.},
journal = {American journal of botany},
volume = {112},
number = {3},
pages = {e70010},
doi = {10.1002/ajb2.70010},
pmid = {39985228},
issn = {1537-2197},
support = {//California Conservation Genomics Project, with funding provided to the University of California by the State of California, State Budget Act of 2019 [UC Award ID RSI-19-690224]./ ; },
mesh = {*Ferns/microbiology/genetics/physiology ; *Microbiota ; *Symbiosis ; *Nitrogen Fixation ; California ; },
abstract = {PREMISE: Azolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of transmission are unknown.

METHODS: We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes to identify the common bacterial endosymbionts and assess their patterns of interaction.

RESULTS: Four genera were found across all samples, establishing that multiple Azolla endosymbionts were consistently present. We found varying degrees of cophylogenetic signal across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which demonstrates that multiple processes underlie how this endosymbiotic community is constituted. We also characterized the entire Azolla leaf pocket microbiome.

CONCLUSIONS: These results show that the Azolla symbiotic community is complex and features members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.},
}

*Ferns/microbiology/genetics/physiology
*Microbiota
*Symbiosis
*Nitrogen Fixation
California

@article {pmid40117176,
year = {2025},
author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP},
title = {Healthy microbiome-moving towards functional interpretation.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf015},
pmid = {40117176},
issn = {2047-217X},
support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Metagenome ; Phylogeny ; Dysbiosis/microbiology ; Principal Component Analysis ; COVID-19/virology ; },
abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.

FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.

CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).},
}

Humans
*Gastrointestinal Microbiome/genetics
*Inflammatory Bowel Diseases/microbiology
*Metagenomics/methods
Metagenome
Phylogeny
Dysbiosis/microbiology
Principal Component Analysis
COVID-19/virology

@article {pmid40115125,
year = {2025},
author = {Pavloudi, C and Santi, I and Azua, I and Baña, Z and Bastianini, M and Belser, C and Bilbao, J and Bitz-Thorsen, J and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Daguin, C and Díaz de Cerio, O and Exter, K and Fauvelot, C and Frada, MJ and Galand, PE and Garczarek, L and González Fernández, J and Guillou, L and Hablützel, PI and Heynderickx, H and Houbin, C and Kervella, AE and Krystallas, A and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhaes, C and Maidanou, M and Margiotta, F and Montresor, M and Not, F and Paredes, E and Percopo, I and Péru, E and Poulain, J and Præbel, K and Rigaut-Jalabert, F and Romac, S and Stavroulaki, M and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Trano, AC and Wincker, P and Pade, N},
title = {First release of the European marine omics biodiversity observation network (EMO BON) shotgun metagenomics data from water and sediment samples.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e143585},
pmid = {40115125},
issn = {1314-2828},
abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is an initiative of the European Marine Biological Resource Centre (EMBRC) to establish a persistent genomic observatory amongst designated European coastal marine sites, sharing the same protocols for sampling and data curation. Environmental samples are collected from the water column and, at some sites, soft sediments and hard substrates (Autonomous Reef Monitoring Structures - ARMS), together with a set of mandatory and discretionary metadata (including Essential Ocean Variables - EOVs). Samples are collected following standardised protocols at regular and specified intervals and sequenced in large six-monthly batches at a centralised sequencing facility. The use of standard operating procedures (SOPs) during data collection, library preparation and sequencing aims to provide uniformity amongst the data collected from the sites. Coupled with strict adherence to open and FAIR (Findable, Accessible, Interoperable, Reusable) data principles, this ensures maximum comparability amongst samples and enhances reusability and interoperability of the data with other data sources. The observatory network was launched in June 2021, when the first sampling campaign took place.},
}

@article {pmid40115072,
year = {2025},
author = {Li, J and Hu, X and Tao, X and Li, Y and Jiang, W and Zhao, M and Ma, Z and Chen, B and Sheng, S and Tong, J and Zhang, H and Shen, B and Gao, X},
title = {Deconstruct the link between gut microbiota and neurological diseases: application of Mendelian randomization analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1433131},
pmid = {40115072},
issn = {2235-2988},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Nervous System Diseases/genetics/microbiology ; Brain-Gut Axis ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: Recent research on the gut-brain axis has deepened our understanding of the correlation between gut bacteria and the neurological system. The inflammatory response triggered by gut microbiota may be associated with neurodegenerative diseases. Additionally, the impact of gut microbiota on emotional state, known as the "Gut-mood" relationship, could play a role in depression and anxiety disorders.

RESULTS: This review summarizes recent data on the role of gut-brain axis in the pathophysiology of neuropsychiatric and neurological disorders including epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke. Also, we conducted a Mendelian randomization study on seven neurological disorders (Epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke). MR-Egger and MR-PRESSO tests confirmed the robustness of analysis against horizontal pleiotropy.

CONCLUSIONS: By comparing the protective and risk factors for neurological disorders found in our research and other researches, we can furtherly determine valuable indicators for disease evolution tracking and potential treatment targets. Future research should explore extensive microbiome genome-wide association study datasets using metagenomics sequencing techniques to deepen our understanding of connections and causality between neurological disorders.},
}

Humans
*Mendelian Randomization Analysis
*Gastrointestinal Microbiome/genetics
*Nervous System Diseases/genetics/microbiology
Brain-Gut Axis
Genome-Wide Association Study

@article {pmid40114290,
year = {2025},
author = {Demina, T and Marttila, H and Pessi, IS and Männistö, MK and Dutilh, BE and Roux, S and Hultman, J},
title = {Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {79},
pmid = {40114290},
issn = {2049-2618},
mesh = {*Soil Microbiology ; *Genome, Viral ; *Virome ; *Tundra ; *Phylogeny ; *Metagenome ; Arctic Regions ; Finland ; Bacteriophages/genetics/classification/isolation & purification ; Acidobacteria/genetics/classification/isolation & purification ; Soil ; DNA, Viral/genetics ; },
abstract = {BACKGROUND: Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils.

RESULTS: Five virus isolates, Tunturi 1-5, were obtained from Arctic tundra soils, Kilpisjärvi, Finland (69°N), using Tunturiibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63-98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjärvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjärvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between the Tunturi viruses, Kilpisjärvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils.

CONCLUSIONS: This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic. Video Abstract.},
}

*Soil Microbiology
*Genome, Viral
*Virome
*Tundra
*Phylogeny
*Metagenome
Arctic Regions
Finland
Bacteriophages/genetics/classification/isolation & purification
Acidobacteria/genetics/classification/isolation & purification
Soil
DNA, Viral/genetics

@article {pmid40114168,
year = {2025},
author = {Wu, Y and Qu, Z and Wu, Z and Zhuang, J and Wang, Y and Wang, Z and Chu, J and Qi, Q and Han, S},
title = {Multiple primary malignancies and gut microbiome.},
journal = {BMC cancer},
volume = {25},
number = {1},
pages = {516},
pmid = {40114168},
issn = {1471-2407},
support = {2022E50008, 2024ZY01056//Zhejiang Provincial Clinical Research Center for CANCER/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Metagenomics/methods ; *Neoplasms, Multiple Primary/microbiology/virology ; Colorectal Neoplasms/microbiology/virology ; Adult ; Aged ; Bacteria/classification/genetics/isolation & purification ; Enterovirus/isolation & purification/genetics ; Case-Control Studies ; Feces/microbiology/virology ; },
abstract = {BACKGROUND: Multiple primary malignancies (MPM) are two or more independent primary malignancies. Recently, the relationship between microbiome and various tumors has been gradually focused on.

OBJECTIVE: To describe the relationship between MPM patients (MPMs) and gut microbiome.

METHODS: A total of 27 MPMs, 30 colorectal cancer patients (CRCs), and 30 healthy individuals were included to obtain metagenomic sequencing data. The knowledge graphs of gut bacteria and enteroviruses were plotted based on metagenomics. Wilcoxon rank-sum test was used to screen the characteristic gut microbiome.

RESULTS: The knowledge graph of gut microbiome in MPM patients was plotted. A total of 26 different gut bacteria, including Dialister, Fecalibacterium and Mediterraneibacter, were found between MPMs and healthy individuals. Twenty gut bacteria, including Parvimonas, Dialister and Mediterraneibacter, were more abundant in MPM complicated by CRC compared with CRCs. Twenty-one different enterovirus, including Triavirus, Punavirus and Lilyvirus, were screened between MPMs and healthy individuals. Triavirus, Punavirus and Lilyvirus were less abundant in MPM than healthy individuals. The abundance of Triavirus, Punavirus and Lilyvirus in CRC patients were also lower than MPM complicated by CRC patients.

CONCLUSION: The knowledge graph of gut microbiome in MPM patients was plotted. It may provide basic data support for future research of MPM.},
}

Humans
*Gastrointestinal Microbiome
Female
Male
Middle Aged
*Metagenomics/methods
*Neoplasms, Multiple Primary/microbiology/virology
Colorectal Neoplasms/microbiology/virology
Adult
Aged
Bacteria/classification/genetics/isolation & purification
Enterovirus/isolation & purification/genetics
Case-Control Studies
Feces/microbiology/virology

@article {pmid40037607,
year = {2025},
author = {Antaliya, K and Godhaniya, M and Galawala, J and Vansia, A and Mangrola, A and Ghelani, A and Patel, R},
title = {Microbial community transition in Surti buffalo-based fermented formulations sustainably enhances soil fertility and plant growth.},
journal = {Letters in applied microbiology},
volume = {78},
number = {3},
pages = {},
doi = {10.1093/lambio/ovaf030},
pmid = {40037607},
issn = {1472-765X},
support = {GSBTM/JD(R&D)661/2022-2023/00172813//Gujarat State Biotechnology Mission/ ; },
mesh = {*Soil Microbiology ; Animals ; *Fermentation ; *Soil/chemistry ; *Buffaloes/growth & development ; Microbiota ; Fertilizers/analysis ; Bacteria/classification/genetics/metabolism/growth & development/isolation & purification ; Plant Development ; Vigna/growth & development/microbiology ; },
abstract = {This study investigates the role of microbial dynamics during the fermentation of buffalo dung and urine-fermented plant growth-promoting formulation, a natural biofertilizer, and its impact on plant growth and soil health. This formulation was prepared using Surti buffalo dung, urine, jaggery, gram flour, and soil and fermented for up to 14 days. Metagenomic analysis revealed microbial succession from a diverse initial community to a Bacillus-dominated population, especially the Lactic Acid Bacteria, after 8 days of fermentation. The changes were accompanied by increases in the plant growth-promoting genes related to nutrient acquisition, phytohormone production, and stress resistance. The pot experiment revealed a significant increase in mung bean growth, with the maximum effect obtained from the eighth-day fermented formulation. The experiment showed considerable improvement in the physicochemical properties of soil, including increased organic carbon and nutrient availability. These findings underscore the ecological importance of microbial input preparation in enhancing soil fertility and plant growth sustainably. Future research should delve deeper into the specific mechanisms these microbes facilitate nutrient cycling and resilience in various agroclimatic conditions.},
}

*Soil Microbiology
Animals
*Fermentation
*Soil/chemistry
*Buffaloes/growth & development
Microbiota
Fertilizers/analysis
Bacteria/classification/genetics/metabolism/growth & development/isolation & purification
Plant Development
Vigna/growth & development/microbiology

@article {pmid39999339,
year = {2025},
author = {Hohmann, M and Iliasov, D and Larralde, M and Johannes, W and Janßen, KP and Zeller, G and Mascher, T and Gulder, TAM},
title = {Heterologous Expression of a Cryptic BGC from Bilophila sp. Provides Access to a Novel Family of Antibacterial Thiazoles.},
journal = {ACS synthetic biology},
volume = {14},
number = {3},
pages = {967-978},
doi = {10.1021/acssynbio.5c00042},
pmid = {39999339},
issn = {2161-5063},
mesh = {*Thiazoles/metabolism ; *Anti-Bacterial Agents/pharmacology ; Humans ; Gastrointestinal Microbiome/drug effects ; Multigene Family ; Siderophores/metabolism ; },
abstract = {Human health is greatly influenced by the gut microbiota and microbiota imbalance can lead to the development of diseases. It is widely acknowledged that the interaction of bacteria within competitive ecosystems is influenced by their specialized metabolites, which act, e.g., as antibacterials or siderophores. However, our understanding of the occurrence and impact of such natural products in the human gut microbiome remains very limited. As arylthiazole siderophores are an emerging family of growth-promoting molecules in pathogenic bacteria, we analyzed a metagenomic data set from the human microbiome and thereby identified the bil-BGC, which originates from an uncultured Bilophila strain. Through gene synthesis and BGC assembly, heterologous expression and mutasynthetic experiments, we discovered the arylthiazole natural products bilothiazoles A-F. While established activities of related molecules indicate their involvement in metal-binding and -uptake, which could promote the growth of pathogenic strains, we also found antibiotic activity for some bilothiazoles. This is supported by biosensor-experiments, where bilothiazoles C and E show PrecA-suppressing activity, while bilothiazole F induces PblaZ, a biosensor characteristic for β-lactam antibiotics. These findings serve as a starting point for investigating the role of bilothiazoles in the pathogenicity of Bilophila species in the gut.},
}

*Thiazoles/metabolism
*Anti-Bacterial Agents/pharmacology
Humans
Gastrointestinal Microbiome/drug effects
Multigene Family
Siderophores/metabolism

@article {pmid39864798,
year = {2025},
author = {Nehra, C and Harshini, V and Shukla, N and Chavda, P and Bhure, M and Savaliya, K and Patil, S and Shah, T and Pandit, R and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Joshi, M and Joshi, CG},
title = {Ruminal microbial responses to Moringa oleifera feed in lactating goats (Capra hircus): A metagenomic exploration.},
journal = {New biotechnology},
volume = {86},
number = {},
pages = {87-96},
doi = {10.1016/j.nbt.2025.01.006},
pmid = {39864798},
issn = {1876-4347},
mesh = {Animals ; *Goats/microbiology ; *Moringa oleifera ; *Lactation/drug effects ; *Animal Feed ; *Metagenomics ; *Rumen/microbiology/metabolism ; Female ; Bacteria/genetics/metabolism/classification ; Milk/metabolism/microbiology ; Gastrointestinal Microbiome/drug effects ; },
abstract = {The purpose of the current study was to explore the effects of Moringa oleifera feed on the taxonomy and function of the rumen microbial community, and further to evaluate its impact on milk yield and body weight in lactating goats. Nineteen goats were divided into moringa leaf diet (ML; n = 10) and masoor straw (MS; n = 9) groups. For each group fortnight milk yield and body weight was recorded. Rumen solid and liquid fraction samples were processed for metagenomic shotgun sequencing and further analysed. The pairwise comparison between the two groups showed a significant increase (p-value- <0.01) in milk yield of the ML goats after the 4th fortnight interval onwards. The metagenomic analysis revealed Bacteroidetes and Firmicutes are the most abundant phyla, with increased Bacteroidetes in response to the moringa diet. The ML group exhibited a reduction in microbial diversity, with an increase in Prevetolla and Bacteroidales populations which are positively associated with carbohydrate, protein, and VFA metabolism, and an increased proportions of Treponema sp., Ruminococcus sp., Ruminobacter amylophilus, and Aeromonas, indicating improved cellulose and nitrogen metabolism. KEGG analysis revealed significant changes in microbial gene pool and metabolic pathways, particularly in carbohydrate metabolism, propanoate metabolism, and fatty acid synthesis genes. These microbial and functional shifts are correlated with improvements in milk yield, growth rates, and potentially reduced methane emissions.This study highlighted the potential benefits of feeding moringa in the animal production system. However, furthermore experimental evidence including genetic and environmental effects is needed for a comprehensive understanding of moringa feed's impact on goat health and productivity.},
}

Animals
*Goats/microbiology
*Moringa oleifera
*Lactation/drug effects
*Animal Feed
*Metagenomics
*Rumen/microbiology/metabolism
Female
Bacteria/genetics/metabolism/classification
Milk/metabolism/microbiology
Gastrointestinal Microbiome/drug effects

@article {pmid38735389,
year = {2025},
author = {Tan, X and Wu, J and Zhang, H and Li, Y and Huang, Y and Zheng, P and Xie, P},
title = {Biogeography of intestinal mucus-associated microbiome: Depletion of genus Pseudomonas is associated with depressive-like behaviors in female cynomolgus macaques.},
journal = {Journal of advanced research},
volume = {70},
number = {},
pages = {393-404},
doi = {10.1016/j.jare.2024.05.013},
pmid = {38735389},
issn = {2090-1224},
mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; *Depression/microbiology ; *Macaca fascicularis/microbiology ; *Pseudomonas ; Dysbiosis/microbiology ; Intestinal Mucosa/microbiology/metabolism ; Behavior, Animal ; Mucus/metabolism/microbiology ; },
abstract = {INTRODUCTION: Depression is a debilitating and poorly understood mental disorder. There is an urgency to explore new potential biological mechanisms of depression and the gut microbiota is a promising research area.

OBJECTIVES: Our study was aim to understand regional heterogeneity and potential molecular mechanisms underlying depression induced by dysbiosis of mucus-associated microbiota.

METHODS: Here, we only selected female macaques because they are more likely to form a natural social hierarchy in a harem-like environment. Because high-ranking macaques rarely displayed depressive-like behaviors, we selected seven monkeys from high-ranking individuals as control group (HC) and the same number of low-ranking ones as depressive-like group (DL), which displayed significant depressive-like behaviors. Then, we collected mucus from the duodenum, jejunum, ileum, cecum and colon of DL and HC monkeys for shotgun metagenomic sequencing, to profile the biogeography of mucus-associated microbiota along duodenum to colon.

RESULTS: Compared with HC, DL macaques displayed noticeable depressive-like behaviors such as longer duration of huddle and sit alone behaviors (negative emotion behaviors), and fewer duration of locomotion, amicable and ingestion activities (positive emotion behaviors). Moreover, the alpha diversity index (Chao) could predict aforementioned depressive-like behaviors along duodenum to colon. Further, we identified that genus Pseudomonas was consistently decreased in DL group throughout the entire intestinal tract except for the jejunum. Specifically, there were 10, 18 and 28 decreased Pseudomonas spp. identified in ileum, cecum and colon, respectively. Moreover, a bacterial module mainly composed of Pseudomonas spp. was positively associated with three positive emotion behaviors. Functionally, Pseudomonaswas mainly involved in microbiota derived lipid metabolisms such as PPAR signaling pathway, cholesterol metabolism, and fat digestion and absorption.

CONCLUSION: Different regions of intestinal mucus-associated microbiota revealed that depletion of genus Pseudomonas is associated with depressive-like behaviors in female macaques, which might induce depressive phenotypes through regulating lipid metabolism.},
}

Animals
Female
*Gastrointestinal Microbiome
*Depression/microbiology
*Macaca fascicularis/microbiology
*Pseudomonas
Dysbiosis/microbiology
Intestinal Mucosa/microbiology/metabolism
Behavior, Animal
Mucus/metabolism/microbiology

@article {pmid40111684,
year = {2025},
author = {de Barros Santos, HS and Pagnussatti, MEL and Arthur, RA},
title = {Symbiosis Between the Oral Microbiome and the Human Host: Microbial Homeostasis and Stability of the Host.},
journal = {Advances in experimental medicine and biology},
volume = {1472},
number = {},
pages = {31-51},
pmid = {40111684},
issn = {0065-2598},
mesh = {Humans ; *Symbiosis ; *Mouth/microbiology ; *Microbiota/physiology ; *Homeostasis ; *Host Microbial Interactions ; Bacteria/metabolism/genetics/classification ; Metagenomics/methods ; Oral Health ; },
abstract = {The oral cavity presents a highly diverse microbial composition. All the three domains of life, Bacteria, Eukarya, and Archaea, as well as viruses constitute the oral microbiome. Bacteria are among the most abundant microorganisms in the oral cavity, followed by viruses, fungi, and Archaea. These microorganisms tend to live in harmony with each other and with the host by preventing the colonization of oral sites by exogenous microorganisms. Interactions between the host and its microbiota are crucial for keeping ecological stability in the oral cavity and a condition compatible with oral health. This chapter focuses on describing the oral microbiota in healthy individuals based on both targeted and nontargeted genome sequencing methods and the functional activity played by those microorganisms based on metagenomic, metatranscriptomic, metaproteomic, and metabolomic analyses. Additionally, this chapter explores mutualistic and antagonistic microbe-microbe relationships. These interactions are mediated by complex mechanisms like cross-feeding networks, production of bacteriocins and secondary metabolites, synthesis of pH-buffering compounds, and the use of universal signaling molecules. At last, the role played by host-microbe interactions on colonization resistance and immune tolerance will help provide a better understanding about the harmonious and peaceful coexistence among host and microbial cells under oral health-related conditions.},
}

Humans
*Symbiosis
*Mouth/microbiology
*Microbiota/physiology
*Homeostasis
*Host Microbial Interactions
Bacteria/metabolism/genetics/classification
Metagenomics/methods
Oral Health

@article {pmid40108202,
year = {2025},
author = {Redgwell, TA and Thorsen, J and Petit, MA and Deng, L and Vestergaard, G and Russel, J and Chawes, B and Bønnelykke, K and Bisgaard, H and Nielsen, DS and Sørensen, S and Stokholm, J and Shah, SA},
title = {Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {46},
pmid = {40108202},
issn = {2055-5008},
mesh = {*Gastrointestinal Microbiome ; *Prophages/genetics/physiology ; Humans ; Infant ; *Metagenome ; Virome ; Female ; Feces/microbiology/virology ; Bacteria/genetics/classification/virology ; Bacteroides/genetics/virology ; },
abstract = {Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.},
}

*Gastrointestinal Microbiome
*Prophages/genetics/physiology
Humans
Infant
*Metagenome
Virome
Female
Feces/microbiology/virology
Bacteria/genetics/classification/virology
Bacteroides/genetics/virology

@article {pmid40056581,
year = {2025},
author = {Wu, Y and Xu, L and He, F and Song, X and Ding, J and Ma, J},
title = {Effects of micro-magnetite on anaerobic co-digestion of waste activated sludge and slaughterhouse waste: Microbial community and metabolism analyses.},
journal = {Journal of environmental management},
volume = {379},
number = {},
pages = {124896},
doi = {10.1016/j.jenvman.2025.124896},
pmid = {40056581},
issn = {1095-8630},
mesh = {*Sewage/microbiology ; Anaerobiosis ; *Abattoirs ; *Ferrosoferric Oxide/metabolism ; *Methane/metabolism ; Bacteria/metabolism ; Bioreactors ; Microbiota ; },
abstract = {Micro-magnetite has been widely applied to improve anaerobic digestion (AD) performance, while comprehensive investigation of microbial community succession, metabolic pathway and magnetite fate remains unclear. In the current study, the effects of micro-magnetite (Fe3O4) on anaerobic co-digestion (AcD) of waste activated sludge and slaughterhouse waste were investigated. Experimental results indicated that the cumulative methane production was significantly increased from 484.6 mL/g VS to 524.4 mL/g VS with 0.8 g/L Fe3O4 addition. Recycled magnetite remained the initial physicochemical properties, including morphology, particle size and crystal structure, as evidenced by various characterization methods. Microbial community analysis indicated that magnetite addition enriched syntrophic bacteria (Armatimonadota, Syntrophomonas and Petrimonas) and methanogens (Methanosarcina). Metagenomic sequencing analysis demonstrated that hydrolysis and acidogenesis metabolic pathways were reinforced by magnetite addition. Meanwhile, the magnetite stimulated the direct interspecies electron transfer via enriching syntrophic microbes (Syntrophomonas and Methanosarcina) and conductive pili functional genes (pilA, mshA and mshC), finally achieving higher cumulative methane yield. This study provided in-depth investigation of the methane production facilitated by micro-magnetite addition and the magnetite fate during the AcD process.},
}

*Sewage/microbiology
Anaerobiosis
*Abattoirs
*Ferrosoferric Oxide/metabolism
*Methane/metabolism
Bacteria/metabolism
Bioreactors
Microbiota

@article {pmid39946816,
year = {2025},
author = {Laredo-Tiscareño, SV and Garza-Hernandez, JA and Tangudu, CS and Dankaona, W and Rodríguez-Alarcón, CA and Gonzalez-Peña, R and Adame-Gallegos, JR and Beristain-Ruiz, DM and Barajas-López, IN and Hargett, AM and Munderloh, UG and Blitvich, BJ},
title = {Detection of multiple novel viruses in argasid and ixodid ticks in Mexico.},
journal = {Ticks and tick-borne diseases},
volume = {16},
number = {2},
pages = {102455},
doi = {10.1016/j.ttbdis.2025.102455},
pmid = {39946816},
issn = {1877-9603},
mesh = {Animals ; Mexico ; *Argasidae/virology ; Ixodidae/virology ; Virome ; Viruses/classification/isolation & purification/genetics ; Metagenomics ; },
abstract = {We examined ticks from Mexico using viral metagenomics to increase our understanding of the composition and diversity of the tick virome. The analysis was performed using 3,127 ticks of four Ixodidae spp. and one Argasidae spp. collected in 2019 to 2021 from domestic animals in four states of Mexico (Chiapas, Chihuahua, Guerrero, and Michoacán). All ticks were homogenized and tested for viruses using two approaches. In the first approach, an aliquot of each homogenate underwent two blind passages in Ixodes scapularis (ISE6) cells. Supernatants from all second passage cultures were subjected to polyethylene glycol (PEG) precipitation to enrich for virions then RNAs were extracted from the precipitates and analyzed by unbiased high-throughput sequencing (UHTS). In the second approach, an aliquot of every homogenate was subjected to PEG precipitation then RNAs were extracted and analyzed by UHTS, allowing for the detection of viruses unable to replicate in ISE6 cells. We identified seven novel species of viruses from multiple taxonomic groups (Bunyavirales, Flaviviridae, Nodaviridae, Nyamivirdae, Rhabdoviridae, Solemoviridae, and Totiviridae), some of which are highly divergent from all classified viruses and cannot be assigned to any established genus. Twelve recognized species of viruses were also identified. In summary, multiple novel and recognized viruses were detected in ticks from Mexico, highlighting the remarkable diversity of the tick virome.},
}

Animals
Mexico
*Argasidae/virology
Ixodidae/virology
Virome
Viruses/classification/isolation & purification/genetics
Metagenomics

@article {pmid39377977,
year = {2025},
author = {Tufail, MA and Schmitz, RA},
title = {Exploring the Probiotic Potential of Bacteroides spp. Within One Health Paradigm.},
journal = {Probiotics and antimicrobial proteins},
volume = {17},
number = {2},
pages = {681-704},
pmid = {39377977},
issn = {1867-1314},
support = {031B0846D//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Probiotics ; Humans ; *Bacteroides/genetics ; *Gastrointestinal Microbiome ; One Health ; Animals ; },
abstract = {Probiotics are pivotal in maintaining or restoring the balance of human intestinal microbiota, a crucial factor in mitigating diseases and preserving the host's health. Exploration into Bacteroides spp. reveals substantial promise in their development as next-generation probiotics due to their profound interaction with host immune cells and capability to regulate the microbiome's metabolism by significantly impacting metabolite production. These beneficial bacteria exhibit potential in ameliorating various health issues such as intestinal disorders, cardiovascular diseases, behavioral disorders, and even cancer. Though it's important to note that a high percentage of them are as well opportunistic pathogens, posing risks under certain conditions. Studies highlight their role in modifying immune responses and improving health conditions by regulating lymphocytes, controlling metabolism, and preventing inflammation and cancer. The safety and efficacy of Bacteroides strains are currently under scrutiny by the European Commission for authorization in food processing, marking a significant step towards their commercialization. The recent advancements in bacterial isolation and sequencing methodologies, coupled with the integration of Metagenome-Assembled Genomes (MAGs) binning from metagenomics data, continue to unveil the potential of Bacteroides spp., aiding in the broader understanding and application of these novel probiotics in health and disease management.},
}

*Probiotics
Humans
*Bacteroides/genetics
*Gastrointestinal Microbiome
One Health
Animals

@article {pmid38214674,
year = {2025},
author = {Zhang, H and Zhang, H and Du, H and Yu, X and Xu, Y},
title = {The insights into the phage communities of fermented foods in the age of viral metagenomics.},
journal = {Critical reviews in food science and nutrition},
volume = {65},
number = {9},
pages = {1656-1668},
doi = {10.1080/10408398.2023.2299323},
pmid = {38214674},
issn = {1549-7852},
mesh = {*Bacteriophages/genetics/physiology ; *Metagenomics/methods ; *Fermented Foods/microbiology ; *Fermentation ; *Food Microbiology ; Microbiota ; Bacteria/virology/genetics/classification ; },
abstract = {Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.},
}

*Bacteriophages/genetics/physiology
*Metagenomics/methods
*Fermented Foods/microbiology
*Fermentation
*Food Microbiology
Microbiota
Bacteria/virology/genetics/classification

@article {pmid40102546,
year = {2025},
author = {Lechleiter, N and Wedemeyer, J and Schütz, A and Sehl-Ewert, J and Schaufler, K and Homeier-Bachmann, T},
title = {Metagenomic analysis of the faecal microbiota and AMR in roe deer in Western Pomerania.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {9288},
pmid = {40102546},
issn = {2045-2322},
mesh = {Animals ; *Deer/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; Escherichia coli/genetics/isolation & purification ; Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; Germany ; Metagenome ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; Anti-Bacterial Agents/pharmacology ; },
abstract = {As an integral part of the global wellbeing, the health of wild animals should be regarded just as important as that of humans and livestock. The investigation of wildlife health, however, is limited by the availability of samples. In an attempt to implement a method with little invasiveness and broad areas of application, shotgun metagenomics were utilised to investigate the faecal microbiome and its antimicrobial resistance genes (AMRG) in roe deer. These genes can facilitate antimicrobial resistances (AMR) in bacteria and are therefore of increasing importance in global health. Accordingly, the abundance in potential vectors like wildlife needs to be assessed. The samples were additionally investigated for ESBL-E. coli, an antibiotic resistant pathogen of global concern, via cultivation. Twenty-seven hunt-harvested animals in Western Pomerania were sampled. This study is the first to our knowledge to describe the faecal microbiome of the European roe deer (Capreolus capreolus), providing insights into the bacterial and archaeal composition. Among the animals, the microbiome was mostly similar and showed a comparable composition to what has been reported in related species, with a ratio of 1.76 between Bacillota and Bacteroidota. The normalised abundance of AMR genes was found to be 0.035 on average, which is similar to other investigations on wild ruminants. Selective cultivation found no ESBL-E. coli in the animals. The prevalence of AMRG in roe deer of Western Pomerania was found to be in line with previous results. The use of shotgun metagenomics allowed for the simultaneous investigation of composition and AMR genes in the faecal microbiome of roe deer, which suggests it as a promising method for the health monitoring of wildlife. This study is the first to describe the prokaryotic assemblage in the faeces of roe deer and its differences to the microbiomes published on other cervids were discussed.},
}

Animals
*Deer/microbiology
*Feces/microbiology
*Metagenomics/methods
Escherichia coli/genetics/isolation & purification
Microbiota/genetics
Drug Resistance, Bacterial/genetics
Germany
Metagenome
Gastrointestinal Microbiome/genetics
Bacteria/genetics/classification
Anti-Bacterial Agents/pharmacology

@article {pmid40102379,
year = {2025},
author = {Deng, L and Taelman, S and Olm, MR and Toe, LC and Balini, E and Ouédraogo, LO and Bastos-Moreira, Y and Argaw, A and Tesfamariam, K and Sonnenburg, ED and Hanley-Cook, GT and Ouédraogo, M and Ganaba, R and Van Criekinge, W and Huybregts, L and Stock, M and Kolsteren, P and Sonnenburg, JL and Lachat, C and Dailey-Chwalibóg, T},
title = {Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2683},
pmid = {40102379},
issn = {2041-1723},
support = {OPP1175213//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; *Dietary Supplements ; Infant ; Pregnancy ; Adult ; Burkina Faso ; *Carbohydrate Metabolism ; Infant, Newborn ; Feces/microbiology ; Dietary Proteins/metabolism ; Male ; Lactation ; },
abstract = {Balanced energy-protein (BEP) supplementation during pregnancy and lactation can improve birth outcomes and infant growth, with the gut microbiome as a potential mediator. The MISAME-III randomized controlled trial (ClinicalTrial.gov: NCT03533712) assessed the effect of BEP supplementation, provided during pregnancy and the first six months of lactation, on small-for-gestational age prevalence and length-for-age Z-scores at six months in rural Burkina Faso. Nested within MISAME-III, this sub-study examines the impact of BEP supplementation on maternal and infant gut microbiomes and their mediating role in birth outcomes and infant growth. A total of 152 mother-infant dyads (n = 71 intervention, n = 81 control) were included for metagenomic sequencing, with stool samples collected at the second and third trimesters, and at 1-2 and 5-6 months postpartum. BEP supplementation significantly altered maternal gut microbiome diversity, composition, and function, particularly those with immune-modulatory properties. Pathways linked to lipopolysaccharide biosynthesis were depleted and the species Bacteroides fragilis was enriched in BEP-supplemented mothers. Maternal BEP supplementation also accelerated infant microbiome changes and enhanced carbohydrate metabolism. Causal mediation analyses identified specific taxa mediating the effect of BEP on birth outcomes and infant growth. These findings suggest that maternal supplementation modulates gut microbiome composition and influences early-life development in resource-limited settings.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Female
*Dietary Supplements
Infant
Pregnancy
Adult
Burkina Faso
*Carbohydrate Metabolism
Infant, Newborn
Feces/microbiology
Dietary Proteins/metabolism
Male
Lactation

@article {pmid40019271,
year = {2025},
author = {Milani, C and Longhi, G and Alessandri, G and Fontana, F and Viglioli, M and Tarracchini, C and Mancabelli, L and Lugli, GA and Petraro, S and Argentini, C and Anzalone, R and Viappiani, A and Carli, E and Vacondio, F and van Sinderen, D and Turroni, F and Mor, M and Ventura, M},
title = {Functional modulation of the human gut microbiome by bacteria vehicled by cheese.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {3},
pages = {e0018025},
doi = {10.1128/aem.00180-25},
pmid = {40019271},
issn = {1098-5336},
support = {GR-2018-12365988//Ministero della Salute (Italy Ministry of Health)/ ; SFI/12/RC/2273a//Science Foundation Ireland (SFI)/ ; SFI/12/RC/2273b//Science Foundation Ireland (SFI)/ ; },
mesh = {*Cheese/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Feces/microbiology ; },
abstract = {Since cheese is one of the most commonly and globally consumed fermented foods, scientific investigations in recent decades have focused on determining the impact of this dairy product on human health and well-being. However, the modulatory effect exerted by the autochthonous cheese microbial community on the taxonomic composition and associated functional potential of the gut microbiota of human is still far from being fully dissected or understood. Here, through the use of an in vitro human gut-simulating cultivation model in combination with multi-omics approaches, we have shown that minor rather than dominant bacterial players of the cheese microbiota are responsible for gut microbiota modulation of cheese consumers. These include taxa from the genera Enterococcus, Bacillus, Clostridium, and Hafnia. Indeed, they contribute to expand the functional potential of the intestinal microbial ecosystem by introducing genes responsible for the production of metabolites with relevant biological activity, including genes involved in the synthesis of vitamins, short-chain fatty acids, and amino acids. Furthermore, tracing of cheese microbiota-associated bacterial strains in fecal samples from cheese consumers provided evidence of horizontal transmission events, enabling the detection of particular bacterial strains transferred from cheese to humans. Moreover, transcriptomic and metabolomic analyses of a horizontally transmitted (cheese-to-consumer) bacterial strain, i.e., Hafnia paralvei T10, cultivated in a human gut environment-simulating medium, confirmed the concept that cheese-derived bacteria may expand the functional arsenal of the consumer's gut microbiota. This highlights the functional and biologically relevant contributions of food microbes acquired through cheese consumption on the human health.IMPORTANCEDiet is universally recognized as the primary factor influencing and modulating the human intestinal microbiota both taxonomically and functionally. In this context, cheese, being a fermented food with its own microbiota, serves not only as a source of nourishment for humans, but also as a source of nutrients for the consumer's gut microbiota. Additionally, it may act as a vehicle for autochthonous food-associated microorganisms which undergo transfer from cheese to the consumer, potentially influencing host gut health. The current study highlights not only that cheese microbiota-associated bacteria can be traced in the human gut microbiota, but also that they may expand the functional repertoire of the human gut microbiota, with potentially significant implications for human health.},
}

*Cheese/microbiology
Humans
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Feces/microbiology

@article {pmid39912643,
year = {2025},
author = {Hotchkiss, MZ and Poulain, AJ and Forrest, JRK},
title = {Bumble bee gut microbial community structure differs between species and commercial suppliers, but metabolic potential remains largely consistent.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {3},
pages = {e0203624},
doi = {10.1128/aem.02036-24},
pmid = {39912643},
issn = {1098-5336},
support = {//Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Species Specificity ; },
abstract = {Bumble bees are key pollinators for natural and agricultural plant communities. Their health and performance are supported by a core gut microbiota composed of a few bacterial taxa. However, the taxonomic composition and community structure of bumble bee gut microbiotas can vary with bee species, environment, and origin (i.e., whether colonies come from the wild or a commercial rearing facility), and it is unclear whether metabolic capabilities therefore vary as well. Here we used metagenomic sequencing to examine gut microbiota community composition, structure, and metabolic potential across bumble bees from two different commercial Bombus impatiens suppliers, wild B. impatiens, and three other wild bumble bee species sampled from sites within the native range of all four species. We found that the community structure of gut microbiotas varied between bumble bee species, between populations from different origins within species, and between commercial suppliers. Notably, we found that Apibacter is consistently present in some wild bumble bee species-suggesting it may be a previously unrecognized core phylotype of bumble bees-and that commercial B. impatiens colonies can lack core phylotypes consistently found in wild populations. However, despite variation in community structure, the high-level metabolic potential of gut microbiotas was largely consistent across all hosts, including for metabolic capabilities related to host performance, though metabolic activity remains to be investigated.IMPORTANCEOur study is the first to compare genome-level taxonomic structure and metabolic potential of whole bumble bee gut microbiotas between commercial suppliers and between commercial and wild populations. In addition, we profiled the full gut microbiotas of three wild bumble bee species for the first time. Overall, our results provide new insight into bumble bee gut microbiota community structure and function and will help researchers evaluate how well studies conducted in one bumble bee population will translate to other populations and species. Research on taxonomic and metabolic variation in bumble bee gut microbiotas across species and origins is of increasing relevance as we continue to discover new ways that social bee gut microbiotas influence host health, and as some bumble bee species decline in range and abundance.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/metabolism/isolation & purification
Species Specificity

@article {pmid39804518,
year = {2025},
author = {Claytor, JD and Lin, DL and Magnaye, KM and Guerrero, YS and Langelier, CR and Lynch, SV and El-Nachef, N},
title = {Effect of Fecal Microbiota Transplant on Antibiotic Resistance Genes Among Patients with Chronic Pouchitis.},
journal = {Digestive diseases and sciences},
volume = {70},
number = {3},
pages = {982-990},
pmid = {39804518},
issn = {1573-2568},
mesh = {Humans ; *Pouchitis/microbiology/therapy ; *Fecal Microbiota Transplantation ; Male ; Female ; Adult ; Middle Aged ; Chronic Disease ; Anti-Bacterial Agents/therapeutic use ; Gastrointestinal Microbiome ; Colitis, Ulcerative/microbiology/surgery/therapy ; Feces/microbiology ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {BACKGROUND: Pouchitis is common among patients with ulcerative colitis (UC) who have had colectomy with ileal pouch-anal anastomosis. Antibiotics are first-line therapy for pouch inflammation, increasing the potential for gut colonization with multi-drug resistant organisms (MDRO). Fecal microbial transplant (FMT) is being studied in the treatment of pouchitis and in the eradication of MDRO. Prior work using aerobic antibiotic culture disks suggests that some patients with chronic pouchitis may regain fluoroquinolone sensitivity after FMT. However, gut MDRO include anaerobic, fastidious organisms that are difficult to culture using traditional methods.

AIM: We aimed to assess whether FMT reduced the abundance of antibiotic resistance genes (ARG) or affected resistome diversity, evenness, or richness in patients with chronic pouchitis.

METHODS: We collected clinical characteristics regarding infections and antibiotic exposures for 18 patients who had previously been enrolled in an observational study investigating FMT as a treatment for pouchitis. Twenty-six pre- and post-FMT stool samples were analyzed using FLASH (Finding Low Abundance Sequences by Hybridization), a CRISPR/Cas9-based shotgun metagenomic sequence enrichment technique that detects acquired and chromosomal bacterial ARGs. Wilcoxon rank sum tests were used to assess differences in clinical characteristics, ARG counts, resistome diversity and ARG richness, pre- and post-FMT.

RESULTS: All 13 of the patients with sufficient stool samples for analysis had recently received antibiotics for pouchitis prior to a single endoscopic FMT. Fecal microbiomes of all patients had evidence of multi-drug resistance genes and ESBL resistance genes at baseline; 62% encoded fluoroquinolone resistance genes. A numerical decrease in overall ARG counts was noted post-FMT, but no statistically significant differences were noted (P = 0.19). Richness and diversity were not significantly altered. Three patients developed infections during the 5-year follow-up period, none of which were associated with MDRO.

CONCLUSION: Antibiotic resistance genes are prevalent among antibiotic-exposed patients with chronic pouchitis. FMT led to a numerical decrease, but no statistically significant change in ARG, nor were there significant changes in the diversity, richness, or evenness of ARGs. Further investigations to improve FMT engraftment and to optimize FMT delivery in patients with inflammatory pouch disorders are warranted.},
}

Humans
*Pouchitis/microbiology/therapy
*Fecal Microbiota Transplantation
Male
Female
Adult
Middle Aged
Chronic Disease
Anti-Bacterial Agents/therapeutic use
Gastrointestinal Microbiome
Colitis, Ulcerative/microbiology/surgery/therapy
Feces/microbiology
Drug Resistance, Bacterial/genetics
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid39410870,
year = {2025},
author = {Matsubara, K and Li, J and Enomoto, Y and Takahashi, T and Ma, M and Ninomiya, R and Kazami, D and Miura, K and Hirayama, K},
title = {Beneficial Role of Heat-Treated Lactobacillus sakei HS-1 on Growth Performance, Nutritional Status and Gut Microbiota in Weaned Piglets.},
journal = {Journal of animal physiology and animal nutrition},
volume = {109},
number = {2},
pages = {362-375},
doi = {10.1111/jpn.14056},
pmid = {39410870},
issn = {1439-0396},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Animal Nutritional Physiological Phenomena ; *Diet/veterinary ; *Probiotics/pharmacology/administration & dosage ; *Hot Temperature ; *Latilactobacillus sakei ; Nutritional Status ; Weaning ; },
abstract = {In the swine industry, there is a strong need to replace an antibiotic growth promoter (AGP) used as feed additives in weaned piglets to enhance nutrient utilization in their diets and improve growth performance. Lactobacillus sakei HS-1 strain is a microbial preparation isolated from pickles. The study aim is to investigate the effectiveness of heat-treated L. sakei HS-1 strain (HT-LS) as a growth promoter in weaned piglets compared to colistin (CS), a widely used AGP. Eighteen crossbred weaned piglets (Landrace × Yorkshire × Duroc) of 21 days (average body weight [BW]: 7.06 ± 0.59 kg) were divided into three groups: fed the control diet (CT group), fed a diet supplemented with 30 ppm colistin sulphate (CS group), fed a diet supplemented with HT-LS at a concentration of 2.0 × 10[5] cells/g (LS group) until 49 days. The results indicated that LS group exhibited significantly higher average daily gain (p < 0.05) and higher BW (p < 0.1) compared with CT group, even higher than CS group. CS group showed higher growth performance compared to CT group but the differences were not statistically significant. In addition, LS group had higher (p < 0.05) or tended to higher (p < 0.1) concentrations of several plasma amino acids than the other two groups at 35 and 49 days. Faecal acetate concentration was higher (p < 0.1) in LS group than in CT group at 35 days. Blood immunoglobulin G concentration in LS group was significantly lower (p < 0.05) than in CT group at 35 and 49 days, and blood immunoglobulin A tended to be lower (p < 0.1) at 35 days than in CT group. LS group showed an increased abundance of g_Prevotella 7, g_Streptococcus and g_Lactobacillus (linear discriminant analysis [LDA] score ≥ 2.0). Predictive metagenomic analysis revealed an enrichment of the mixed acid fermentation pathway (LDA score ≥ 2.0). Furthermore, several gut microbes exhibited correlations with plasma amino acids (p < 0.01) and short-chain fatty acids in faeces (p < 0.01). These findings demonstrate that HT-LS improves the growth performance of weaned piglets by enhancing the efficient utilization of nutrients through gut microbiota modification.},
}

Animals
Swine
*Gastrointestinal Microbiome/drug effects
*Animal Feed/analysis
*Animal Nutritional Physiological Phenomena
*Diet/veterinary
*Probiotics/pharmacology/administration & dosage
*Hot Temperature
*Latilactobacillus sakei
Nutritional Status
Weaning

@article {pmid38902926,
year = {2025},
author = {Niosi, A and Võ, NH and Sundaramurthy, P and Welch, C and Penn, A and Yuldasheva, Y and Alfareh, A and Rausch, K and Amin-Rahbar, T and Cavanaugh, J and Yadav, P and Peterson, S and Brown, R and Hu, A and Ardon-Castro, A and Nguyen, D and Crawford, R and Lee, W and Morris, EJ and Jensen, MH and Mulligan, K},
title = {Kismet/CHD7/CHD8 affects gut microbiota, mechanics, and the gut-brain axis in Drosophila melanogaster.},
journal = {Biophysical journal},
volume = {124},
number = {6},
pages = {933-941},
doi = {10.1016/j.bpj.2024.06.016},
pmid = {38902926},
issn = {1542-0086},
mesh = {Animals ; *Drosophila melanogaster/microbiology/physiology ; *Gastrointestinal Microbiome ; *Drosophila Proteins/metabolism/genetics ; Brain-Gut Axis/physiology ; Biomechanical Phenomena ; Mutation ; DNA-Binding Proteins/genetics/metabolism ; DNA Helicases/metabolism/genetics ; Mechanical Phenomena ; },
abstract = {The gut microbiome affects brain and neuronal development and may contribute to the pathophysiology of neurodevelopmental disorders. However, it is unclear how risk genes associated with such disorders affect gut physiology in a manner that could impact microbial colonization and how the mechanical properties of the gut tissue might play a role in gut-brain bidirectional communication. To address this, we used Drosophila melanogaster with a null mutation in the gene kismet, an ortholog of chromodomain helicase DNA-binding protein (CHD) family members CHD7 and CHD8. In humans, these are risk genes for neurodevelopmental disorders with co-occurring gastrointestinal symptoms. We found that kismet mutant flies have a significant increase in gastrointestinal transit time, indicating the functional homology of kismet with CHD7/CHD8 in vertebrates. Rheological characterization of dissected gut tissue revealed significant changes in the mechanics of kismet mutant gut elasticity, strain stiffening behavior, and tensile strength. Using 16S rRNA metagenomic sequencing, we also found that kismet mutants have reduced diversity and abundance of gut microbiota at every taxonomic level. To investigate the connection between the gut microbiome and behavior, we depleted gut microbiota in kismet mutant and control flies and quantified the flies' courtship behavior. Depletion of gut microbiota rescued courtship defects of kismet mutant flies, indicating a connection between gut microbiota and behavior. In striking contrast, depletion of the gut microbiome in the control strain reduced courtship activity, demonstrating that antibiotic treatment can have differential impacts on behavior and may depend on the status of microbial dysbiosis in the gut prior to depletion. We propose that Kismet influences multiple gastrointestinal phenotypes that contribute to the gut-microbiome-brain axis to influence behavior. We also suggest that gut tissue mechanics should be considered as an element in the gut-brain communication loop, both influenced by and potentially influencing the gut microbiome and neurodevelopment.},
}

Animals
*Drosophila melanogaster/microbiology/physiology
*Gastrointestinal Microbiome
*Drosophila Proteins/metabolism/genetics
Brain-Gut Axis/physiology
Biomechanical Phenomena
Mutation
DNA-Binding Proteins/genetics/metabolism
DNA Helicases/metabolism/genetics
Mechanical Phenomena

@article {pmid40100697,
year = {2025},
author = {Sun, J and Hirai, M and Takaki, Y and Evans, PN and Nunoura, T and Rinke, C},
title = {Metagenomic insights into taxonomic and functional patterns in shallow coastal and deep subseafloor sediments in the Western Pacific.},
journal = {Microbial genomics},
volume = {11},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001351},
pmid = {40100697},
issn = {2057-5858},
mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Metagenome ; Phylogeny ; Pacific Ocean ; Microbiota/genetics ; },
abstract = {Marine sediments are vast, underexplored habitats and represent one of the largest carbon deposits on our planet. Microbial communities drive nutrient cycling in these sediments, but the full extent of their taxonomic and metabolic diversity remains to be explored. Here, we analysed shallow coastal and deep subseafloor sediment cores from 0.01 to nearly 600 metres below the seafloor, in the Western Pacific Region. Applying metagenomics, we identified several taxonomic clusters across all samples, which mainly aligned with depth and sediment type. Inferring functional patterns provided insights into possible ecological roles of the main microbial taxa. These included Chloroflexota, the most abundant phylum across all samples, whereby the classes Dehalococcoida and Anaerolineae dominated deep-subsurface and most shallow coastal sediments, respectively. Thermoproteota and Asgardarchaeota were the most abundant phyla among Archaea, contributing to high relative abundances of Archaea reaching over 50% in some samples. We recovered high-quality metagenome-assembled genomes for all main prokaryotic lineages and proposed names for three phyla, i.e. Tangaroaeota phyl. nov. (former RBG-13-66-14), Ryujiniota phyl. nov. (former UBA6262) and Spongiamicota phyl. nov. (former UBA8248). Metabolic capabilities across all samples ranged from aerobic respiration and photosynthesis in the shallowest sediment layers to heterotrophic carbon utilization, sulphate reduction and methanogenesis in deeper anoxic sediments. We also identified taxa with the potential to be involved in nitrogen and sulphur cycling and heterotrophic carbon utilization. In summary, this study contributes to our understanding of the taxonomic and functional diversity in benthic prokaryotic communities across marine sediments in the Western Pacific Region.},
}

*Geologic Sediments/microbiology
*Archaea/genetics/classification
*Metagenomics/methods
*Bacteria/genetics/classification
*Metagenome
Phylogeny
Pacific Ocean
Microbiota/genetics

@article {pmid40098558,
year = {2025},
author = {Di Rienzi, SC and Danhof, HA and Forshee, MD and Roberts, A and Britton, RA},
title = {Limosilactobacillus reuteri promotes the expression and secretion of enteroendocrine- and enterocyte-derived hormones.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {6},
pages = {e70408},
doi = {10.1096/fj.202401669R},
pmid = {40098558},
issn = {1530-6860},
support = {T15 LM007093/LM/NLM NIH HHS/United States ; F32 AI136404/AI/NIAID NIH HHS/United States ; //Weston Family Foundation (WFF)/ ; //BioGaia/ ; },
mesh = {*Limosilactobacillus reuteri/metabolism ; *Enteroendocrine Cells/metabolism ; *Enterocytes/metabolism/microbiology ; Humans ; Organoids/metabolism ; Gastrointestinal Hormones/metabolism/genetics ; Gastrointestinal Microbiome ; Animals ; },
abstract = {Intestinal microbes can beneficially impact host physiology, prompting investigations into the therapeutic usage of such microbes in a range of diseases. For example, human intestinal microbe Limosilactobacillus reuteri strains ATCC PTA 6475 and DSM 17938 are being considered for use for intestinal ailments, including colic, infection, and inflammation, as well as for non-intestinal ailments, including osteoporosis, wound healing, and autism spectrum disorder. While many of their beneficial properties are attributed to suppressing inflammatory responses, we postulated that L. reuteri may also regulate intestinal hormones to affect physiology within and outside of the gut. To determine if L. reuteri secreted factors impact the secretion of enteric hormones, we treated an engineered jejunal organoid line, NGN3-HIO, which can be induced to be enriched in enteroendocrine cells, with L. reuteri 6475 or 17938 conditioned medium and performed transcriptomics. Our data suggest that these L. reuteri strains affect the transcription of many gut hormones, including vasopressin and luteinizing hormone subunit beta, which have not been previously recognized as produced in the gut epithelium. Moreover, we find that these hormones appear to be produced in enterocytes, in contrast to canonical gut hormones produced in enteroendocrine cells. Finally, we show that L. reuteri conditioned media promote the secretion of enteric hormones, including serotonin, GIP, PYY, vasopressin, and luteinizing hormone subunit beta, and identify by metabolomics metabolites potentially mediating these effects on hormones. These results support L. reuteri affecting host physiology through intestinal hormone secretion, thereby expanding our understanding of the mechanistic actions of this microbe.},
}

*Limosilactobacillus reuteri/metabolism
*Enteroendocrine Cells/metabolism
*Enterocytes/metabolism/microbiology
Humans
Organoids/metabolism
Gastrointestinal Hormones/metabolism/genetics
Gastrointestinal Microbiome
Animals

@article {pmid40098172,
year = {2025},
author = {Raziq, MF and Khan, N and Manzoor, H and Tariq, HMA and Rafiq, M and Rasool, S and Kayani, MUR and Huang, L},
title = {Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {343},
pmid = {40098172},
issn = {1479-5876},
mesh = {Humans ; *Polymorphism, Single Nucleotide/genetics ; *Carcinoma, Non-Small-Cell Lung/genetics/microbiology/drug therapy ; *Computational Biology/methods ; *Gastrointestinal Microbiome/genetics ; *Lung Neoplasms/genetics/drug therapy/microbiology ; *Immunotherapy ; Treatment Outcome ; Male ; Female ; Metagenome/genetics ; },
abstract = {BACKGROUND: The human gut microbiome has emerged as a potential modulator of treatment efficacy for different cancers, including non-small cell lung cancer (NSCLC) patients undergoing immune checkpoint inhibitor (ICI) therapy. In this study, we investigated the association of gut microbial variations with response against ICIs by analyzing the gut metagenomes of NSCLC patients.

METHODS: Strain identification from the publicly available metagenomes of 87 NSCLC patients, treated with nivolumab and collected at three different timepoints (T0, T1, and T2), was performed using StrainPhlAn3. Variant calling and annotations were performed using Snippy and associations between microbial genes and genomic variations with treatment responses were evaluated using MaAsLin2. Supervised machine learning models were developed to prioritize single nucleotide polymorphisms (SNPs) predictive of treatment response. Structural bioinformatics approaches were employed using MUpro, I-Mutant 2.0, CASTp and PyMOL to access the functional impact of prioritized SNPs on protein stability and active site interactions.

RESULTS: Our findings revealed the presence of strains for several microbial species (e.g., Lachnospira eligens) exclusively in Responders (R) or Non-responders (NR) (e.g., Parabacteroides distasonis). Variant calling and annotations for the identified strains from R and NR patients highlighted variations in genes (e.g., ftsA, lpdA, and nadB) that were significantly associated with the NR status of patients. Among the developed models, Logistic Regression performed best (accuracy > 90% and AUC ROC > 95%) in prioritizing SNPs in genes that could distinguish R and NR at T0. These SNPs included Ala168Val (lpdA) in Phocaeicola dorei and Tyr233His (lpdA), Leu330Ser (lpdA), and His233Arg (obgE) in Parabacteroides distasonis. Lastly, structural analyses of these prioritized variants in objE and lpdA revealed their involvement in the substrate binding site and an overall reduction in protein stability. This suggests that these variations might likely disrupt substrate interactions and compromise protein stability, thereby impairing normal protein functionality.

CONCLUSION: The integration of metagenomics, machine learning, and structural bioinformatics provides a robust framework for understanding the association between gut microbial variations and treatment response, paving the way for personalized therapies for NSCLC in the future. These findings emphasize the potential clinical implications of microbiome-based biomarkers in guiding patient-specific treatment strategies and improving immunotherapy outcomes.},
}

Humans
*Polymorphism, Single Nucleotide/genetics
*Carcinoma, Non-Small-Cell Lung/genetics/microbiology/drug therapy
*Computational Biology/methods
*Gastrointestinal Microbiome/genetics
*Lung Neoplasms/genetics/drug therapy/microbiology
*Immunotherapy
Treatment Outcome
Male
Female
Metagenome/genetics

@article {pmid40097931,
year = {2025},
author = {Boutin, S and Käding, N and Belheouane, M and Merker, M and Rupp, J and Nurjadi, D},
title = {Towards unraveling antimicrobial resistance dynamics: a longitudinal exploration of rectal swab metagenomes.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {150},
pmid = {40097931},
issn = {1471-2180},
mesh = {Humans ; *Rectum/microbiology ; *Metagenome ; *Metagenomics/methods ; Bacteria/genetics/drug effects/isolation & purification/classification ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Longitudinal Studies ; Male ; Microbial Sensitivity Tests ; Female ; Middle Aged ; Microbiota/genetics/drug effects ; Aged ; Genome, Bacterial/genetics ; Adult ; },
abstract = {The increasing prevalence of antimicrobial resistance (AMR) poses significant challenges in clinical settings. In particular, early screening and detection of colonization by multidrug-resistant organisms (MDROs) in patients at admission is crucial. In this context, the clinical use of metagenomics (mNGS) holds promise for fast and untargeted diagnostic methods. Here, we aimed to evaluate the long-term stability of the rectal microbiome and the diagnostic accuracy of mNGS in comparison to culture and whole-genome sequencing (WGS) of MDROs. We analyzed rectal swabs from 26 patients with two consecutive admissions over a four-year period. The detected antimicrobial resistance genes and assembled metagenomes were compared to those obtained via classical culture-based antimicrobial susceptibility testing and WGS of isolated MDROs. Our results showed that the rectal microbiome is variable during the two timepoints, highlighting the variability in the niche. Nevertheless, we also observed strong co-occurrence of taxa, suggesting that the rectal swab microbiome is also a regulated environment with cooperative biotic interactions. In total, we isolated and sequenced 6 MDROs from 6 patients at individual timepoints. Almost all AMR genes from the genomes of the isolates (median: 100%, range: 84.6-100%) could be detected by mNGS of the rectal swabs at the time of isolation of the MDRO but not at the time of culture negativity. In addition, we detected AMR genes and potentially pathogenic species in patients with negative cultures. In conclusion, our study showed that, in principle, mNGS of rectal swabs can detect clinically relevant AMR profiles. However, the cooccurrence of AMR genes and potentially-pathogenic species does not always correlate with culture-based diagnostic results but rather indicates a potential risk of horizontal AMR gene transfer. However, it is unclear whether the observed discrepancies are due to transient or locally confined colonization of MDROs, limits of detection, or variability of the sampling method and specimens.},
}

Humans
*Rectum/microbiology
*Metagenome
*Metagenomics/methods
Bacteria/genetics/drug effects/isolation & purification/classification
Anti-Bacterial Agents/pharmacology
Drug Resistance, Multiple, Bacterial/genetics
Whole Genome Sequencing
Longitudinal Studies
Male
Microbial Sensitivity Tests
Female
Middle Aged
Microbiota/genetics/drug effects
Aged
Genome, Bacterial/genetics
Adult