@article {pmid41778161,
year = {2026},
author = {Wang, D and Han, J and Wang, X and Wang, J and You, C and Wu, Z},
title = {Lacticaseibacillus rhamnosus B6 alleviates metabolic dysfunction-associated fatty liver disease by suppressing intestinal LPS synthesis and regulating lipid metabolism.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1755982},
pmid = {41778161},
issn = {1664-2392},
mesh = {Animals ; *Lacticaseibacillus rhamnosus/physiology ; *Probiotics/pharmacology ; Mice ; *Lipid Metabolism/drug effects ; Male ; *Gastrointestinal Microbiome ; *Lipopolysaccharides/biosynthesis/metabolism ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Metabolic Diseases/metabolism ; },
abstract = {INTRODUCTION: Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a global epidemic with an unclear etiology and no effective therapeutic options. Disruption of the gut-liver axis driven by intestinal dysbiosis is closely implicated in MAFLD pathogenesis, making gut microbiota-targeted probiotic interventions promising preventive strategies.

METHODS: Lacticaseibacillus rhamnosus B6, a probiotic strain isolated from homemade Bulgarian fermented milk, synthesizes immunomodulatory macromolecules and regulates the intestinal flora. In the present study, we comprehensively investigated the colonization ability and MAFLD-alleviating effects of L. rhamnosus B6 in a high-fat diet (HFD)-induced murine MAFLD model using an integrated approach encompassing metagenomics, untargeted metabolomics, serum biochemical assays, and liver histopathological analysis.

RESULTS: Supplementation with L. rhamnosus B6 markedly decreased the relative abundance of Cupriavidus, Desulfovibrionaceae, and Enterobacteriacea, and inhibited the predicted lipopolysaccharide (LPS) synthesis pathway, thereby suppressing the inflammatory response. Furthermore, L. rhamnosus B6 intervention elevated unsaturated fatty acid levels by modulating lipid metabolic pathways, specifically mitochondrial β-oxidation of long-chain saturated fatty acids, α-linolenic acid, linoleic acid, and sphingolipid metabolism, while downregulating predicted myo-inositol degradation pathways, collectively contributing to MAFLD alleviation. In vitro, the metabolites of L. rhamnosus B6 exerted potent inhibitory activity against LPS-producing bacteria (e.g., Escherichia coli and Salmonella enterica).

DISCUSSION: These findings demonstrate that L. rhamnosus B6 is a promising probiotic for MAFLD alleviation via dual mechanisms of attenuating inflammation and regulating lipid metabolism. This study provides compelling evidence for the specific protective effects of L. rhamnosus B6 against MAFLD and offers a novel probiotic-based therapeutic strategy for MAFLD.},
}

Animals
*Lacticaseibacillus rhamnosus/physiology
*Probiotics/pharmacology
Mice
*Lipid Metabolism/drug effects
Male
*Gastrointestinal Microbiome
*Lipopolysaccharides/biosynthesis/metabolism
Mice, Inbred C57BL
Diet, High-Fat/adverse effects
*Non-alcoholic Fatty Liver Disease/metabolism
*Metabolic Diseases/metabolism

@article {pmid41775849,
year = {2026},
author = {Plewnia, A and Hildwein, T and Quezada Riera, AB and Terán-Valdez, A and Crawford, AJ and Heine, C and Franco-Mena, D and Székely, D and Armijos-Ojeda, D and Siavichay, FR and Arpi, JD and Salazar, J and Erens, J and Páez-Vacas, MI and Székely, P and Böning, P and Stassen, R and Carvajal-Endara, S and Lötters, S and Guayasamin, JM},
title = {Environmental DNA metabarcoding facilitates integrative conservation assessments and species rediscoveries in tropical biodiversity hotspots.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41775849},
issn = {2045-2322},
abstract = {UNLABELLED: Environmental DNA (eDNA) metabarcoding is an emerging and versatile tool in biodiversity research. With recent advances in field sampling techniques, this approach becomes increasingly suited for application in tropical ecosystems where biodiversity monitoring gaps remain significant and species detection is particularly challenging. Using amphibians as a model, we harness eDNA metabarcoding in 52 localities in the Tropical Andean biodiversity hotspot to rapidly trace elusive, threatened, or presumed extinct species as a baseline for conservation action. Metabarcoding ‘bycatch’ of non-target species further revealed specific environmental threats through the detection of invasive species and pathogens, thus facilitating integrative conservation assessments despite the incompleteness of reference data and the vast species richness hampering biodiversity assessments in complex tropical communities. Consequently, we call for more intense employment of eDNA metabarcoding in conservation to rapidly bridge critical knowledge gaps on elusive species or declining populations in tropical biodiversity hotspots.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41937-x.},
}

@article {pmid41774204,
year = {2026},
author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M},
title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41774204},
issn = {1432-0991},
abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.},
}

@article {pmid41770401,
year = {2026},
author = {Han, T and Yang, T and Liu, Y and He, Z and Hao, Y and Cao, W and Ren, J and Wang, G and Gong, C and Hou, J},
title = {Dietary supplementation with allicin enhances growth performance and antioxidant capacity, and reduces gut pathogens and antibiotic resistance genes in Trachidermus fasciatus.},
journal = {Fish physiology and biochemistry},
volume = {52},
number = {2},
pages = {},
pmid = {41770401},
issn = {1573-5168},
support = {2025JNZ-C01//the earmarked fund of Hebei Agricultural S&T Achievements Transformation/ ; 21326307D//the Key R&D Program of Hebei Province, China and the National Marine Genetic Resource Center/ ; },
mesh = {Animals ; *Sulfinic Acids/pharmacology/administration & dosage ; Disulfides ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Animal Feed/analysis ; *Drug Resistance, Microbial/genetics ; Diet/veterinary ; *Fishes/growth & development/microbiology ; },
abstract = {Allicin, a bioactive sulfur compound from garlic known for its antimicrobial and immunomodulatory properties, was evaluated in this study for its effects on growth, antioxidant activity, gut microbiota, and antibiotic resistance genes (ARGs) in Trachidermus fasciatus. Fish were administered allicin at concentrations of 100 mg/kg, 200 mg/kg, and 300 mg/kg. The 200 mg/kg allicin group had significantly higher WGR, LGR, and SGR than the control group. Hepatic SOD and LZM activities were also higher in the 200 mg/kg group. Metagenomics showed that allicin altered the gut microbiota composition, decreased the diversity, and altered the community structure. Allicin-treated fish had significantly reduced levels of potentially damaging bacteria, including Pseudomonas and Vibrio species. The ARGs showed that genes associated with multidrug resistance, including specific subtypes, were markedly reduced in the 200 mg/kg allicin-treated fish. The control group had a markedly decreased number of genes resistant to β-lactam antibiotics. Allicin reduced the number of genes resistant to rpoB2 and mdtC, suggesting the potential for antibiotic resistance. Network analysis of co-occurrence patterns showed that genes resistant to multiple drugs, tetracyclines, and peptides were prevalent, with most possible potential host taxa belonging to Ascomycota and Firmicutes. These results indicate the importance of allicin for fish health as a sustainable alternative to antibiotic resistance and provide a viable alternative to antibiotic resistance for fish farming.},
}

Animals
*Sulfinic Acids/pharmacology/administration & dosage
Disulfides
*Antioxidants/metabolism
*Gastrointestinal Microbiome/drug effects
*Dietary Supplements
Animal Feed/analysis
*Drug Resistance, Microbial/genetics
Diet/veterinary
*Fishes/growth & development/microbiology

@article {pmid41769343,
year = {2026},
author = {Yan, X and Zhang, X and Wang, L and Song, W and Qi, T and Wang, Z and Tang, Y and Sun, J and Xu, S and Yang, J and Shao, Y and Chen, Y and Wang, J and Chen, J and Zhang, R and Liu, L and Shen, Y},
title = {Gut microbiota alterations and microbial translocation in HIV/SARS-CoV-2 co-infected patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1688580},
pmid = {41769343},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/complications ; *HIV Infections/microbiology/complications ; Male ; Female ; *Bacterial Translocation ; *Coinfection/microbiology/virology ; Middle Aged ; Adult ; Lipopolysaccharide Receptors/blood ; Lipopolysaccharides/blood ; Feces/microbiology ; SARS-CoV-2 ; Cohort Studies ; Severity of Illness Index ; Haptoglobins ; Protein Precursors/blood ; },
abstract = {OBJECTIVE: To characterize gut microbiome alterations and microbial translocation in human immunodeficiency virus (HIV)/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected patients and identify microbial signatures associated with COVID-19 severity.

METHODS: In this cohort study, blood and fecal samples from 38 HIV/AIDS patients (20 SARS-CoV-2 co-infected [PC group]; 18 SARS-CoV-2-negative [NC group]) were analyzed. The PC group was stratified by COVID-19 severity: mild-to-moderate (PC1, n=13), severe-to-critical (PC2, n=3), and mixed infections (PC3, n=4). Serum lipopolysaccharide (LPS), soluble CD14 (sCD14), and zonulin levels were measured to assess microbial translocation and gut barrier integrity. Fecal metagenomic profiling was performed via whole-genome shotgun sequencing (Illumina NovaSeq/HiSeq).

RESULTS: Co-infected patients exhibited significantly elevated plasma LPS (78.09 vs 48.72 pg/mL, p=0.032) and sCD14 (2667 vs 1927 ng/mL, p=0.0015) compared to controls. Although no differences in α-diversity or overall taxonomic abundance were observed between the PC and NC groups, 329 PC-unique and 216 NC-unique microbial species were identified. Nine genera demonstrated diagnostic potential for co-infection [Area Under the Curve (AUC), >0.7] with Akkermansia showing the highest predictive value (AUC = 0.811). Critically, Blautia abundance was significantly reduced in severe-to-critical cases (PC2) versus mild-moderate cases (PC1, p=0.043) and controls (NC, p=0.006). Besides, our function prediction for gut microbiota suggested that SARS-CoV-2 may exacerbate lipid metabolic dysregulation in HIV-infected individuals.

CONCLUSIONS: HIV/SARS-CoV-2 co-infection is characterized by heightened microbial translocation and species-specific microbiota alterations rather than global dysbiosis. Blautia depletion may correlate with COVID-19 severity.},
}

Humans
*Gastrointestinal Microbiome
*COVID-19/microbiology/complications
*HIV Infections/microbiology/complications
Male
Female
*Bacterial Translocation
*Coinfection/microbiology/virology
Middle Aged
Adult
Lipopolysaccharide Receptors/blood
Lipopolysaccharides/blood
Feces/microbiology
SARS-CoV-2
Cohort Studies
Severity of Illness Index
Haptoglobins
Protein Precursors/blood

@article {pmid41762228,
year = {2026},
author = {Liu, T and Ding, H and Lv, Z and Yan, C and Feng, S and Lu, D and Hang, F and Meng, X},
title = {Lactobacillus Taiwanensis Inhibits Gallstone Formation by Regulating Ileal Metabolism.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41762228},
issn = {1432-0991},
support = {82270598//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Lactobacillus/physiology ; *Ileum/metabolism/microbiology ; Mice ; *Gallstones/microbiology/prevention & control/metabolism ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; Male ; *Probiotics/administration & dosage ; Disease Models, Animal ; Colon/microbiology ; },
abstract = {In recent years, gut microbiota has been recognized to participate in gallstone formation via the gut-liver axis, yet the specific changes and roles of ileal microbiota remain unclear. This study aims to investigate the effects of microbial communities in different digestive tract segments on the formation of gallstones and the underlying mechanisms. Six-week-old C57BL/6J mice were randomly divided into a lithogenic diet group and a normal diet group. Ileal and colonic contents were collected separately for metagenomic sequencing.The Lactobacillus taiwanensis gavage model was constructed to compare its effects on gallstone formation and ileal metabolism. An intraperitoneal injection model of Lipoxin A4 (LXA4) was established to investigate the mechanisms by which Lactobacillus taiwanensis and LXA4 inhibit gallstone through Western blot analysis and ELISA methods. We found that there were significant differences in the intestinal microbiota between the group with gallstone formation and the control group in the small intestine and colon. Species-level analysis indicated that the lithogenic diet reduced the abundance of Lactobacillus taiwanensis in the small intestine. When Lactobacillus taiwanensis was administered intragastrically to mice, the incidence of gallstones decreased. Through metabolomics analysis and experimental verification, we demonstrated that Lactobacillus taiwanensis could down-regulate the expression of NETs in the liver and bile by increasing the level of LXA4, thereby reducing gallstone. The ileal and colonic microbiota exert site-specific effects in gallstone formation. Lactobacillus taiwanensis may inhibit gallstone formation by regulating ileal metabolism, may contribute to prevention and treatment of gallstones.},
}

Animals
*Lactobacillus/physiology
*Ileum/metabolism/microbiology
Mice
*Gallstones/microbiology/prevention & control/metabolism
Mice, Inbred C57BL
*Gastrointestinal Microbiome
Male
*Probiotics/administration & dosage
Disease Models, Animal
Colon/microbiology

@article {pmid41758194,
year = {2026},
author = {Chen, J and Wang, Y and Xu, L and Li, X and Zhao, L},
title = {Exploring the gut microbiome and metabolomic interactions of antimetabolite drugs to optimize therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638009},
pmid = {41758194},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Antimetabolites/pharmacology/therapeutic use/pharmacokinetics ; Dysbiosis/chemically induced/microbiology ; Bacteria/metabolism/drug effects/genetics/classification ; Animals ; Metabolomics ; Neoplasms/drug therapy ; },
abstract = {Antimetabolite drugs are cornerstones in treating various cancers and autoimmune diseases; however, their clinical utility is often hampered by systemic toxicity caused by drug-induced gut microbiota dysbiosis. Predicting patient responses remains a significant challenge. Several studies have highlighted the influence of gut microbiota on antimetabolite treatment outcomes, revealing complex bidirectional interactions between the drugs and microbial communities. This review synthesizes the effects of common antimetabolites (including 5-fluorouracil, methotrexate, gemcitabine, capecitabine, 6-mercaptopurine, and thioguanine) on gut microbial communities and outlines a framework (pharmacokinetics, endogenous metabolite production, immune modulation, and apoptotic pathway modulation) for assessing chemotherapy-microbiota interactions. Additionally, potential microbial biomarkers for predicting treatment responses and strategies for manipulating the gut microbiota to enhance therapeutic efficacy are discussed. Therefore, advances in methodologies such as metagenomics and real-time microbial monitoring will be essential for unraveling these interactions and promoting the precise application of antimetabolite drugs.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Antimetabolites/pharmacology/therapeutic use/pharmacokinetics
Dysbiosis/chemically induced/microbiology
Bacteria/metabolism/drug effects/genetics/classification
Animals
Metabolomics
Neoplasms/drug therapy

@article {pmid41754473,
year = {2026},
author = {Vilela, C and Mendoza, L and Vilela, R and Moreira Jardilino, FD and Brilhante Bhering, CL and Moreno, A},
title = {Microbial Diversity and Composition Uncovered on Obturator Prosthesis Biofilms: Exploratory Findings from a Pilot Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754473},
issn = {2076-0817},
mesh = {*Biofilms/growth & development ; Humans ; Pilot Projects ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Microbiota ; *Biodiversity ; Archaea/genetics/isolation & purification/classification ; Fungi/genetics/classification/isolation & purification ; Male ; Viruses/classification/genetics/isolation & purification ; Female ; Middle Aged ; },
abstract = {Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery.},
}

*Biofilms/growth & development
Humans
Pilot Projects
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Microbiota
*Biodiversity
Archaea/genetics/isolation & purification/classification
Fungi/genetics/classification/isolation & purification
Male
Viruses/classification/genetics/isolation & purification
Female
Middle Aged

@article {pmid41754400,
year = {2026},
author = {Wang, X and Duan, R and Ming, A and Zhang, Y and Liu, T and Wang, X and Diao, M},
title = {Age-Dependent Dynamics of the Biliary Microbiome in Children with Choledochal Cysts: Functional Remodeling Underlying Taxonomic Conservation.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754400},
issn = {2076-0817},
mesh = {Humans ; Child, Preschool ; *Choledochal Cyst/microbiology ; Infant ; Male ; Female ; Child ; Age Factors ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; *Biliary Tract/microbiology ; },
abstract = {Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1-5 years), and later childhood (5-12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1-5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of "taxonomic conservation coupled with functional remodeling" in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies.},
}

Humans
Child, Preschool
*Choledochal Cyst/microbiology
Infant
Male
Female
Child
Age Factors
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Metagenomics/methods
*Biliary Tract/microbiology

@article {pmid41754175,
year = {2026},
author = {Wang, Z and Wei, J and Huang, Z and Liu, X and Li, S and Fang, Z and Hu, L and Li, R and Tao, L and Li, C and Chen, H},
title = {Metagenomics and Machine Learning Identify TMA-Producing Serratia Induced by High-Fat/Choline Diet: A Novel Obesity Target for TMA.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754175},
issn = {2072-6643},
support = {2023ZYD0129//Sichuan Province Central Leading Local Science and Technology Development Special Project/ ; 2024YFD2101003//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Methylamines/metabolism/blood ; *Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; *Choline/administration & dosage/metabolism ; *Gastrointestinal Microbiome ; *Obesity/microbiology/metabolism/etiology ; Mice ; *Metagenomics ; *Machine Learning ; Liver/metabolism/pathology ; Feces/microbiology ; },
abstract = {BACKGROUND: High-fat diet-induced metabolic disorders are associated with trimethylamine (TMA)/trimethylamine N-oxide (TMAO), whose production is linked to gut microbial choline metabolism. However, changes in specific gut microbiota under a high-fat diet and the relationship between these changes and choline in TMA/TMAO production remain unclear.

METHODS: A total of 48 7-week-old male C57BL/6J mice were subjected to one-week acclimatization feeding, and then randomly divided into four groups (12 mice per group) to establish a 2 × 2 factorial design animal experiment: the control group (CON, basal diet), the choline-supplemented control group (CON + C, basal diet supplemented with 1% choline), the high-fat diet group (HF, high-fat diet), and the high-fat plus choline group (HF + C, high-fat diet supplemented with 1% choline). The experiment lasted for 9 weeks, during which dynamic monitoring of TMAO levels in mice was performed in the first 4 weeks. At the ninth week, the mice were sacrificed and samples were collected for subsequent assays, including the concentrations of TMA and TMAO in serum, colonic contents and feces; the pathological morphology of liver tissue, adipocyte staining characteristics and serum biochemical parameters; and the expression levels of key genes and proteins in liver, small intestine and colon tissues. Meanwhile, metagenomic analysis was conducted on colonic contents, combined with machine learning to predict the correlation between gut microbiota and TMA. In addition, gene cloning, multiple sequence alignment, molecular simulation and in vitro culture experiments were carried out to verify the TMA-producing function of the target strain.

RESULTS: This study elucidated that high-fat diet and high choline exert a significant interaction in TMA/TMAO production through a 2 × 2 animal experiment; meanwhile, the significantly increased TMA/TMAO levels co-induced by the two factors further exacerbate metabolic disorders. Notably, through combined metagenomics and machine learning, we identified Serratia marcescens as the primary TMA-producing microorganism under high-fat/choline diet induction. In vitro cultures simulating the intestinal environment revealed that the TMA conversion ability of Serratia marcescens is time-dependent, reaching 60 ± 2.49% after 24 h of anaerobic culture with choline chloride. Multiple sequence alignment and molecular simulation further demonstrated that the CutC enzyme of Serratia marcescens has a conserved amino acid sequence and high affinity for choline.

CONCLUSIONS: We uncovered a two-factor synergistic effect of a high-fat/choline diet on TMA/TMAO, and for the first time identified the genus Serratia as a TMA-producing bacterium. These findings provide a new potential target for intervening in metabolic disorders mediated by high-fat diet-induced TMAO elevation.},
}

Animals
*Methylamines/metabolism/blood
*Diet, High-Fat/adverse effects
Male
Mice, Inbred C57BL
*Choline/administration & dosage/metabolism
*Gastrointestinal Microbiome
*Obesity/microbiology/metabolism/etiology
Mice
*Metagenomics
*Machine Learning
Liver/metabolism/pathology
Feces/microbiology

@article {pmid41754080,
year = {2026},
author = {Qin, P and Berzina, L and Geiker, NRW and Sandby, K and Krarup, T and Kristiansen, K and Magkos, F},
title = {Associations Between Gut Microbiome Enterotypes and Body Weight Change During Whole Milk Consumption.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754080},
issn = {2072-6643},
support = {NA//Arla Food for Health/ ; NA//Danish Milk Levy Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; *Milk ; Animals ; Feces/microbiology/chemistry ; Adult ; Bacteroides ; *Body Weight ; Obesity/microbiology/diet therapy ; Middle Aged ; Streptococcus thermophilus ; },
abstract = {Background: Evidence is accumulating that gut bacterial communities modulate the outcome of dietary interventions. Objective: To assess how gut microbial enterotypes correlate with obesity-related outcomes during one month of whole milk consumption. Methods: This post hoc analysis used data from a previously published trial, which included a lead-in phase during which men with abdominal adiposity replaced habitual dairy product consumption with 400 g/day of whole milk for one month. We compared body weight, urinary metabolites, fecal metabolites, and gut microbiome composition and function based on shotgun metagenomic sequencing at the beginning and at the end of the lead-in phase between individuals with the two most prevalent enterotypes, the Bacteroides1 (B1) enterotype (n = 24) and the Ruminococcaceae (R) enterotype (n = 38). Results: Individuals with the B1 enterotype, but not those with the R enterotype, exhibited decreases in body weight and the relative abundance of Streptococcus thermophilus. Multiple linear regression analysis identified enterotype as a strong predictor of body weight change (p = 0.0034). In addition, urinary taurine level change was positively associated with body weight change in B1 individuals, not in R individuals. Conclusions: Our findings reveal an enterotype-specific response to an identical dietary modification, underscoring the value of integrating enterotype information into nutrition-intervention design and personalized nutrition strategies.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
*Milk
Animals
Feces/microbiology/chemistry
Adult
Bacteroides
*Body Weight
Obesity/microbiology/diet therapy
Middle Aged
Streptococcus thermophilus

@article {pmid41752220,
year = {2026},
author = {Kareem, HA and Khan, MF},
title = {Current Research Advances and Future Prospects on Microbial Consortia for Sustainable PFAS Remediation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752220},
issn = {1422-0067},
support = {82930-NP//University College Dublin Internal Fund/ ; },
mesh = {Biodegradation, Environmental ; *Microbial Consortia ; *Soil Pollutants/metabolism ; *Fluorocarbons/metabolism ; Soil Microbiology ; *Environmental Restoration and Remediation/methods ; },
abstract = {Soil contamination by per- and polyfluoroalkyl substances (PFAS) represents a pressing environmental and public health concern due to the exceptional persistence of carbon-fluorine bonds, which prevent natural attenuation and limit the effectiveness of conventional remediation. Agricultural and industrial soils serve as long-term sinks for PFAS, continuously releasing these pollutants into groundwater and facilitating their transfer through the food chain. Conventional chemical and physical remediation methods are often costly, energy-intensive, and yield incomplete removal, underscoring the need for sustainable and biologically driven alternatives. Microbial consortia have emerged as a promising solution due to their metabolic complementarities, cross-feeding interactions, and ecological resilience, which together enable PFAS transformation and partial defluorination under complex soil and subsurface conditions. Key enzymes such as oxygenases, reductive dehalogenases, and hydrolases are often operating within co-metabolic networks, which play central roles in these processes. Advances in metagenomics, CRISPR-based functional screening, and metabolic modelling are rapidly uncovering novel PFAS-degrading microbes and pathways. Integration of machine learning with multi-omics and environmental datasets further enables the prediction of degradation mechanisms, identification of keystone degraders, and rational design of synthetic consortia. Emerging sustainable strategies, including biochar- and nutrient-amended soil microcosms, plant-microbe partnerships for coupled soil-groundwater phytoremediation, and bioelectrochemical systems that offer new avenues for enhancing PFAS biodegradation in situ. This review synthesises recent research progress and provides critical perspectives on the mechanistic, ecological, and engineering dimensions of PFAS bioremediation, proposing an integrated conceptual framework linking microbial consortia dynamics, enzymatic pathways, and environmental engineering interventions to guide scalable field applications and sustainable management of PFAS-contaminated soil-groundwater ecosystems.},
}

Biodegradation, Environmental
*Microbial Consortia
*Soil Pollutants/metabolism
*Fluorocarbons/metabolism
Soil Microbiology
*Environmental Restoration and Remediation/methods

@article {pmid41752202,
year = {2026},
author = {Jung, S},
title = {Microbiome-Genome Crosstalk in Colorectal Cancer: Colibactin Signatures and Fusobacterium nucleatum in Epidemiology, Driver Selection, and Translation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752202},
issn = {1422-0067},
support = {RS-2022-NR069378//National Research Foundation of Korea/ ; RS-2025-18732993//National Research Foundation of Korea/ ; },
mesh = {*Colorectal Neoplasms/epidemiology/genetics/microbiology ; Humans ; *Fusobacterium nucleatum/genetics ; *Polyketides/metabolism ; *Peptides/metabolism ; *Gastrointestinal Microbiome ; Mutation ; *Bacteriocins/metabolism/genetics ; *Microbiota ; },
abstract = {Colibactin, a genotoxin produced by pks[+]E. coli, imprints highly specific mutational signatures SBS88 and ID18 in colorectal cancer (CRC) and even in normal colonic crypts. Population-scale analyses show these signatures are enriched in early-onset CRC, vary geographically, and are imprinted early during tumor evolution, where probabilistic attribution indicates that colibactin contributes to a measurable fraction of APC driver mutations in colibactin-positive cancers. Beyond colibactin, Fusobacterium nucleatum exerts clade-specific effects on tumor ecology and therapy response, with data supporting both chemoresistance and sensitization to anti-PD-1 in microsatellite stable (MSS) CRC. This article covers mechanistic, genomic, and molecular epidemiology evidence, outlines analytic standards for signature detection (whole-genome sequencing (WGS)/whole-exome sequencing (WES), single-sample fitting, and limits at low mutation counts), and charts translational paths spanning noninvasive screening (stool metagenomics + mutational signatures in tissue/circulating tumor DNA (ctDNA)), risk stratification, and microbial-targeted interventions (antibiotics, phages, ClbP inhibitors). Framing microbiome-genome crosstalk as a tractable axis enables testable clinical hypotheses for precision oncology.},
}

*Colorectal Neoplasms/epidemiology/genetics/microbiology
Humans
*Fusobacterium nucleatum/genetics
*Polyketides/metabolism
*Peptides/metabolism
*Gastrointestinal Microbiome
Mutation
*Bacteriocins/metabolism/genetics
*Microbiota

@article {pmid41746975,
year = {2026},
author = {Wang, G and Liu, L and Zhang, H and Mao, P and Lu, S and Zhang, X and Li, X and Song, C},
title = {Effects of tacrolimus treatment on the gut microbiota and metabolites in liver transplant recipients.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0343817},
pmid = {41746975},
issn = {1932-6203},
mesh = {Humans ; *Tacrolimus/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Liver Transplantation/adverse effects ; Male ; Female ; Middle Aged ; *Immunosuppressive Agents/therapeutic use/pharmacology ; Adult ; Feces/microbiology ; Aged ; Dysbiosis ; Transplant Recipients ; Tandem Mass Spectrometry ; Metabolome/drug effects ; },
abstract = {BACKGROUND: Liver transplantation (LT) is an effective treatment for patients with end-stage liver disease. In recent years, more and more evidence has supported the association between gut microbiota dysbiosis and the pathogenesis and progression of liver diseases.

METHODS: The study included 36 patients who received tacrolimus treatment after liver transplantation. Patients were stratified into subgroups according to three key variables: tacrolimus treatment duration, whole-blood tacrolimus concentration, and tacrolimus concentration-to-dose (C/D) ratio. Fecal samples and whole-blood specimens were collected from all participants. The Illumina HiSeq X platform was used to detect the gut metagenome, analyzing the composition and characteristics of the gut microbiota. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology was employed to detect metabolites of the gut microbiota, revealing their metabolic profiles.

RESULTS: As the duration of tacrolimus use increased, the diversity of the gut microbiota also increased, and the abundance of Escherichia coli_D and Bacteroides stercoris rose. Additionally, the abundance of Brunovirus and Uetakevirus tended to decrease. The abundance of gene functions related to chemical carcinogenesis and bacterial invasion of epithelial cells significantly decreased. In the gut microbiota metabolites, 16 substances like Astragaloside A and Acetyl-L-carnitine significantly increased, while 108 substances like Capsaicin and TLK significantly decreased. Within a certain range, as the concentration of tacrolimus in whole blood increased, the diversity of the gut microbiota increased. The abundance of Phocaeicola and Klebsiella increased, and the abundance of Peduovirus among viruses also rose. However, excessively high concentrations may lead to a decrease in the diversity of the gut microbiota and a decrease in the abundance of Phocaeicola. With respect to the C/D ratio, increased ratios were linked to significantly higher levels of 57 fecal metabolites (e.g., PC 34:2, 5-Methyl-2'-deoxycytidine), whereas 13 metabolites (e.g., FAHFA 2:0/16:0) showed substantial declines.

CONCLUSIONS: Tacrolimus treatment is associated with distinct alterations in gut microbiota and metabolites among LT recipients. These findings provide a preliminary framework for future investigations aimed at optimizing immunosuppressive regimens, although their clinical translational potential requires validation in larger-scale, prospective cohort studies.},
}

Humans
*Tacrolimus/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
*Liver Transplantation/adverse effects
Male
Female
Middle Aged
*Immunosuppressive Agents/therapeutic use/pharmacology
Adult
Feces/microbiology
Aged
Dysbiosis
Transplant Recipients
Tandem Mass Spectrometry
Metabolome/drug effects

@article {pmid41729067,
year = {2026},
author = {Liu, Y and Zhang, T and Liu, J and Dong, X},
title = {Lactiplantibacillus plantarum Fermentation Enhances the Bioactivity of Polymeric Proanthocyanidins: Gut Microbiota Regulation via Caffeic Acid Production.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {8},
pages = {6824-6839},
doi = {10.1021/acs.jafc.5c14510},
pmid = {41729067},
issn = {1520-5118},
mesh = {*Proanthocyanidins/metabolism/chemistry ; *Caffeic Acids/metabolism ; Fermentation ; *Gastrointestinal Microbiome ; *Lactiplantibacillus plantarum/metabolism/isolation & purification/genetics ; Probiotics/metabolism ; Humans ; *Polymers/metabolism/chemistry ; Feces/microbiology ; *Lactobacillaceae/metabolism/genetics/isolation & purification ; Animals ; },
abstract = {Polymeric proanthocyanidins (PPC) typically exhibit low bioavailability. While probiotic metabolism can enhance polyphenol bioactivity, the interaction between Lactiplantibacillus plantarum and PPC remains underexplored. In this study, L. plantarum SFFI23, a strain exhibiting excellent capacity to metabolize PPC, was selectively isolated. During in vitro digestion and fecal fermentation, SFFI23 reduced the degree of polymerization of PPC and enhanced overall antioxidant capacity. Metagenomic analysis revealed that SFFI23-PPC metabolism resulted in Firmicutes enrichment, accompanied by opportunistic pathogen reduction and an upregulation of health-associated pathways such as quorum sensing. Metabolomics analysis showed significant enrichment in 17 metabolic pathways. Multiomics analyses revealed that caffeic acid, derived from SFFI23-PPC metabolism, contributes to improved gut health by regulating gut microbiota and promoting metabolic reprogramming. This study outlines a triadic mechanism: "biotransformation by L. plantarum-metabolic activation of PPC-gut microbiota regulation", highlighting the potential of SFFI23 as an adjunct for enhancing PPC bioactivity.},
}

*Proanthocyanidins/metabolism/chemistry
*Caffeic Acids/metabolism
Fermentation
*Gastrointestinal Microbiome
*Lactiplantibacillus plantarum/metabolism/isolation & purification/genetics
Probiotics/metabolism
Humans
*Polymers/metabolism/chemistry
Feces/microbiology
*Lactobacillaceae/metabolism/genetics/isolation & purification
Animals

@article {pmid41719987,
year = {2026},
author = {Dang, X and Xu, S},
title = {Exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate is associated with aberrant barbering behavior in diabetic mice.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119906},
doi = {10.1016/j.ecoenv.2026.119906},
pmid = {41719987},
issn = {1090-2414},
mesh = {Animals ; Male ; Mice ; Hippocampus/drug effects ; *Behavior, Animal/drug effects ; Molecular Docking Simulation ; Diabetes Mellitus, Experimental ; *Alkanesulfonic Acids/toxicity ; Salmonella enterica ; Gastrointestinal Microbiome/drug effects ; *Environmental Pollutants/toxicity ; Molecular Dynamics Simulation ; Colon/microbiology ; Fluorobenzenes ; },
abstract = {This study originated from an incidental behavioral observation. We found that exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate (OBS; 3 μg/L), as reported in a previous field measurement study, was associated with aberrant barbering behavior in diabetic mice. To investigate the underlying mechanisms, sixteen 8-week-old male db/db mice were administered OBS at 3 μg/L for 91 days. Biochemical assays of endothelial- and barrier-related markers, hippocampal OBS quantification, stereotaxic hippocampal OBS administration, and metagenomic sequencing of the colonic contents and hippocampal tissues were performed. Based on the metagenomic results, computational biology analyses, including molecular docking, molecular dynamics simulations, and protein functional annotation, were conducted to assess potential OBS-bacterial protein interactions. The results showed that exposure to environmentally relevant concentration of OBS was associated with aberrant barbering behavior in the experimental mice (100 % prevalence). Circulating markers of endothelial activation and basal lamina injury were significantly elevated. Metagenomic analysis revealed that the abundance of Salmonella enterica subsp. diarizonae was significantly increased in both the colonic contents and hippocampal tissues, with hippocampal abundance positively correlated with colonic abundance. Molecular docking and molecular dynamics simulations indicated that OBS binds effectively to two bacterial proteins. Functional annotation suggested that these proteins are associated with central metabolic and biosynthetic processes relevant to bacterial proliferation. Together, these findings suggest that exposure to environmentally relevant concentration of OBS is associated with aberrant barbering behavior in diabetic mice and may be associated with increased colonic S. enterica subsp. diarizonae abundance and its presence in the hippocampus.},
}

Animals
Male
Mice
Hippocampus/drug effects
*Behavior, Animal/drug effects
Molecular Docking Simulation
Diabetes Mellitus, Experimental
*Alkanesulfonic Acids/toxicity
Salmonella enterica
Gastrointestinal Microbiome/drug effects
*Environmental Pollutants/toxicity
Molecular Dynamics Simulation
Colon/microbiology
Fluorobenzenes

@article {pmid41715225,
year = {2026},
author = {Ding, L and Yang, S and Wu, F and Pilling, D and Zhang, J and Pool, K and Nishvanthi, M and Babington, S and Maloney, SK and Chen, L and Shi, J and Wang, Y and Blache, D and Wang, M},
title = {Association between the gut microbiome and plasma metabolites linked to vocalization-based temperament in Merino sheep.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41715225},
issn = {2049-2618},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Sheep/microbiology/physiology/blood ; *Temperament/physiology ; *Vocalization, Animal/physiology ; Rumen/microbiology ; *Metabolome ; Female ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; gamma-Aminobutyric Acid/metabolism ; },
abstract = {BACKGROUND: Temperament, as a determinant of behavioural and emotional responses, has a substantial adaptive value in different environments. This study aims to investigate the association between the gut microbiota and temperament plasticity, and clarify the potential metabolic mechanism that underpins that association by running a multi-omics study in sheep.

METHODS: The TrackSheep research cohort was generated using 200 healthy juvenile Merino ewes, and the rumen microbiota, plasma metabolome, and temperament phenotype was measured.

RESULTS: Rumen metagenomic analysis identified 25 microbial species and 16 MetaCyc pathways that explained 37.5% and 11.1%, respectively, of the variation in temperament as estimated using the vocal reactivity to stress. Among these, the γ-aminobutyric acid (GABA) shunt and allantoin degradation pathways showed the strongest associations with vocal behaviour. Multi-omic integration linked these microbial pathways to plasma metabolites that are involved in neurotransmission, antioxidant defense, and energy metabolism, including acetyl-L-carnitine (ALCAR) and urocortisone, which partially mediated the effects of microbial pathways on vocalisations. Notably, functional genomic and mediation analyses indicated that the abundance of Cryptobacteroides sp902761655 was associated with the activity of GABA shunt pathway, where GABA co-occurred with succinate production, in turn correlating with reduced inhibitory effects of ALCAR on stress-susceptible temperament. Although plasma metabolite shifts observed immediately after behavioural tests reflected stress exposure, their associations with rumen microbiota highlight microbiome-metabolite interplay that could underly behavioural variation.

CONCLUSIONS: Our study provides the first large-scale multi-omics evidence linking the rumen microbiome to a dimension of emotional reactivity in livestock, while underscoring the need for longitudinal and experimental validation to establish causal mechanisms. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/physiology
Sheep/microbiology/physiology/blood
*Temperament/physiology
*Vocalization, Animal/physiology
Rumen/microbiology
*Metabolome
Female
Metagenomics
Bacteria/classification/genetics/isolation & purification
gamma-Aminobutyric Acid/metabolism

@article {pmid41691814,
year = {2026},
author = {Guo, H and Liu, Q and Han, H and Xu, W and Shi, W and Zhao, M and Xiao, X and Liu, J and Li, T},
title = {Unveiling the adaptive evolution of halotolerant aceticlastic methanogenesis: Multi-scale responses and energy partition.},
journal = {Water research},
volume = {294},
number = {},
pages = {125552},
doi = {10.1016/j.watres.2026.125552},
pmid = {41691814},
issn = {1879-2448},
mesh = {Methane/metabolism ; Wastewater ; Microbiota ; Acetates/metabolism ; },
abstract = {The high concentration of salt ions in saline organic wastewater poses significant challenges for wastewater treatment technologies, particularly impacting the stability of anaerobic digesters. Aceticlastic methanogenesis is a crucial pathway for converting acetate into methane through methanoarchaea whose metabolism is adversely impacted by salt stress. To address this, long-term adaptive laboratory evolution (ALE) was conducted to cultivate halotolerant aceticlastic methanoarchaea, incorporating metagenomics, metatranscriptomic sequencing, metabolomics, and metabolic modeling to delineate genetic and metabolic responses. The evolved microbiome achieved a substantial increase in methanogenic activity at 5 % sodium chloride, reaching 82.25 % theoretical conversion of acetate to methane, significantly outperforming the original microbiome. This ALE process overcame the natural scarcity of aceticlastic methanogens in hypersaline environments. Key adaptation mechanisms were confirmed at the transcriptional level, primarily involving the upregulation of genes for inorganic ion transport, compatible solute uptake, and de novo biosynthesis. Horizontal gene transfer also contributed significantly through the transfer of osmoregulation genes, particularly those for compatible solute transport, suggesting an energy-efficient adaptation strategy of accumulating rather than synthesizing solutes. Metabolic flux analysis revealed that adjustments in energy distribution under salt stress are driven by the energetic cost of synthesizing compatible solutes, which highlights the importance of solute transporters for energy conservation. This study elucidates the complex interplay between metabolic reprogramming and gene transfer in enhancing microbial resilience under salt stress, thereby deepening our understanding of microbial adaptations in extreme environments and advancing biotechnological approaches for saline wastewater treatment.},
}

Methane/metabolism
Wastewater
Microbiota
Acetates/metabolism

@article {pmid41669888,
year = {2026},
author = {Yeo, LF and Palmu, J and Havulinna, AS and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T},
title = {Prospective association between the gut microbiome and incident hypertension: a 20-year cohort study.},
journal = {Journal of hypertension},
volume = {44},
number = {4},
pages = {673-681},
pmid = {41669888},
issn = {1473-5598},
mesh = {Humans ; *Hypertension/epidemiology/microbiology ; Middle Aged ; Female ; Male ; *Gastrointestinal Microbiome ; Adult ; Aged ; Prospective Studies ; Finland/epidemiology ; Incidence ; Risk Factors ; Cohort Studies ; },
abstract = {INTRODUCTION: Hypertension remains the leading modifiable risk factor attributable to 10.8 million premature deaths. Hence the study of hypertension and gut microbiome as a therapeutic target is very important. Yet the links between the gut microbiome and long-term incidence of hypertension are unknown.

AIM: This study assessed the association between gut microbiome and incident hypertension.

METHOD: The study sample consisted of 3311 nonhypertensive individuals (60.7% women) aged 25-74  years who were drawn from the general population in Finland. In the baseline examination performed in the year 2002, the participants underwent a health examination and provided a stool sample. The gut microbiome was assessed using shallow shotgun metagenomic sequencing. Microbiome analyses were performed with Cox proportional hazards model.

RESULTS: In total, 675 participants developed hypertension over a follow-up period of nearly 20 years. In multivariable-adjusted models, overall gut microbiome composition was not related to risk of future hypertension. Eight genera, including Agathobaculum, Blautia_A_141780, Blautia_A_141781, Mediterraneibacter_A_155590, Enterocloster , Bariatricus , CAG-317-146760 , and CAG-628 were significantly associated with incident hypertension in the age-adjusted and sex-adjusted models, but none remained significant in the multivariable-adjusted models. No functional pathways were associated with hypertension risk.

CONCLUSION: Our results do not provide strong evidence for an association between the gut microbiome and risk of future hypertension, especially after adjusting for covariates that are known to influence the gut microbiome.},
}

Humans
*Hypertension/epidemiology/microbiology
Middle Aged
Female
Male
*Gastrointestinal Microbiome
Adult
Aged
Prospective Studies
Finland/epidemiology
Incidence
Risk Factors
Cohort Studies

@article {pmid41653958,
year = {2026},
author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ},
title = {Household environmental characteristics influence the house dust metagenome.},
journal = {Environmental research},
volume = {295},
number = {},
pages = {123889},
doi = {10.1016/j.envres.2026.123889},
pmid = {41653958},
issn = {1096-0953},
mesh = {*Dust/analysis ; *Metagenome ; Humans ; *Microbiota ; *Family Characteristics ; Housing ; *Air Pollution, Indoor/analysis ; *Environmental Exposure ; },
abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.},
}

*Dust/analysis
*Metagenome
Humans
*Microbiota
*Family Characteristics
Housing
*Air Pollution, Indoor/analysis
*Environmental Exposure

@article {pmid41636495,
year = {2026},
author = {Kopp, OS and Morandi, SC and Kreuzer, M and Uldry, A-C and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC},
title = {Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.},
journal = {Microbiology spectrum},
volume = {14},
number = {3},
pages = {e0226425},
pmid = {41636495},
issn = {2165-0497},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; },
mesh = {Humans ; Female ; *Tears/chemistry/metabolism ; Male ; *Dry Eye Syndromes/microbiology/etiology ; *Proteome/analysis ; *Microbiota ; Adult ; *Contact Lenses/adverse effects ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; Middle Aged ; Eye Proteins ; },
abstract = {Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.},
}

Humans
Female
*Tears/chemistry/metabolism
Male
*Dry Eye Syndromes/microbiology/etiology
*Proteome/analysis
*Microbiota
Adult
*Contact Lenses/adverse effects
Bacteria/classification/genetics/isolation & purification
Young Adult
Middle Aged
Eye Proteins

@article {pmid41634815,
year = {2026},
author = {Hao, X and Wang, X and Wang, X and Wang, C and Li, C and Lu, Y and Cheng, Q and Chen, Z and Zhu, L and Li, C and Shen, X},
title = {Synthetic community derived from the root core microbes of a desert shrub Caragana korshinskii enhances wheat drought tolerance.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41634815},
issn = {2049-2618},
mesh = {*Triticum/growth & development/microbiology/physiology ; *Droughts ; *Caragana/microbiology ; *Plant Roots/microbiology ; Biofilms/growth & development ; *Microbiota ; Desert Climate ; Quorum Sensing ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; Drought Resistance ; },
abstract = {BACKGROUND: Drought, intensified by climate change, poses a mounting threat to global food security by severely constraining crop productivity. While microbial inoculants offer promise for drought tolerance, their poor adaptability remains insufficient for extremely water-deficient environments. Desert plants host unique drought-adapted microbiomes that remain largely unexplored for agricultural applications.

RESULTS: Here, we investigated the microbial community of the desert shrub Caragana korshinskii and identified a core set of drought-responsive strains. A synthetic microbial community (SynCom) derived from these strains significantly improved wheat growth under drought stress. Metagenomic analyses revealed that microbial functions related to biofilm formation, quorum sensing, and carbon metabolism were enriched, with Pseudomonas identified as a key functional taxon. Guided by inter-strain interactions in biofilm assembly, we streamlined the consortium into a five-member synthetic community, where quorum-sensing signals promoted community-wide biofilm formation. Community biofilm production improved strain colonization and conferred greater drought tolerance compared to monocultures. In plants, mechanistic investigations indicated that the simplified SynCom inoculation universally upregulated MAPK and jasmonic acid signaling pathways. Furthermore, carbohydrate metabolic pathways such as starch and sucrose metabolism were specifically activated, suggesting a multi-level mechanism underlying SynCom-mediated drought tolerance.

CONCLUSIONS: These findings demonstrate that SynCom constructed on the endophytic flora of desert plants can significantly enhance crop drought tolerance. Our work highlights the pivotal role of community biofilm synthesis in facilitating root colonization and activating a multidimensional drought tolerance network in plants. This study not only gives an ecological perspective on desert microbiome adaptations but also offers a strategic framework for developing effective microbial inoculants for arid-region agriculture. Video Abstract.},
}

*Triticum/growth & development/microbiology/physiology
*Droughts
*Caragana/microbiology
*Plant Roots/microbiology
Biofilms/growth & development
*Microbiota
Desert Climate
Quorum Sensing
Metagenomics/methods
Bacteria/classification/genetics/isolation & purification
Drought Resistance

@article {pmid41619209,
year = {2026},
author = {Tang, R and Wang, J and Wang, X and Zeng, M and Gao, W and Yang, K and Xu, L and Li, Y and Zhou, C and Yue, B and Fan, Z and Song, Z},
title = {Large-scale metagenomic analysis reveals host genetics shapes microbiomes in wild freshwater fish gut and skin.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116930},
doi = {10.1016/j.celrep.2026.116930},
pmid = {41619209},
issn = {2211-1247},
mesh = {Animals ; *Skin/microbiology ; *Metagenomics/methods ; Fresh Water ; *Fishes/microbiology/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Microbiota/genetics ; },
abstract = {Wild freshwater fish microbiomes remain underexplored despite their ecological and economic importance. Through metagenomic sequencing of 903 gut/skin samples from 121 species in southwest China, we constructed the Wild Freshwater Fish Microbiome Catalog, comprising 705 metagenome-assembled genomes and 3,271 viral operational taxonomic units. Host phylogeny dominates microbial community variation, explaining 48.2% (skin) and 22.28% (gut) of the variation. Significant phylosymbiosis occurs in wild freshwater fish, particularly Cyprinidae, with a stronger skin than gut signal. Deterministic selection underpins phylosymbiosis via host-specific ecological filtering. Lifestyle factors (diet, living water layer) and geographical location also impact microbial communities. Notably, wild freshwater fish microbiota harbor a complete set of vitamin B12de novo biosynthesis genes, with Cetobacterium as a keystone genus with probiotic potential. Our work expands gut and skin microbial genome resources, reveals host-microbe coevolution in freshwater fishes, and provides probiotic resources for aquaculture.},
}

Animals
*Skin/microbiology
*Metagenomics/methods
Fresh Water
*Fishes/microbiology/genetics
Phylogeny
*Gastrointestinal Microbiome/genetics
Metagenome/genetics
*Microbiota/genetics

@article {pmid41617733,
year = {2026},
author = {Thangaraj, S and Sun, J},
title = {Depth Resolved Metagenomic Dataset from Surface and Deep Chlorophyll Maximum Layers in the Western Pacific Ocean.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41617733},
issn = {2052-4463},
mesh = {Pacific Ocean ; *Metagenomics ; *Metagenome ; *Chlorophyll/analysis ; *Seawater/microbiology ; *Microbiota ; },
abstract = {Stratified microbial communities are central to ocean biogeochemical cycles, yet their vertical structure and functional potential remain under characterized in oligotrophic regions. We present a metagenomic dataset from surface ocean and the deep chlorophyll maximum (DCM) layers of the stratified Western Pacific Ocean, sampled at four stations spanning approximately 800 kilometres. Each of the eight samples generated over 22.9 Gb of high-quality Illumina HiSeq 2500 paired end reads (Q20 > 95%, Q30 > 90%). De novo assemblies yielded 1.3-1.9 million contigs per sample, with total assembly sizes of 948 Mb to 1.33 Gb and N50 values of 632-749 bp. Gene prediction identified ~5.26 million non-redundant genes across all samples, reflecting substantial microbial diversity and depth-specific variation. Assembly statistics, taxonomic profiles, and functional annotations of genes are included for technical validation of the dataset, demonstrating data completeness and analytical depth. This dataset offers annotated sequence data and environmental metadata suitable for benchmarking, method development, and comparative studies of marine metagenomes.},
}

Pacific Ocean
*Metagenomics
*Metagenome
*Chlorophyll/analysis
*Seawater/microbiology
*Microbiota

@article {pmid41617710,
year = {2026},
author = {Shrestha, B and Romero, MF and Villada, JC and , and Blaby-Haas, CE and Schulz, F},
title = {Global metagenomics reveals plastid diversity and unexplored algal lineages.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41617710},
issn = {2041-1723},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
mesh = {*Plastids/genetics/classification ; *Metagenomics/methods ; Phylogeny ; Symbiosis/genetics ; Cyanobacteria/genetics/classification ; Biodiversity ; Genetic Variation ; Haptophyta/genetics/classification ; Cryptophyta/genetics/classification ; Genome, Plastid ; Alveolata/genetics ; Photosynthesis/genetics ; Evolution, Molecular ; },
abstract = {Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We capture 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights into plastid evolution in haptophytes and cryptophytes. Our results confirm that Archaeplastida plastids originate from an early branching cyanobacterial lineage closely related to Gloeomargaritales and identify the closest extant relative of Paulinella plastids. Additionally, our findings suggest two independent origins of secondary red-algal plastids, contributing to plastid diversity in CASH lineages and challenging the prevailing model of single secondary plastid origin. Our study highlights the importance of metagenomic data in uncovering biological diversity and advancing understanding of plastid relationships across photosynthetic eukaryotes.},
}

*Plastids/genetics/classification
*Metagenomics/methods
Phylogeny
Symbiosis/genetics
Cyanobacteria/genetics/classification
Biodiversity
Genetic Variation
Haptophyta/genetics/classification
Cryptophyta/genetics/classification
Genome, Plastid
Alveolata/genetics
Photosynthesis/genetics
Evolution, Molecular

@article {pmid41587576,
year = {2026},
author = {Mburu, D and Kumar, S and Wang, Y and Namagerdi, AA and Bai, K and Ali, B and Minalla, A and Gonzales, KO and Abdelhalim, KA},
title = {The oxalobiome: unraveling the role of gut microbiota in oxalate metabolism and its implications for kidney health and disease management.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {584},
number = {},
pages = {120852},
doi = {10.1016/j.cca.2026.120852},
pmid = {41587576},
issn = {1873-3492},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Oxalates/metabolism ; *Kidney/metabolism ; Hyperoxaluria/metabolism ; Disease Management ; },
abstract = {The oxalobiome, comprising microbial communities involved in oxalate metabolism, plays a critical role in maintaining oxalate homeostasis and preventing associated health issues, particularly calcium oxalate nephrolithiasis. Key organisms, notably Oxalobacter formigenes, are essential for degrading oxalate, yet their abundance is influenced by factors such as diet, genetics, and antibiotic use. Recent advances in research have elucidated the complex interactions between the gut microbiome and oxalate metabolism, highlighting the potential for therapeutic interventions. Innovative strategies, including RNA interference therapies (e.g., lumasiran, nedosiran), engineered probiotics, and gene-editing technologies, show promise in managing conditions like primary hyperoxaluria. However, challenges remain, including limitations in oxalate measurement techniques and variability in microbial populations. Multi-omics approaches and metagenomic analyses have enhanced our understanding of the oxalobiome, revealing novel microbial taxa and metabolic pathways involved in oxalate degradation. Despite the potential of emerging therapies, clinical translation is still in its infancy, necessitating further research to establish efficacy and safety. Future studies should focus on mechanistic insights, standardized methodologies, and targeted microbiome-based therapies to optimize management strategies for hyperoxaluria and related systemic diseases. A comprehensive understanding of the oxalobiome is essential for developing precision medicine approaches that effectively address oxalate dysregulation and improve patient outcomes.},
}

Humans
*Gastrointestinal Microbiome
*Oxalates/metabolism
*Kidney/metabolism
Hyperoxaluria/metabolism
Disease Management

@article {pmid41540332,
year = {2026},
author = {Wang, Y and Wu, C and Zhu, Q and Fan, C and Zhu, Y and Chen, Y and Wei, X and Feng, L},
title = {Comparative metagenomic characterization of gut microbiota and antibiotic resistome in multi-facility SPF mice.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41540332},
issn = {1471-2180},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; Mice ; *Metagenomics/methods ; Mice, Inbred C57BL ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; Mice, Inbred BALB C ; Specific Pathogen-Free Organisms ; Cecum/microbiology ; Metagenome ; *Drug Resistance, Microbial/genetics ; },
abstract = {Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.},
}

Animals
*Gastrointestinal Microbiome/genetics/drug effects
Mice
*Metagenomics/methods
Mice, Inbred C57BL
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/classification/drug effects/isolation & purification
Mice, Inbred BALB C
Specific Pathogen-Free Organisms
Cecum/microbiology
Metagenome
*Drug Resistance, Microbial/genetics

@article {pmid41527291,
year = {2026},
author = {Chen, W and Guo, R and Zhang, W and Yan, Q and Wang, X and Chen, R and Hu, X and Liang, J and Xing, G and Xu, D and Ma, X and Chen, Q and Sha, S and Tao, E and Cheng, L and Fan, S and Liu, H and Lu, T and Yu, H and Su, J and Xu, J and Qin, Y and Liu, J and Zhong, X and Hu, X and Hu, X and Zheng, W and Hu, Z and Kang, J and Yang, J},
title = {Alterations of the gut virome in patients with Parkinson's disease.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {81},
number = {3},
pages = {},
doi = {10.1093/gerona/glag001},
pmid = {41527291},
issn = {1758-535X},
support = {82370563//National Natural Science Foundation of China/ ; 2024JJ7423//Natural Science Foundation of Hunan Province/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; },
mesh = {Humans ; *Parkinson Disease/virology/microbiology ; *Gastrointestinal Microbiome ; *Virome ; Male ; Female ; Aged ; Case-Control Studies ; Middle Aged ; Metagenomics ; },
abstract = {Gut microbiota plays a pivotal role in Parkinson's disease (PD) pathogenesis. However, the role of enteric viruses remains underexplored. Here, we reanalyzed publicly available metagenomic datasets from two independent cohorts, including 79 PD patients and 79 controls, to characterize gut virome profiles and explore the potential role of enteric viruses in PD pathogenesis and early diagnosis. Our findings indicate increased richness and diversity of the gut virome in PD, with 640 vOTUs differing in abundance between groups. Notably, Siphoviridae and Myoviridae were more abundant in PD patients. A variety of viruses enriched in PD or healthy subjects (HS) preferentially infect bacterial hosts that produce short-chain fatty acids. Furthermore, specific viral functional orthologs, such as thymidylate synthase (K00560) and integrases (K14059), displayed notable differences in prevalence between PD-enriched and HS-enriched vOTUs. Finally, we constructed a random forest model using the top 22 most significant vOTUs, which achieved an AUC of 0.822, demonstrating strong performance in distinguishing PD patients from healthy controls. This is the first study to characterize the gut virome profile in PD, laying a robust foundation for future investigations into the underlying mechanisms and early diagnosis strategies for PD as well as other neurodegenerative disorders.},
}

Humans
*Parkinson Disease/virology/microbiology
*Gastrointestinal Microbiome
*Virome
Male
Female
Aged
Case-Control Studies
Middle Aged
Metagenomics

@article {pmid41468749,
year = {2026},
author = {Liu, X and Ma, T and Khan, I and Chen, L and Zhang, H},
title = {Age-dependent variations in aerosol-borne particulates and microbial communities in multi-tier broiler housing systems: A metagenomics environmental health risk assessment.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106308},
pmid = {41468749},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology/physiology ; *Particulate Matter/analysis ; *Housing, Animal ; Metagenomics ; *Microbiota ; Risk Assessment ; *Air Microbiology ; Aerosols/analysis ; *Air Pollutants/analysis ; Bacteria/isolation & purification/classification ; Age Factors ; Animal Husbandry ; },
abstract = {By investigating the temporal dynamics of airborne microbial communities associated with particulate matter in multi‑tier broiler housing, this study offers a systematic reference for understanding how environmental microbiota shift with broiler age. Fine particulate matter (PM2.5) and total suspended particulate (TSP) were collected from the housing environment at three growth stages: D10 (10-day-old), D24 (24-day-old), and D38 (38-day-old). The concentration and LPS content of the collected TSP and PM2.5 samples from each stage were measured, followed by metagenomic sequencing. Results revealed that the concentrations of TSP and PM2.5 peaked at D24 (P < 0.05), showing a trend of first increasing and then decreasing, and the change trend of mortality in the early stage was similar. Metagenomic results identified that Faecalibacterium, Pseudomonas, and Acinetobacter were the dominant genera at D24, whereas Enterococcus and Macrococcus were the dominant genera at D10 and D38, respectively. Correlation analysis further indicated that TSP was positively associated with mortality and g_Pseudomonas, while PM2.5 was positively associated with g_Faecalibacterium. Significant enrichment was observed in metabolic pathways such as glycosyltransferase 35 and glycoside hydrolase 23, macB, LOS(CVF494), and other antibiotic resistance and virulence genes in TSP and PM2.5 (P < 0.05). Collectively, these findings elucidate the stage‑specific dynamics of environmental microbiota in broiler housing and underscore particulate matter as a potential driver of both microbial shifts and health outcomes, thereby providing evidence to inform interventions aimed at improving environmental and flock health.},
}

Animals
*Chickens/microbiology/physiology
*Particulate Matter/analysis
*Housing, Animal
Metagenomics
*Microbiota
Risk Assessment
*Air Microbiology
Aerosols/analysis
*Air Pollutants/analysis
Bacteria/isolation & purification/classification
Age Factors
Animal Husbandry

@article {pmid41413233,
year = {2026},
author = {Ikagawa, Y and Okamoto, S and Taniguchi, K and Mizoguchi, R and Hashimoto, A and Imamura, R and Arakawa, H and Ogura, K and Yanagihara, M and Tsujiguchi, H and Hara, A and Nakamura, H and Hosomichi, K and Karashima, S},
title = {Gut microbiota-derived polyamine pathways associated with mean blood pressure.},
journal = {Hypertension research : official journal of the Japanese Society of Hypertension},
volume = {49},
number = {3},
pages = {958-968},
pmid = {41413233},
issn = {1348-4214},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Male ; *Blood Pressure/physiology ; *Polyamines/metabolism ; Female ; *Hypertension/microbiology/metabolism/physiopathology ; Aged ; Adult ; Feces/microbiology ; },
abstract = {Hypertension is a common lifestyle-related disease and is influenced by various factors, including excessive salt intake. Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood. Sixty participants aged ≥40 years from Shika Town, Japan, were stratified into four groups (n = 15 each) based on mean blood pressure and urinary sodium chloride (u-NaCl) excretion. The clinical parameters were evaluated, and fecal samples were analyzed using shotgun metagenomic sequencing to assess the microbial composition and abundance of genes related to arginine-polyamine metabolism. Three major findings were observed: (1) Significant differences in the α-diversity of GM were observed between salt-sensitive and non-salt-sensitive hypertensive groups; (2) The abundance of spermidine synthase (EC 2.5.1.16), a key enzyme in polyamine metabolism with known antihypertensive effects, was significantly higher in normotensive individuals, independent of u-NaCl excretion; and (3) Bacterial species harboring polyamine metabolic enzyme genes, including EC 2.5.1.16, differed significantly between groups, suggesting group-specific microbial metabolic traits. These findings suggest that GM-mediated polyamine metabolism may contribute to the regulation of salt-sensitive blood pressure. While variations in spermidine-producing bacteria and the involvement of EC 2.5.1.16 were observed, these factors alone do not fully account for the intergroup differences related to salt intake. Thus, polyamine metabolism likely plays a part in salt sensitivity, but additional microbial and host factors are also involved. Further studies are needed to validate these findings and to explore microbiota-targeted strategies for the prevention and treatment of hypertension.},
}

Humans
*Gastrointestinal Microbiome/physiology
Middle Aged
Male
*Blood Pressure/physiology
*Polyamines/metabolism
Female
*Hypertension/microbiology/metabolism/physiopathology
Aged
Adult
Feces/microbiology

@article {pmid41401693,
year = {2026},
author = {Chen, J and Li, J and Lin, Z and Zhang, Y and Lin, L and Guo, S and Huang, S and Li, X and Ma, J},
title = {Research note: Virome of Alectoris chukars by metagenomic analysis in Guangdong, southern China.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106246},
pmid = {41401693},
issn = {1525-3171},
mesh = {China/epidemiology ; Animals ; *Virome ; Metagenomics ; *Galliformes/virology ; *Metagenome ; },
abstract = {Alectoris Chukar (Chukar) has been introduced to numerous countries for stocking farms or release for hunting purposes. China imported commercial chuckars in the 1980s, and Guangdong Province was the first province in mainland China to feed on this species on stock farms; however, few reports have described the species and amount of virus circulating in it. In this study, meta-transcriptome analysis was conducted to reveal the virome in 34 unexplained dead chukars in Guangdong, southern China, which identified 2 novel viruses and 1 known virus, including the Alectoris chukar Avian leukosis-like virus (ACALLV) in the family Retroviridae, the GD-Alectoris chukar orthobunya virus (GD-ACOBV) in the family Peribunyaviridae, and an infectious bronchitis virus strain GD-Alectoris chukar strain (IBV-GDAC). These findings are the first to reveal the virome of chukars in Guangdong Province, providing more information to identify the virus circulating in chukars.},
}

China/epidemiology
Animals
*Virome
Metagenomics
*Galliformes/virology
*Metagenome

@article {pmid41364878,
year = {2026},
author = {Yoon, SE and Kang, W and Cho, J and Cho, HJ and Chalita, M and Oh, HS and Hyun, DW and Han, S and Kim, H and Sung, H and Lee, JY and Park, B and Ryu, KJ and Kim, HY and Cho, D and Kim, WS and Kim, SJ},
title = {Microbiome and metabolite biomarkers of CAR T-cell therapy outcomes in relapsed/refractory diffuse large B-cell lymphoma.},
journal = {Blood advances},
volume = {10},
number = {5},
pages = {1634-1645},
pmid = {41364878},
issn = {2473-9537},
mesh = {Humans ; *Lymphoma, Large B-Cell, Diffuse/therapy/microbiology/metabolism/mortality ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Immunotherapy, Adoptive/adverse effects/methods ; Aged ; Biomarkers ; Treatment Outcome ; Adult ; Recurrence ; },
abstract = {CD19 chimeric antigen receptor (CAR) T-cell therapy has revolutionized treatment for relapsed/refractory diffuse large B-cell lymphoma (R/R-DLBCL), but challenges such as posttreatment failure and immune-related adverse events (AEs) persist. This study explores the gut microbiome as a predictive biomarker for CAR T-cell therapy outcomes and toxicity. Stool and serum samples from patients with R/R-DLBCL were analyzed at apheresis (47 samples) and 1 month after infusion (32 samples) using whole-genome sequencing metagenomics. When compared with healthy controls and newly-diagnosed DLBCL, R/R-DLBCL showed significant gut dysbiosis, characterized by increased Proteobacteria and Enterobacteriaceae. Responders had higher levels of Bacteroides fragilis, whereas nonresponders exhibited higher levels of Faecalibacterium prausnitzii. Functional metagenomic analysis suggested enrichment of inosine biosynthesis pathways in responders, and elevated serum inosine demonstrated an exploratory association with improved progression-free survival. Distinct microbial taxa and serum fatty acid profiles were also linked to CAR T-cell-related AEs, with higher acetate and butyrate levels in patients without AEs and increased isovalerate in those with AEs. These findings indicate that gut microbiome features-particularly Bacteroides fragilis and inosine metabolism-may serve as candidate biomarkers for CAR T-cell therapy outcomes and toxicity. However, given the exploratory nature of these analyses and the limited cohort size, results should be interpreted cautiously. Larger, prospective studies will be required to validate these observations and to assess the potential of microbiome-based strategies to optimize CAR T-cell therapy in R/R-DLBCL.},
}

Humans
*Lymphoma, Large B-Cell, Diffuse/therapy/microbiology/metabolism/mortality
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Immunotherapy, Adoptive/adverse effects/methods
Aged
Biomarkers
Treatment Outcome
Adult
Recurrence

@article {pmid41093027,
year = {2026},
author = {Li, KY and Zhou, JL and Tian, ZH and Gao, F},
title = {N-acyl-homoserine lactone regulation of nutrient removal, microbial community assembly, and process efficacy in dialysis membrane-algal-bacterial photobioreactors.},
journal = {Bioresource technology},
volume = {440},
number = {},
pages = {133502},
doi = {10.1016/j.biortech.2025.133502},
pmid = {41093027},
issn = {1873-2976},
mesh = {Serine/analogs & derivatives/analogs & derivatives ; Quorum Sensing ; Microbial Consortia ; Microbiota ; *Photobioreactors/microbiology ; Microalgae/physiology ; Nitrogen/analysis/metabolism ; Phosphorus/analysis/metabolism ; Biomass ; Membranes, Artificial ; 4-Butyrolactone/analogs & derivatives/metabolism ; Bacteria/metabolism ; Metagenomics ; Chlorella/physiology ; Water Purification/methods ; },
abstract = {Quorum sensing is a central mechanism by which signal bacteria sense and integrate signaling molecules to coordinate gene expression and physiological activities at the community level. To investigate how exogenous signal molecules regulate the maintenance of algal-bacterial symbiosis, this study constructed a dialysis membrane-coupled algal-bacterial photobioreactor and separately amended it with N-butyryl-l-homoserine lactone (C4-HSL), N-hexanoyl-l-homoserine lactone (C6-HSL), and N-(3-oxodecanoyl)-l-homoserine lactone (3-oxo-C10-HSL), systematically investigated their effects on nutrient removal, microbial community composition, and functional characteristics within the system. Compared with the control, all three N-acyl-homoserine lactones (AHLs) enhanced total nitrogen and total phosphorus removal and stimulated biomass (sludge) growth, while redirecting microalgal carbon allocation toward lipid accumulation; notably, the C6-HSL treatment achieved the highest nitrogen (80.39 %) and phosphorus (53.01 %) removal efficiencies. Metagenomic analyses revealed that exogenous AHLs exerted selective effects on the microbial assemblage, enriching dominant signal-responsive bacteria whose relative abundance was positively correlated with nitrogen and phosphorus removal performance. Furthermore, genes associated with nitrogen metabolism, the tricarboxylic acid cycle, and glycolysis were more abundant in the 3-oxo-C10-HSL and C6-HSL groups, indicating that strengthened metabolic coupling likely underpins the observed biomass increase and enhanced nutrient removal. Collectively, these findings demonstrate that AHL-mediated signaling is a key driver shaping algal-bacterial interactions, community assembly, and functional expression.},
}

Serine/analogs & derivatives/analogs & derivatives
Quorum Sensing
Microbial Consortia
Microbiota
*Photobioreactors/microbiology
Microalgae/physiology
Nitrogen/analysis/metabolism
Phosphorus/analysis/metabolism
Biomass
Membranes, Artificial
4-Butyrolactone/analogs & derivatives/metabolism
Bacteria/metabolism
Metagenomics
Chlorella/physiology
Water Purification/methods

@article {pmid40814761,
year = {2026},
author = {Qin, P and Kragsnaes, MS and Holm, DK and Horn, HC and Nilsson, AC and Kjeldsen, J and Kristiansen, K and Ellingsen, T},
title = {Clinical Significance of Gut Microbiota Community Types for Long-Term Response to Fecal Microbiota Transplantation in Patients With Psoriatic Arthritis.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {78},
number = {2},
pages = {320-331},
pmid = {40814761},
issn = {2326-5205},
support = {Sundhedsdonationer 2022-0026//Sygeforsikringen "danmark"/ ; //Fabrikant Vilhelm Pedersen's Mindelegat (on recommendation by the Novo Nordisk Foundation)/ ; //Medicine Fund of the Danish Regions (Regionernes Medicin- og behandlingspulje)/ ; //University of Southern Denmark Research Fund/ ; //the Danish Rheumatism Association/ ; //the Danish Psoriasis Research Foundation/ ; //Research Fund of Odense University Hospital/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Male ; Female ; Middle Aged ; *Arthritis, Psoriatic/therapy/microbiology ; Bacteroides ; Adult ; Prevotella ; Treatment Outcome ; Feces/microbiology ; Clinical Relevance ; },
abstract = {OBJECTIVE: Fecal microbiota transplantation (FMT) holds promises as a beneficial supplement to methotrexate in patients with psoriatic arthritis (PsA). We therefore investigated how gut bacterial signatures in patients and donor strain engraftment were associated with long-term response to FMT.

METHODS: This exploratory study is based on the FLORA trial cohort, encompassing 31 patients with moderate-to-high PsA disease activity and four FMT donors. Of the 15 patients receiving one single-donor FMT, 13 were included in the per-protocol (PP) population. Stool samples were collected before and after FMT (week 4, 12, and 26). We performed shotgun metagenomics to characterize gut microbiota features.

RESULTS: At baseline, 17 patients (55%) had a gut microbiota community type dominated by the Bacteroides genus (B-type), whereas 14 (45%) had a Prevotella-driven community type (P-type). The B- and P-type patients did not differ in disease activity or demographics, but the B-type had a significantly higher species diversity compared to the P-type (P = 0.005). In the PP population, five of seven B-type patients versus none of six P-type patients (P = 0.021) achieved a long-term clinical beneficial response at week 26. Bacterial strain richness increased significantly from baseline to week 4 and week 26 in B-type (P = 0.016), but not in P-type, patients. Eighteen engrafted strains persisted only in B-type recipients by week 26, including a Bacteroides clarus strain, which demonstrated a negative effect size regarding arthritis pain and the patients' global assessment of disease.

CONCLUSION: Recipients with a Bacteroides-dominated community structure were more likely to achieve long-term beneficial response following one FMT.},
}

Humans
*Gastrointestinal Microbiome
*Fecal Microbiota Transplantation
Male
Female
Middle Aged
*Arthritis, Psoriatic/therapy/microbiology
Bacteroides
Adult
Prevotella
Treatment Outcome
Feces/microbiology
Clinical Relevance

@article {pmid40554061,
year = {2026},
author = {Yang, W and Zou, P and He, S and Cui, H and Yang, Z and An, H and Chen, Q and Huang, W and Guo, H and Liu, J and Ling, X and Cao, J and Ao, L},
title = {Perfluorooctane sulfonic acid impairs spermatogenesis via the liver-gut microbiota-testis axis: a central role of chenodeoxycholic acid metabolism.},
journal = {Journal of advanced research},
volume = {81},
number = {},
pages = {897-914},
pmid = {40554061},
issn = {2090-1224},
mesh = {Male ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Testis/drug effects/metabolism ; Mice ; *Chenodeoxycholic Acid/metabolism ; *Alkanesulfonic Acids/toxicity ; *Spermatogenesis/drug effects ; *Fluorocarbons/toxicity ; *Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Fecal Microbiota Transplantation ; Metabolome/drug effects ; },
abstract = {INTRODUCTION: Perfluorooctane sulfonic acid (PFOS) as a global contaminant is ubiquitously presented in the environmental media and human body. The association between PFOS exposure and reduced male fertility has been recently discovered. However, the relevant mechanism remains unexplored.

OBJECTIVES: Our study aimed to investigate the effect and mechanism of PFOS exposure on male reproductive function.

METHODS: In a murine PFOS exposure model, single-nucleus transcriptome sequencing was performed to delineate the transcriptomic landscape of mouse testes at the single-cell resolution. We examined the serum metabolomic profile and conducted in-depth analysis of hepatic transcriptome datasets to explore the metabolic connections between liver and testis under PFOS exposure. Through integrating chenodeoxycholic acid intervention, fecal microbiota transplantation (FMT), metagenomic sequencing, testicular metabolome, Ligilactobacillus murinus (L. murinus) metabolome, and administration of L. murinus, we confirmed the role of the liver-gut microbiota-testis axis and screened the critical gut microbiota involved in PFOS-mediated spermatogenic disorders.

RESULTS: The results showed that PFOS exposure led to spermatogenic arrest and abnormal spermatogenic microenvironment in the mouse testis. The PFOS-repressed hepatic chenodeoxycholic acid (CDCA) synthesis contributed to the reduced serum/testicular levels of essential fatty acid (linoleic acid) and lipid-soluble vitamins (retinol, vitamin D3), which was responsible for the spermatogenic arrest. Beyond this, PFOS-mediated impaired CDCA production decreased the abundance of gut L. murinus, which affected spermatogenesis through the potential involvement of aspartic acid metabolism. For the first time to our knowledge, we comprehensively assessed the effects of PFOS exposure on the spermatogenic process and elucidated the unrecognized role of liver-gut microbiota-testis axis in PFOS-induced abnormal spermatogenesis.

CONCLUSIONS: The unveiled organ crosstalks provide new insights into the metabolism-disrupting properties, hepatotoxicity, and reproductive toxicity of PFOS, which may facilitate the development of molecule-, metabolite-, and microbe-based strategies for PFOS-induced metabolic diseases and reproductive disorders.},
}

Male
Animals
*Gastrointestinal Microbiome/drug effects
*Testis/drug effects/metabolism
Mice
*Chenodeoxycholic Acid/metabolism
*Alkanesulfonic Acids/toxicity
*Spermatogenesis/drug effects
*Fluorocarbons/toxicity
*Liver/metabolism/drug effects
Mice, Inbred C57BL
Fecal Microbiota Transplantation
Metabolome/drug effects

@article {pmid41766731,
year = {2026},
author = {Peddle, SD and Cando-Dumancela, C and Costin, S and Davies, T and Doane, MP and Edwards, RA and Hodgson, RJ and Krauss, SL and Liddicoat, C and Breed, MF},
title = {Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73172},
pmid = {41766731},
issn = {2045-7758},
abstract = {Soil microbiomes are fundamental ecosystem components that are increasingly used to monitor the efficacy of restoration efforts. However, given high levels of functional redundancy among soil microbial taxa and the subsequent lack of definitive taxa-function links, taxonomic assessments (e.g., via metabarcoding) alone are limited for inferring ecological recovery. Here, we used shotgun metagenomics on soils from six post-agricultural restoration sites in southwest Western Australia to test whether soil microbial functional potential recovers following restoration plantings. We compared taxonomic and functional gene diversity and composition across degraded, passively regenerated, revegetated, and remnant land conditions. Effective number of functions (alpha diversity) did not differ across land conditions. However, functional composition (beta diversity) differed between remnant and revegetated conditions and associated with altered soil abiotic properties, especially elevated phosphorus. Remnant soils supported a greater diversity of phosphorus metabolism functions despite lower available phosphorus, indicating a microbial adaptation to nutrient limitation in phosphorus deficient soils. Rather than indicating a lack of functional recovery, these results suggest a functional response to persistent agricultural legacies that may reflect a shift toward an alternative state. Restoration interventions that aim to target the soil microbiome (e.g., soil inoculations) or directly address abiotic legacies (e.g., phosphorus mining plants) may therefore be required to facilitate recovery of the soil microbial functions and the wider ecosystem.},
}

@article {pmid41115830,
year = {2025},
author = {Yang, F and Xu, W and Zhu, L and Tian, X and Duan, Y and Xu, Y and Huang, Q and Zhao, F},
title = {Multiple Roles of Extracellular Vesicles in Promoting Microbial-Driven Manganese Reduction.},
journal = {Environmental science & technology},
volume = {59},
number = {43},
pages = {23275-23288},
doi = {10.1021/acs.est.5c05310},
pmid = {41115830},
issn = {1520-5851},
mesh = {*Extracellular Vesicles/metabolism ; *Manganese/metabolism ; Electron Transport ; Soil Microbiology ; Metagenomics ; *Shewanella/metabolism ; Biofilms ; Microbiota ; },
abstract = {Microbial-driven manganese (Mn) reduction influences the geochemical cycling of Mn and the environmental fate of various organic and inorganic substances. Extracellular vesicles (EVs) are known to impact microbial metabolic activities, but their specific role in Mn reduction remains arcane. Here, we explored the potential involvement of environmental EVs in this process through metagenomic analysis and validated their function using representative functional strains. There are 8.05 and 12.89% of EVs originating from electroactive microorganisms in soil and wastewater, respectively. The addition of EVs increases the birnessite reduction rate of Shewanella oneidensis MR-1 from 2.31 μmol/(L·h) to 20.86 μmol/(L·h). Microbial physiological assays and in situ electrochemical analyses revealed that EVs enhanced cellular metabolism, promoted biofilm formation, and facilitated extracellular electron transfer (EET). The presence of diverse redox enzymes and metabolites in EVs contributed to more efficient substrate utilization and energy conservation, which promoted biomass accumulation and increased substrate consumption by 45.33%. The inner and outer membrane c-type cytochromes, along with flavins contained in the EVs, are essential for promoting microbial EET. These findings highlight the multifaceted role of EVs in microbial-driven Mn reduction, which might also participate in other element cycles in the same way.},
}

*Extracellular Vesicles/metabolism
*Manganese/metabolism
Electron Transport
Soil Microbiology
Metagenomics
*Shewanella/metabolism
Biofilms
Microbiota

@article {pmid41747902,
year = {2026},
author = {Corso, D and Melita, M and Massaccesi, N and Quero, GM and Basili, M and Di Cesare, A and Sabatino, R and Sbaffi, T and Fazi, S and Rakaj, A and Luna, GM and Amalfitano, S},
title = {Constructed wetlands for aquaculture wastewater treatment: Insights on the structural and functional shifts of the aquatic microbial community.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134278},
doi = {10.1016/j.biortech.2026.134278},
pmid = {41747902},
issn = {1873-2976},
abstract = {Aquaculture practices generate nutrient-rich effluents with associated microbiological hazards, such as pathogens and antimicrobial resistance genes (ARGs). Despite their growing popularity as nature-based solutions, little is known about how constructed wetlands (CWs) affect the dynamics of microbial communities at the field scale. By combining flow cytometry, 16S rRNA gene sequencing, shotgun metagenomics, and metabolic potential assays, we investigated the structural and functional responses of the aquatic microbial community following the recurrent exposure to CW-treated effluents from an intensive marine fish farm (Orbetello lagoon, Italy). While the CW promoted abundant, metabolically active, and functionally redundant microbial communities, the phylogenetic composition diverged primarily between water and sediments. Microbial profiles in CW outlet waters converged towards those of the lagoon baselines, suggesting gradual ecological recovery. The CW attenuated the occurrence of potential pathogens, such as members of the genera Francisella and Campylobacter, and acted as a buffer system in ARG dissemination, with sediments serving as reservoirs of microbial and genetic signatures. Functional profiles, dominated by chemoheterotrophy, denitrification, and sulfur respiration, remained stable across environments, reflecting microbial resilience. Our results highlight CWs as effective, field-proven solutions to mitigate aquaculture wastewater impacts while preserving core ecosystem services.},
}

@article {pmid41736978,
year = {2026},
author = {Ling, Y and Yang, DX and Xia, YN and Bao, CP and Zhang, F and Xu, XJ and Sun, BH},
title = {Effects of Age, Sex, and Social Network on Antibiotic Resistance Genes in the Gut Microbiome of Tibetan Macaques (Macaca thibetana).},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73137},
pmid = {41736978},
issn = {2045-7758},
abstract = {The transmission and dissemination of antibiotic resistance genes (ARGs) have increasingly drawn global attention. However, our knowledge of the antibiotic resistance gene pool in wild primates' gut microbiomes and its influencing factors remains limited. In this study, we focus on a social group of Tibetan macaques (Macaca thibetana) in Huangshan, utilizing behavioral and metagenomic data to investigate the effects of host sex, age, and social network on the ARG profiles of the gut microbiome. Our results demonstrate a high diversity of ARGs in the gut microbiota of Tibetan macaques, with multidrug, glycopeptide, and peptide resistance genes being the most prevalent. Although host age, sex, and social networks did not significantly affect the overall diversity of ARGs, these factors were significantly correlated with the relative abundance of several highly abundant ARG types, including gryB, rpoB, macB, novA, efrA, patB, Staphylococcus aureus mupA conferring mupirocin resistance, RanA, and cdeA. Further analysis revealed extensive interactions between gut bacteria and ARGs, with age emerging as a potentially key factor in this covariation process. These findings provide new insights into the formation and transmission mechanisms of antibiotic resistance in the gut microbiome of wildlife, particularly in social primates.},
}

@article {pmid41736795,
year = {2026},
author = {Pan, H and Wu, L and Sheng, S},
title = {Metagenomic profiling of the gut microbiome to predict orthopedic healing responses in postmenopausal women.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1771312},
pmid = {41736795},
issn = {2235-2988},
mesh = {Humans ; Female ; *Postmenopause ; *Gastrointestinal Microbiome/genetics ; Aged ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; *Wound Healing ; },
abstract = {INTRODUCTION: Recovery following orthopedic procedures in postmenopausal women is often prolonged and more complex due to age-related physiological changes, including reduced bone mineral density, altered hormonal profiles, impaired immune regulation, and delayed tissue regeneration. Conventional recovery assessment methods such as radiographic imaging, range-of-motion evaluation, and functional mobility tests provide valuable clinical information but offer limited insight into the underlying biological processes that influence healing. Emerging evidence indicates that the gut microbiome plays a critical role in regulating inflammation, immune homeostasis, and tissue repair, highlighting its potential as a predictive biomarker for post-surgical recovery outcomes. This study investigated the association between gut microbiome dynamics and recovery following orthopedic surgery in postmenopausal women.

METHODS: Stool samples were collected from preoperative (baseline) and 6 weeks postoperative time points. Microbial profiling was performed using 16S rRNA gene sequencing on the Illumina MiSeq platform, and data processing and taxonomic analysis were conducted using QIIME2. Microbial diversity was evaluated through alpha diversity metrics to assess community richness and beta diversity to characterize compositional differences over time. Clinical recovery was assessed using radiographic imaging, the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), and the Timed Up and Go (TUG) functional mobility test. To evaluate the predictive potential of the gut microbiome, a random forest machine learning model was trained using microbial abundance data and correlated with clinical recovery outcomes.

RESULTS: The results revealed significant temporal shifts in gut microbial composition during the recovery period. Bacterial diversity varied across time points, with Firmicutes and Bacteroidetes identified as the dominant phyla. Increased abundance of these taxa was strongly associated with improved functional outcomes and faster recovery. In contrast, elevated levels of Proteobacteria and Escherichia were linked to delayed healing and poorer clinical performance. The predictive model achieved an accuracy of 85%, demonstrating the robustness of gut microbiome signatures as indicators of postoperative recovery.

DISCUSSION: Overall, this study highlights the significant influence of gut microbiome composition on orthopedic recovery in postmenopausal women. Identification of microbial biomarkers associated with favorable healing outcomes provides a foundation for developing microbiome-guided, personalized therapeutic strategies to enhance postoperative recovery and improve long-term musculoskeletal health.},
}

Humans
Female
*Postmenopause
*Gastrointestinal Microbiome/genetics
Aged
Middle Aged
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Metagenomics/methods
Bacteria/classification/genetics/isolation & purification
*Wound Healing

@article {pmid41736790,
year = {2026},
author = {Yu, S and Niu, H and Zhang, Y and Yu, L and Zhang, Q and Liu, X and Sang, Y and Wang, R and Zhang, M},
title = {Characterization of gut microbiota in patients with diabetic kidney disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1713005},
pmid = {41736790},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Diabetic Nephropathies/microbiology ; Feces/microbiology ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: Diabetic kidney disease (DKD) is a major complication of diabetes mellitus (DM). Although dysbiosis of the gut microbiota in DKD has been reported, the specific microbial species associated with disease progression from DM to DKD remain insufficiently defined.

METHODS: We conducted shotgun metagenomic sequencing on fecal samples from 55 healthy participants, 47 patients with DM, and 38 patients with DKD. Gut microbiota diversity, composition, and functional pathways were compared across groups; correlations with glycemic and renal indices were evaluated.

RESULTS: Overall alpha-diversity showed no significantly difference between DKD and healthy controls; however, the simpson's index was higher in DKD than in DM (p < 0.05). There was a difference in beta-diversity between DKD and the healthy control (p = 0.002), but no significant difference was observed between the DKD and DM group. Bacteria significantly enriched in DM/DKD include Mediterraneibacter, Enterocloster, Shigella, Limosilactobacillus, and Thomasclavelia, which showed positive correlations with glycemic indicators (HbA1c, fasting blood glucose) and renal indicators (BUN, UACR). In contrast, health-enriched bacteria, Phocaeicola, Faecalibacterium, Lachnospira, Agathobacter, Odoribacter, and Paraprevotella were negatively correlated with these parameters. Functional analysis revealed that compared to the DM group, the DKD group enriched pathways related to aromatic amino acid biosynthesis (phenylalanine, tyrosine, tryptophan), biofilm formation, and lipopolysaccharide biosynthesis. Gut microbial shifts along the DM-DKD correlates with adverse glycemic and renal phenotypes, as well as functional characteristics associated with inflammation and barrier injury. These findings suggest that microbially driven metabolic and structural pathways represent potential targets for mitigating the progression of DKD.

CONCLUSION: This study elucidates the distinct characteristics of the gut microbiota in DKD patients and highlights potential microbial markers involved in the progression from DM to DKD.},
}

Humans
*Gastrointestinal Microbiome
Female
Male
Middle Aged
*Diabetic Nephropathies/microbiology
Feces/microbiology
Dysbiosis/microbiology
*Bacteria/classification/genetics/isolation & purification
Aged
Metagenomics
Adult

@article {pmid41736479,
year = {2026},
author = {Kong, S and Ning, Z and Chen, Z and Zhang, M},
title = {Broad-Spectrum Co-Metabolic Substrates Enhance the Bioremediation of 1,2,3-Trichloropropane in Groundwater by a Non-Dehalogenimonas Consortium.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {3},
pages = {e70318},
doi = {10.1002/wer.70318},
pmid = {41736479},
issn = {1554-7531},
support = {252S7601D//Hebei Province Science and Technology Support Program/ ; 242S4201Z//Hebei Province Science and Technology Support Program/ ; },
mesh = {*Groundwater/chemistry/microbiology ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Propane/analogs & derivatives/metabolism ; *Microbial Consortia ; },
abstract = {1,2,3-Trichloropropane (TCP), a highly mobile chemical byproduct, has severely exacerbated groundwater environment deterioration. Due to the lack of effective natural attenuation pathways, TCP typically exhibits a fate of persistent retention within aquifers. To address this challenge, instead of relying on limited specific strains, this study focused on exploring broad-spectrum co-metabolic substrates to enhance the degradation efficiency of a non-Dehalogenimonas synergistic consortium optimized through long-term directed domestication. Results indicated that the average degradation rate of the domesticated consortium increased to 19.06 μmol L[-1] d[-1], achieving complete removal within 3.5 days, thereby effectively altering the environmental persistence of TCP. Microbial community and metagenomic analyses revealed that this transformation process was driven by a synergistic alliance comprising Fusibacter, Desulfovibrio, Nitratidesulfovibrio, and Parabacteroides, realized through a coupled metabolic module of "hydrogen production, cofactor synthesis, and reductive dechlorination". Crucially, the consortium demonstrated exceptional broad-spectrum adaptability to various co-metabolic substrates, where sodium acetate and lactate significantly enhanced the degradation efficiency. This study confirms that utilizing suitable co-metabolic substrates can effectively activate the non-Dehalogenimonas consortium to regulate the migration and fate of pollutants in complex groundwater environments, offering an efficient bioremediation strategy to arrest groundwater contamination.},
}

*Groundwater/chemistry/microbiology
Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism
*Propane/analogs & derivatives/metabolism
*Microbial Consortia

@article {pmid41736423,
year = {2026},
author = {Dongqi, LI and Tongxing, W and Zixuan, W and Yihui, Y and Jie, LI and Jiaojiao, GU and Cuiru, LI and Aili, W and Lingling, S and Yongjie, M and Zeyu, Z and Yunlong, H and Huailin, G},
title = {Improving glucose tolerance in obese rats: the role of Jinlida granules () in gut microbiota modulation.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {46},
number = {1},
pages = {62-72},
pmid = {41736423},
issn = {2589-451X},
support = {2017YFC700500//National Key Research and Development Program 'Modernization Research of Traditional Chinese Medicine': Cardiovascular Event Chain (Metabolic Syndrome, Atherosclerosis, Myocardial Infarction, Arrhythmia, Heart Failure)/ ; 223777155D//Key R&D Program of Hebei: Traditional Chinese Medicine Innovation Project: Clinical Research on the Treatment of Diabetes Foot with Collateral Drugs and the Mechanism of Its Influence on Collateral Vessel Reconstruction/ ; 2023179//Scientific Research Project of Hebei Provincial Administration of Traditional Chinese Medicine: Clinical Study on Jinlida Granules in Treating Intestinal Dysfunction of diabetes and Its Effect on Short Chain Fatty Acids/ ; 2018200//Scientific Research Project of Hebei Provincial Administration of Traditional Chinese Medicine: Clinical Study on Tongluo Therapy for Diabetes Foot and Its Influence on Microcirculation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; Rats ; *Obesity/drug therapy/microbiology/metabolism/genetics ; Male ; *Drugs, Chinese Herbal/administration & dosage ; Humans ; Glucose Tolerance Test ; Diet, High-Fat/adverse effects ; Zonula Occludens-1 Protein/metabolism/genetics ; Claudin-1/metabolism/genetics ; Blood Glucose/metabolism ; },
abstract = {OBJECTIVE: To investigate the effects of Jinlida granules (, JLD) on body weight, glucose tolerance, intestinal inflammation and barrier function in high-fat diet (HFD)-induced obese rats and explore the regulation of the gut microbiota as a potential treatment mechanism.

METHODS: Sprague-Dawley rats were divided into control, HFD, low-dose JLD (L-JLD), high-dose JLD (H-JLD), and sitagliptin groups. The rats, with the exception of those in the control group, were fed a HFD to establish an obesity model while simultaneously receiving 0.5% carboxymethyl cellulose, L-JLD, H-JLD or sitagliptin for 25 weeks. We assessed body weight, conducted oral glucose tolerance tests, and analysed faecal samples using metagenomic sequencing. Haematoxylin-eosin (HE), Masson and immunohistochemical (IHC) staining were employed to evaluate histological changes in the colon tissue. Immunofluorescence (IF) staining was used to measure the expression levels of Zonula occludens-1 (ZO-1) and Claudin-1 in colon tissue. The colon tissue was also subjected to transcriptomic evaluation.

RESULTS: JLD treatment significantly reduced body weight and enhanced glucose tolerance in obese rats. It alleviated colonic tissue damage, decreased collagen deposition, inhibited macrophage infiltration, and increased the expression of the tight junction proteins ZO-1 and Claudin-1. Metagenomic analysis revealed JLD-induced shifts in the gut microbiota composition (increasing the abundance of Turicibacter, Faecalibaculum, Coriobacteriaceae and Lactobacillus reuteri), enriching beneficial bacteria and metabolic pathways (increasing the biosynthesis of various secondary metabolites, ascorbate and aldarate metabolism, oxidative phosphorylation, C5-branched dibasic acid metabolism and beta-alanine metabolism). Transcriptomic analysis revealed downregulation of inflammatory and immune pathways (inhibition of the tumour necrosis factor signalling pathway, advanced glycation end products-receptor for advanced glycation end products signalling pathway, toll-like receptor signalling pathway, and interleukin-17 signalling pathway), suggesting a comprehensive modulatory effect of JLD on intestinal health and metabolic function.

CONCLUSIONS: JLD granules effectively improve glucose tolerance and ameliorate obesity-related intestinal dysfunctions in HFD-induced obese rats. These benefits are likely mediated through the modulation of the gut microbiota, the suppression of intestinal inflammation, the enhancement of barrier function, and the attenuation of proinflammatory pathways. Our findings offer novel insights into the therapeutic potential of JLD, emphasizing its role in integrating gut microbiota management into the treatment of metabolic disorders.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
Rats
*Obesity/drug therapy/microbiology/metabolism/genetics
Male
*Drugs, Chinese Herbal/administration & dosage
Humans
Glucose Tolerance Test
Diet, High-Fat/adverse effects
Zonula Occludens-1 Protein/metabolism/genetics
Claudin-1/metabolism/genetics
Blood Glucose/metabolism

@article {pmid41734489,
year = {2026},
author = {Sabatino, R and Gini, C and Borgomaneiro, G and Sbaffi, T and Corno, G and Sun, K and Zhang, XH and Di Cesare, A},
title = {Sinking particles as repository of antimicrobial resistome diversity in the Sansha Yongle Blue Hole.},
journal = {The Science of the total environment},
volume = {1021},
number = {},
pages = {181585},
doi = {10.1016/j.scitotenv.2026.181585},
pmid = {41734489},
issn = {1879-1026},
abstract = {The aquatic environment plays a central role in the selection and spread of antimicrobial resistance genes (ARGs). Using metagenomic approaches, several studies have provided a comprehensive view of the antimicrobial resistome across different aquatic ecosystems. However, unique aquatic systems, such as oceanic blue holes, remain largely unexplored. Free-living and particle-associated samples from the Sansha Yongle Blue Hole (South China Sea) were analyzed by shotgun metagenomics to characterize the antimicrobial resistome and the potential mobility of detected ARGs. The diversity of the antimicrobial resistome significantly decreased with increasing water depth. This trend was driven by the free-living bacterial community, whereas it remained stable in particle-associated communities. Additionally, the latter showed a higher frequency of co-occurring ARGs and mobile genetic elements on the same contigs, with a frequent plasmid localization of these genes. Overall, particle-associated bacteria proved essential for sustaining antimicrobial resistome diversity. Furthermore, these findings suggest that horizontal transfer of ARG may be more frequent within particle-associated communities along the water column of the blue holes, potentially contributing to the persistence of resistances in deep marine waters.},
}

@article {pmid41731616,
year = {2026},
author = {Fan, S and Lu, J and Cui, H and Ding, W and Li, S and Sun, J and Li, YX and Zhang, W},
title = {Unlocking the unexplored AMPSphere in marine rare species.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02326-0},
pmid = {41731616},
issn = {2049-2618},
abstract = {BACKGROUND: Antimicrobial peptides (AMPs) have advantages over traditional antibiotics in fighting against drug-resistant bacterial infections. Natural microbial communities are considered as the priority targets for next-generation AMP bioprospecting initiatives. While progress has been made in characterizing AMPs from the dominant microbial taxa in natural ecosystems, current research largely overlooks the biosynthetic potential of rare species. Given their distinct evolutionary pressures, rare species likely produce AMPs with novel structures and unconventional mechanisms of action.

RESULTS: In this study, enrichment cultivation of a marine biofilm was conducted in 138 carbon source- and oxygen level-based conditions, followed by metagenomic sequencing using both Illumina and Nanopore platforms. Analysis of 435 high-quality genomes derived from the metagenomes suggests that these bacterial strains are significantly underrepresented (< 0.01%) in global marine biofilm communities. Through multi-model prediction, we identified 3,054,472 candidate AMPs from the genomes, including 1048 high-confidence ones, thereby significantly expanding the previously known AMPSphere. Furthermore, AMPs derived from the rare bacterial species exhibit unique sequence characteristics, structural diversity, remarkable stability under diverse pH conditions and pepsin exposure, and strong therapeutic potential in animal models, reflecting their specialized adaptive and defensive strategies developed within ecological systems.

CONCLUSIONS: The features of the underexplored AMPs from low-abundance bacteria in marine biofilms provide valuable resources and theoretical foundations for the development of highly effective antimicrobial agents. Video Abstract.},
}

@article {pmid41729207,
year = {2026},
author = {Gouda, MNR and Subramanian, S},
title = {Functional Genomics and Enzymatic Diversity of Gut Bacteria in Apis mellifera: A Multi-Approach Study from India.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41729207},
issn = {1432-0991},
mesh = {Bees/microbiology ; Animals ; India ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/enzymology/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Phylogeny ; Genomics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {The gut microbiota of the western honey bee Apis mellifera plays a vital role in host nutrition, digestion, immunity, and overall colony health. Although the functional and enzymatic capabilities of bee-associated microbes are increasingly recognized, studies integrating culture-dependent screening with metagenomic functional profiling remain scarce. This study characterizes the gut bacterial communities of forager and hive bees from the Indian subcontinent using cultivation, 16S rRNA gene sequencing, enzyme assays, and metagenomic analysis. A total of 165 isolates were obtained, yielding 85 unique strains deposited in GenBank. Metagenomic assembly generated 7.78 million non-redundant genes, including 11,050 KEGG-annotated and 2.43 million CAZy-annotated genes. Forager bees showed pronounced enrichment of carbohydrate-processing pathways such as glycolysis/gluconeogenesis (22.9%), galactose metabolism (4.42%), starch and sucrose metabolism, and ABC transporters (9.80%), consistent with their nectar- and pollen-rich diet. Culture-based biochemical assays revealed substantial enzymatic diversity among isolates belonging to Bacillus, Enterobacter, Serratia, Cedecea, Clostridium, Lysinibacillus, and Aneurinibacillus. High invertase activities were recorded in Xanthomonas sp. HAmf44 (2.509 U/mg), Clostridium argentinense HAmf20 (2.470 U/mg), Lysinibacillus fusiformis HAmh15 (2.509 U/mg), and Bacillus paralicheniformis HAmh05 (2.333 U/mg). Strong lipolytic activities were observed in Cedecea davisae HAmf19 (6.062 U/mg), Pseudomonas aeruginosa HAmh21 (5.927 U/mg), and Enterobacter cloacae HAmf26 (3.349 U/mg). Significant variation among isolates (p = 0.001) underscored the functional diversity of the gut microbiota. Integrating KEGG orthologs with species abundance revealed that dominant taxa-including Gilliamella, Snodgrassella, Lactobacillus, and Bifidobacterium-drive key metabolic pathways. Overall, this study provides the first combined enzymatic and metagenomic assessment of A. mellifera gut microbiota from India and identifies high-performing strains with probiotic potential to enhance honey bee nutrition and colony productivity.},
}

Bees/microbiology
Animals
India
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/enzymology/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Metagenomics
Phylogeny
Genomics
Bacterial Proteins/genetics/metabolism

@article {pmid41686173,
year = {2026},
author = {Yang, Z and Zhang, F and Li, H and Liu, B and Liu, P and Wu, Z and Li, Y and Miao, J and Li, X and Liang, H and Zhong, Y and Xiao, L and Zou, Y and He, N and Li, S},
title = {Gut Commensal Phocaeicola vulgatus AF107-22 Alleviates Obesity-Induced Metabolic Syndrome via Promoting Gut Microbiota-Derived Spermidine Synthesis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14443},
pmid = {41686173},
issn = {1520-5118},
abstract = {Obesity-induced metabolic syndrome (MetS) is a prevalent metabolic disorder, and therapeutic strategies targeting the gut microbiota hold considerable promise. Phocaeicola vulgatus (P. vulgatus) is a gut commensal bacterium that plays an important role in modulating the composition and metabolism of gut microbiota. This study demonstrated that the abundance of P. vulgatus is significantly negatively correlated to obesity-induced MetS and complications in human metagenomic data. Oral gavage of P. vulgatus significantly ameliorated high-fat-diet (HFD)-induced MetS symptoms in mice, reducing body weight, systemic inflammation, and hepatic steatosis. Furthermore, multiomics analyses indicated that P. vulgatus treatment significantly enhanced the production of gut microbiota-derived spermidine and spermine. Subsequently, population-based analysis confirmed a strong negative correlation between plasma spermidine levels and MetS progression, supporting that such parameters may serve as potential biomarkers for MetS. This study reveals a potential mechanism, bridging commensal probiotic and spermidine metabolism, with implications for treating obesity-induced MetS.},
}

@article {pmid41562342,
year = {2026},
author = {Winkler, M and Seel, W and Kornblum, C and Simon, MC and Reimann, J},
title = {The MicroIBioM study: the gut microbiome in inclusion body myositis.},
journal = {Clinical and experimental rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.55563/clinexprheumatol/1b8sv1},
pmid = {41562342},
issn = {0392-856X},
abstract = {OBJECTIVES: Inclusion body myositis (IBM) is a disorder with features of both inflammation and degeneration yet without effective treatment. Influences of the gut microbiome on degenerative as well as inflammatory disorders and immune treatments are known. We sought to investigate whether the gut microbiome might influence the development or recalcitrance of IBM.

METHODS: We appealed to IBM patients and their unaffected spouses/cohabitants for stool samples and data on clinical symptoms, gathering questionnaire data (modified Gastrointestinal Symptom Rating Scale (mGSRS), IBM Functional Rating Scale (IBMFRS) and Bristol Stool Scale) and stool samples for 16S rRNA V3V4 metagenomic analysis from 21 IBM and 20 control probands. Bioinformatic analyses used QIIME2 and MicrobiomeAnalyst software packages. LEfSe and Random Forest analysis aimed to identify group specific biomarkers. PICRUSt was used to perform pathway analysis.

RESULTS: No overall differences of alpha and beta diversity were found between IBM and control group. No impact of immune treatments was found, but a reduction in alpha diversity was identified comparing older (≥ 72 years) IBM and control probands. Increased abundances of some genera, in particular Bacteroides, were detected in the IBM group. Bacteroides, Clostridium CAG 352, and Eggerthella were identified as IBM biomarkers at genus level. Gastrointestinal symptoms (mGSRS) correlated with disease severity (IBMFRS).

CONCLUSIONS: General differences of gut microbiome seem unlikely to play a role in the genesis of IBM. Whether the late occurring or the more specific differences detected are part of the disease course needs to be addressed by investigations of further biosamples.},
}

@article {pmid40990531,
year = {2025},
author = {Del Carratore, F and Breitling, R},
title = {Engineering microbiomes for natural product discovery and production.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5np00038f},
pmid = {40990531},
issn = {1460-4752},
abstract = {Covering: 2021 to 2025Microbial communities represent a vast and largely untapped source of natural products with potential applications in various fields, including medicine, agriculture, and the biomanufacturing industry. Secondary metabolites play a crucial role in mediating interspecies interactions within these communities, influencing their structure and function. Recent advances in microbial genetic engineering and multi-omics technologies have enabled the harnessing of these interactions for enhanced natural product discovery and production. These techniques, coupled with systems biology and mathematical modelling, allow for the rational design and manipulation of microbial consortia to elicit the expression of cryptic biosynthetic gene clusters and to optimize the production of desired compounds. Additionally, direct mining of microbiomes using metagenomics, metatranscriptomics, and metabolomics has revealed a wealth of novel biosynthetic gene clusters and secondary metabolites with potential therapeutic and industrial value. Despite the challenges associated with cultivating and characterizing diverse microbial species, ongoing advancements in computational tools and data analysis are rapidly expanding our ability to explore and exploit the seemingly inexhaustible reservoir of natural products hidden within microbial communities.},
}

@article {pmid41724868,
year = {2026},
author = {Aciole Barbosa, D and de Maria, YNLF and Menegidio, FB and de Oliveira, RC and Jabes, DL and Nunes, LR},
title = {Dysbiosis of the enteric DNA virome correlates with the development of cachexia in a murine Lewis lung carcinoma (LLC) model.},
journal = {Archives of virology},
volume = {171},
number = {3},
pages = {},
pmid = {41724868},
issn = {1432-8798},
mesh = {Animals ; *Cachexia/virology/etiology/microbiology ; *Dysbiosis/virology ; *Virome ; Mice ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Disease Models, Animal ; *Carcinoma, Lewis Lung/complications/virology ; *DNA Viruses/genetics/classification/isolation & purification ; Male ; },
abstract = {Cachexia, a multifaceted wasting syndrome, profoundly impacts quality of life and survival rates in cancer patients. Gut inflammation is identified as a key player among the contributing factors for its development. Consequently, numerous studies have sought to characterize changes in gut microbiota of cachectic individuals, given the well-established roles of the gut microbiota in controlling and/or triggering both local and systemic inflammation in their hosts. Most of these investigations have applied mouse models of tumor-induced cachexia to show correlations between alterations in bacterial and fungal abundance in the digestive tract and the onset of cancer cachexia (CC). However, the role of viral dysbiosis in CC development remains unexplored. The present study aims to address this gap by characterizing the gut virome during the progression of murine cancer cachexia. Although our approach was limited to DNA viruses, our findings reveal that cachectic animals with Lewis lung carcinoma exhibited a subtle yet statistically significant modulation in composition (R[2] = 0.17622; p = 0.05). A linear discriminant analysis effect size (LEfSe) analysis revealed that the dysbiosis observed in the gut virome of CC animals was mostly characterized by a significant enrichment in giant viruses of the family Phycodnaviridae (LDA score, 4.2582; p-value, 0.004; pwrapp, 0.9984) and significantly decreased populations of bacteriophages of the families Microviridae (LDA score, 4.3458; p-value, 0.0127; pwrapp, 0.9065) and Inoviridae (LDA score, 3.3028; p-value, 0.0017; pwrapp, 0.9992). This cachexia-associated viral dysbiosis shares similarities with virome alterations documented in other conditions linked to gut inflammation, including, ulcerative colitis, Crohn's disease, and Clostridioides difficile infection. These new insights suggest the potential contributions of viral communities to the pathophysiology of CC and other inflammation-driven diseases.},
}

Animals
*Cachexia/virology/etiology/microbiology
*Dysbiosis/virology
*Virome
Mice
*Gastrointestinal Microbiome
Mice, Inbred C57BL
Disease Models, Animal
*Carcinoma, Lewis Lung/complications/virology
*DNA Viruses/genetics/classification/isolation & purification
Male

@article {pmid41722974,
year = {2026},
author = {Ji, M and Gong, J and Liu, Z and Liu, X and Wang, X and Ao, C and Tan, J},
title = {Multi-omics investigation of microbial community dynamics and metabolic regulation in mulberry wine fermentation under temperature and acid stress.},
journal = {Food microbiology},
volume = {137},
number = {},
pages = {105022},
doi = {10.1016/j.fm.2025.105022},
pmid = {41722974},
issn = {1095-9998},
mesh = {Fermentation ; *Wine/microbiology/analysis ; *Morus/microbiology/metabolism ; Saccharomyces cerevisiae/metabolism/genetics ; *Microbiota ; Temperature ; Hydrogen-Ion Concentration ; Ethanol/metabolism ; Metabolomics ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics ; *Acids/metabolism ; Lactobacillus/metabolism/genetics ; Stress, Physiological ; Multiomics ; },
abstract = {This study employed an integrated approach of metagenomics and metabolomics to investigate microbial community dynamics during mulberry wine fermentation under varying temperatures (17-29 °C) and pH levels (3.0-4.5). Twenty treatment combinations, spanning 27 days, captured the temporal dynamics of microbial communities and metabolic activity. Environmental stress significantly shaped community assembly, with Saccharomyces cerevisiae acting as the dominant fermentation organism and Lactobacillus spp. associated with organic acids. Core population analysis revealed specialized functions in ethanol production, acid resistance, and flavor biosynthesis. An optimal fermentation efficiency of 82 % and an ethanol content of 9.1 % vol. were achieved with the response surface method, resulting in optimal fermentation conditions of 23 ± 1 °C with a pH of 3.5 ± 0.1. Multi-omics correlation network analysis revealed coordinated associations among gene expression, enzymatic activities, and metabolite profiles, including coordinated expression patterns of flavor compound biosynthesis pathways. This research provides evidence-based optimization strategies for industrial mulberry wine production, enhancing understanding of stress-responsive microbial adaptation mechanisms.},
}

Fermentation
*Wine/microbiology/analysis
*Morus/microbiology/metabolism
Saccharomyces cerevisiae/metabolism/genetics
*Microbiota
Temperature
Hydrogen-Ion Concentration
Ethanol/metabolism
Metabolomics
*Bacteria/metabolism/genetics/classification/isolation & purification
Metagenomics
*Acids/metabolism
Lactobacillus/metabolism/genetics
Stress, Physiological
Multiomics

@article {pmid41718551,
year = {2026},
author = {Gröger, L and Rishik, S and Ludwig, N and Beganovic, A and Koch, M and Rheinheimer, S and Hart, M and König, P and Trampert, T and Paul, P and Boese, A and Lehr, CM and Becker, SL and Fuhrmann, G and Keller, A and Meese, E},
title = {Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2630482},
pmid = {41718551},
issn = {1949-0984},
mesh = {Humans ; *Extracellular Vesicles/metabolism/genetics ; MicroRNAs/metabolism/genetics ; Caco-2 Cells ; *RNA, Bacterial/metabolism/genetics ; *Epithelial Cells/microbiology/metabolism ; *Gastrointestinal Microbiome ; },
abstract = {While extracellular vesicles (EVs) are established mediators of intra-species signaling, their contribution to cross-kingdom communication remains incompletely understood. Here, we investigate the EV-mediated interactions between human colon epithelial cells and both Gram-positive and Gram-negative gut bacteria. We show that bacterial EVs (BEVs) derived from Lacticaseibacillus casei, Enterococcus faecalis, and Proteus mirabilis induce distinct transcriptomic changes in Caco-2 cells depending on the bacterial species, with up to ~6,000 differentially expressed genes, including CCL20, CXCL8, or CXCL10. Transfection of BEV-derived RNA independently induces a subset of similar effects, indicating that the EV-mediated communication is partially driven by the RNA cargo. Conversely, we demonstrate that bacteria interact with Caco-2-derived EVs and miR-192-5p, which is highly abundant (~36.4-fold higher) in EVs isolated from conditioned medium compared with EVs from unconditioned medium, with modest effects on bacterial growth. Furthermore, we show that lipid-based packaging of miR-192-5p modulates its association with the bacteria. Our findings support a conceptual model in which EVs and their RNA cargo contribute to species-dependent host-microbe interactions. This study introduces a framework for understanding EVs as cross-kingdom regulators and underscores the importance of tailored, context-specific analyses for understanding the scope of EV-mediated interactions in microbiome-host homeostasis and disease.},
}

Humans
*Extracellular Vesicles/metabolism/genetics
MicroRNAs/metabolism/genetics
Caco-2 Cells
*RNA, Bacterial/metabolism/genetics
*Epithelial Cells/microbiology/metabolism
*Gastrointestinal Microbiome

@article {pmid41615027,
year = {2025},
author = {Jiménez, DJ and Marasco, R and Schultz, J and Díaz Rodríguez, CA and Nogales, J and Rodriguez-R, LM and Overmann, J and Rosado, AS},
title = {Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag012},
pmid = {41615027},
issn = {1751-7370},
support = {MCIN/AEI/10.13039/501100011033//Spanish Ministry of Science and Innovation/ ; 101081782 (deCYPher)//European Union/ ; 101036768 (PROMISEANG)//European Union/ ; PID2022-139247OB-I00 (Rob3D)//European Union/ ; BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Bacteria/genetics/classification/isolation & purification/growth & development ; Microbiota ; *Archaea/genetics/classification/isolation & purification/growth & development ; },
abstract = {Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.},
}

*Metagenomics/methods
*Artificial Intelligence
*Bacteria/genetics/classification/isolation & purification/growth & development
Microbiota
*Archaea/genetics/classification/isolation & purification/growth & development

@article {pmid41537582,
year = {2026},
author = {Robertson, S and Mosca, A and Ashraf, S and Corral, A and Alegria Terrazas, R and Arnton, C and Thorpe, P and Morris, J and Hedley, PE and Babbi, G and Savojardo, C and Martelli, PL and Møller, FD and Nielsen, HN and Leekitcharoenphon, P and Aarestrup, FM and Halder, R and Laczny, CC and Wilmes, P and Pietrantonio, L and Di Cillo, P and Catara, V and Abbott, J and Bulgarelli, D},
title = {Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants.},
journal = {mSphere},
volume = {11},
number = {2},
pages = {e0084225},
doi = {10.1128/msphere.00842-25},
pmid = {41537582},
issn = {2379-5042},
support = {818290//Horizon 2020 Framework Programme/ ; 2734186/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Solanum lycopersicum/microbiology/growth & development ; *Acinetobacter/genetics/classification/isolation & purification ; Soil Microbiology ; *Microbiota ; Rhizosphere ; Metagenomics ; Plant Roots/microbiology ; Metagenome ; },
abstract = {Tomato is a staple crop and an excellent model to study host-microbiota interactions in the plant food chain. In this study, we describe a "lab-in-the-field" approach to investigate the microbiota of field-grown tomato plants. High-throughput amplicon sequencing revealed a three-microhabitat partition, phyllosphere, rhizosphere, and root interior, differentiating host-associated communities from the environmental microbiota. An individual bacterium, classified as Acinetobacter sp., emerged as a dominant member of the microbiota at the plant-soil continuum. To gain insights into the functional significance of this enrichment, we subjected rhizosphere specimens to shotgun metagenomics. Similar to the amplicon sequencing survey, a "microhabitat effect," defined by a set of rhizosphere-enriched functions, was identified. Mobilization of mineral nutrients, as well as adaptation to salinity and polymicrobial communities, including antimicrobial resistance genes (ARGs), emerged as a functional requirement sustaining metagenomic diversification. A metagenome-assembled genome representative of Acinetobacter calcoaceticus was retrieved, and metagenomic reads associated with this species identified a functional specialization for plant-growth promotion traits, such as phosphate solubilization, siderophore production, and reactive oxygen species detoxification, which were similarly represented in a tomato genotype-independent fashion. Our results revealed that the enrichment of a beneficial bacterium capable of alleviating plant abiotic stresses appears decoupled from ARGs facilitating microbiota persistence at the root-soil interface.IMPORTANCETomatoes are at center stage in global food security due to their high nutritional value, widespread cultivation, and versatility. Tomatoes provide essential vitamins and minerals, contribute to diverse diets, and support farmer livelihoods, making them a cornerstone of sustainable food systems. Beyond direct dietary benefits, the intricate relationship between tomatoes, their associated microbiota, and antimicrobial resistance gene (ARG) is increasingly recognized. Tomato plants host diverse microbial communities in association with their organs, which influence plant health and productivity. Crop management impacts the composition and function of these communities, contributing to the prevalence of ARGs in the soil and on the plants themselves. These genes can potentially transfer to human pathogens, posing a food safety and public health risk. Understanding these complex interactions is critical for developing sustainable agricultural practices capable of mitigating the impact of climatic modifications and the global threat of antimicrobial resistance.},
}

*Solanum lycopersicum/microbiology/growth & development
*Acinetobacter/genetics/classification/isolation & purification
Soil Microbiology
*Microbiota
Rhizosphere
Metagenomics
Plant Roots/microbiology
Metagenome

@article {pmid41460655,
year = {2026},
author = {Oso, TA and Ahmed, MM and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Othman, ZK and Lucero-Prisno, DE},
title = {Exploring the gut-brain-microbiome axis in Alzheimer's disease: Integrating metagenomics, metabolomics, and artificial intelligence for next-generation biomarker discovery.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {109},
number = {4},
pages = {1542-1557},
doi = {10.1177/13872877251407700},
pmid = {41460655},
issn = {1875-8908},
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; *Metabolomics/methods ; *Artificial Intelligence ; Biomarkers/metabolism ; *Metagenomics/methods ; *Brain/metabolism ; Dysbiosis/metabolism ; },
abstract = {Alzheimer's disease (AD), a progressive neurodegenerative disorder, is increasingly understood as a multifactorial condition influenced by systemic and environmental factors beyond the central nervous system. A growing body of evidence shows that the gut-brain-microbiome axis (GBMA), a complex bidirectional communication network, is involved in neural, endocrine, immune, and metabolic pathways in AD pathogenesis. This narrative review synthesizes emerging insights into the role of gut microbiota dysbiosis in promoting neuroinflammation, amyloid-β aggregation, blood-brain barrier disruption, and cognitive decline. We explored recent advancements in metagenomics and metabolomics for profiling microbial communities and their functional metabolites linked to AD. Alterations in microbe-derived compounds, such as short-chain fatty acids and tryptophan metabolites, influence neurodevelopment, glial activation, and mitochondrial dysfunction. Multi-omics integration, enhanced by artificial intelligence (AI), enables precise biomarker discovery, patient stratification, and the development of personalized therapeutic strategies. Translational opportunities include microbiome-based diagnostics, probiotic therapy, and stratified interventions. However, clinical translation faces challenges such as methodological heterogeneity, inter-individual microbiome variation, data governance issues, and algorithmic bias. We emphasize the need for diverse reference panels, longitudinal multimodal cohorts, and shared AI-ready datasets to enhance the reproducibility and global equity of research. Strategic investment in integrative, ethically governed, and interdisciplinary approaches is essential to unlock the full therapeutic and diagnostic potential of GBMA in AD.},
}

Humans
*Alzheimer Disease/metabolism/microbiology
*Gastrointestinal Microbiome/physiology
*Metabolomics/methods
*Artificial Intelligence
Biomarkers/metabolism
*Metagenomics/methods
*Brain/metabolism
Dysbiosis/metabolism

@article {pmid40782151,
year = {2026},
author = {Kumari, P and Tripathi, BM and Eo, KY and Kimura, J and Yamamoto, N},
title = {Spatioseasonal Comparison of Fecal Resistome and Pathogenome of Raccoon Dogs in Korea.},
journal = {EcoHealth},
volume = {23},
number = {1},
pages = {71-83},
pmid = {40782151},
issn = {1612-9210},
support = {2021R1F1A1060259//National Research Foundation of Korea/ ; },
mesh = {Animals ; *Raccoon Dogs/microbiology ; *Feces/microbiology ; Republic of Korea ; Seasons ; *Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome ; },
abstract = {The raccoon dog (Nyctereutes procyonoides) is a medium-sized omnivore native to Asia. Because they live close to human habitation, and therefore, there is likely bidirectional influence between raccoon dogs and humans, it is important to investigate their potential risks. Here, to identify potential risks of carriage of antimicrobial resistance (AMR) and human pathogens by raccoon dogs, we investigated spatioseasonal patterns of fecal resistome (collection of antimicrobial resistance genes: ARGs), pathogenome (collection of virulence factor genes: VFGs), and microbiome (collection of bacterial species) of raccoon dogs inhabiting an urban forest area and a rural rice paddy area in Korea. Metagenomic sequencing revealed that the compositions of fecal resistome, pathogenome, and microbiome were all patterned by season, and we hypothesize that the observed patterns are due to seasonal changes in the diet of omnivorous raccoon dogs. Furthermore, although less pronounced than the seasonal differences, we also observed the geographical differences in the resistome, with aminoglycoside resistance genes being more prevalent in the rural area, which may reflect the geographical difference in selective pressures for AMR emergence, such as the use of manure that may contain antimicrobials in rice cultivation in agricultural areas. Additionally, our network analysis revealed that specific antimicrobial resistance genes were linked to specific bacterial pathogens, e.g., tetA-P to Clostridium. Overall, our study successfully revealed for the first time that not only the microbiome, but also the resistome and pathogenome of wild animals change spatioseasonally, and that the risk of AMR in bacterial pathogens laden by raccoon dogs is spatioseasonal.},
}

Animals
*Raccoon Dogs/microbiology
*Feces/microbiology
Republic of Korea
Seasons
*Drug Resistance, Bacterial/genetics
Gastrointestinal Microbiome

@article {pmid41722379,
year = {2026},
author = {Steinberger, Y and Doniger, T and Marchi, E and Eshel, G and Bocchi, S and Zapperi, S and La Porta, CAM},
title = {Fungal community structure and network connectivity as indicators of soil health under long-term land use.},
journal = {The Science of the total environment},
volume = {1020},
number = {},
pages = {181545},
doi = {10.1016/j.scitotenv.2026.181545},
pmid = {41722379},
issn = {1879-1026},
abstract = {Agriculture practices induce profound changes in soil biological properties and soil functioning. However, we still lack an understanding of how soil fungal biodiversity responds to various practices. Metagenomic tools were used to investigate soil fungal communities and inferred ecological functions based on functional guild classification in response to the effect of climate region and land management. This study assessed how seasonal timing and long-term land management affect soil fungal communities, with the aim of exploring their potential as candidate indicators of soil biological status. We collected soil samples across two regions of Israel (Mediterranean north and semi-arid south), three land-use types-orchard (OR), field crops (FC), and non-cultivated control (CO)-and two seasons-autumn and spring. Abiotic parameters varied significantly by season, region, and depth, underscoring the importance of considering sampling time in soil assessment. Fungal community composition showed marked differences between land uses, suggesting sensitivity to long-term management. CO and OR soils consistently exhibited higher fungal diversity and network connectivity, while FC soils had lower richness and unique taxa. A stable core community of 10 genera was found across treatments. Functional guilds were dominated by saprotrophs, though specific taxa and guild contributions varied by management type and season. Overall, our results emphasize the importance of sampling timing and land-use history in shaping fungal communities and support the potential of fungal-based indicators for assessing soil status across agricultural systems.},
}

@article {pmid41666847,
year = {2026},
author = {Matijašević, D and Kljajević, N and Malešević, M and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K},
title = {Heating-season dynamics of the airborne microbiome, resistome and mobilome in Belgrade, Serbia.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110114},
doi = {10.1016/j.envint.2026.110114},
pmid = {41666847},
issn = {1873-6750},
mesh = {Serbia ; *Microbiota ; Seasons ; *Air Microbiology ; Environmental Monitoring ; Air Pollution/statistics & numerical data ; *Drug Resistance, Microbial/genetics ; *Air Pollutants/analysis ; },
abstract = {Antimicrobial resistance (AMR) and air pollution are critical global health challenges, but their interplay remains poorly understood, particularly in Europe. Serbia, characterized by extensive antibiotic use, high prevalence of multidrug-resistant isolates and severe air pollution, provides a relevant model to study airborne AMR dissemination. During the heating season, air samples were collected at eight locations in Belgrade, representing industrial, traffic loaded and background environments. Shotgun metagenomics, co-occurrence networks and NMDS ordinations were applied to investigate the relationships between atmospheric pollutants, antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Autumn microbiomes were dominated by Lactococcus spp., whereas winter lacked such dominance. ARGs associated with antibiotic inactivation accounted for > 50% in autumn and > 75% in winter, with β-lactam resistance (blaTEM) predominating in both seasons. Winter resistomes also showed more consistent patterns of BRGs and MRGs, with multibiocide/acid and multimetal resistance prevailing. Integron analysis revealed predominance of class 1 integrons (intI1) commonly associated with Escherichia coli. Plasmid-related contigs were most similar to sequences reported in Acinetobacter baumannii and E. coli, while plasmid signatures related to Lactococcus lactis were also detected in autumn. Crucially, the network analysis revealed a seasonal restructuring of the airborne resistome. Autumn networks displayed fragmented structure, showing antagonism between Lactococcus and Escherichia, whereas winter networks coalesced into a densely interconnected superhub that could facilitate horizontal gene transfer and co-selection of resistance determinants. These findings suggest that prolonged air pollution and seasonality jointly shape airborne resistomes, reinforcing the need for integrated environmental and AMR surveillance in highly polluted urban areas.},
}

Serbia
*Microbiota
Seasons
*Air Microbiology
Environmental Monitoring
Air Pollution/statistics & numerical data
*Drug Resistance, Microbial/genetics
*Air Pollutants/analysis

@article {pmid41666834,
year = {2026},
author = {S, H and A, P},
title = {Insights into microbial carbon sequestration mechanisms in the Eastern Arabian Sea using metagenomic analysis.},
journal = {Marine environmental research},
volume = {216},
number = {},
pages = {107903},
doi = {10.1016/j.marenvres.2026.107903},
pmid = {41666834},
issn = {1879-0291},
mesh = {*Carbon Sequestration ; *Seawater/microbiology ; Seasons ; Metagenomics ; *Microbiota ; Bacteria ; *Environmental Monitoring ; Cyanobacteria ; *Water Microbiology ; },
abstract = {This investigation elucidated how depth- and season-dependent environmental gradients shape microbial community composition, metabolic potential, and carbon sequestration pathways in the Eastern Arabian Sea (EAS). The study encompassed six stations (L1-L6) spanning coastal to offshore regimes, three depth zones (surface, 200 m, and 1000 m), and three monsoonal phases: Spring Inter-Monsoon (SIM), Summer Monsoon (SM), and Winter Monsoon (WM). A total of 10,500 taxa were identified across all samples. Alpha-diversity indices showed peak diversity during the SM and SIM periods. Across all depths, Pseudomonadota (53.2 ± 16.2%) remained the dominant phylum, underscoring its broad ecological adaptability. Cyanobacteria (31.3 ± 19%) were abundant in surface waters during SIM and WM, but declined sharply with depth (<2%), where Actinomycetota dominated (25 ± 16%), highlighting strong vertical niche portioning. Distinct seasonal restructuring was evident, particularly during the SM, when upwelling-driven nutrient enrichment resulted in a marked decline in Cyanobacteria and a concomitant increase in copiotrophic taxa such as Rhodobacterales, Flavobacteriales, Pseudomonadales, and Oceanospirillales, indicative of intensified heterotrophic processing of organic matter. In contrast, oligotrophic taxa (Pelagibacterales, Prochlorococcus, Synechococcus) prevailed during SIM and WM, suggesting nutrient-limited and microbially driven carbon cycling. Remarkably, even deep-water communities (200-1000 m) exhibited significant seasonal restructuring (p < 0.05), with Alteromonadales and Oceanospirillales enriched during SM and Sphingomonadales and Rhodobacterales dominating during WM, indicating active coupling between surface productivity and deep microbial assemblages. Functional analyses revealed pronounced depth-dependent stratification of metabolic potential (p < 0.05) reflecting shifts from growth-oriented processes in surface waters to adaptive and recycling strategies at depth. Collectively, these findings reveal robust monsoon-driven and depth-stratified microbial dynamics in the EAS and provide novel evidence inferred based on microbial community structure and functional potential that both the Biological Carbon Pump and the Microbial Carbon Pump operate concurrently across this climatically sensitive and highly productive region.},
}

*Carbon Sequestration
*Seawater/microbiology
Seasons
Metagenomics
*Microbiota
Bacteria
*Environmental Monitoring
Cyanobacteria
*Water Microbiology

@article {pmid41570777,
year = {2026},
author = {Wang, Z and Lu, J and Wang, X and An, W and Zhao, Y and Han, B and Tao, H and Liu, J and Guo, J and Wang, J},
title = {Long-term pet ownership promotes resistome similarity between cats and their owners.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110074},
doi = {10.1016/j.envint.2026.110074},
pmid = {41570777},
issn = {1873-6750},
mesh = {Animals ; Cats ; *Pets/microbiology ; *Ownership ; Humans ; *Gastrointestinal Microbiome ; *Drug Resistance, Microbial/genetics ; Feces/microbiology ; },
abstract = {Pet ownership offers physical and mental health benefits, but the risks of antibiotic resistance genes (ARGs) transmission between pets and humans remain underexplored. In this study, we used metagenomics analysis of fecal samples to compare resistome profiles among four groups: owned cats and their owners, and caged cats and non-cat owners. Our findings show significant similarities in gut microbial composition, ARGs, and mobile genetic elements (MGEs) between owned cats and their owners, identifying 73 shared core ARGs and 80 shared MGEs. In contrast, caged cats and non-cat owners shared only 30 ARGs and 73 MGEs. Long-term contact was positively correlated with a higher number of shared ARGs (from 20 + to 60 +) and MGEs (from 10 + to 40 +), as well as increased resistome risk (2.47- to 4.92-fold) between pet cats and owners. The gut microbiota played a key role in shaping the ARGs and MGEs profiles, with Escherichia coli and Klebsiella pneumoniae identified as primary carriers, each genome harboring 20 to 62 ARGs and 6 to 29 MGEs. ARGs transfer events were more frequent between pet cats and their owners than in other groups. These findings underscore a potential risk of shared antimicrobial resistance between companion animals and humans within the studied population in China.},
}

Animals
Cats
*Pets/microbiology
*Ownership
Humans
*Gastrointestinal Microbiome
*Drug Resistance, Microbial/genetics
Feces/microbiology

@article {pmid41387121,
year = {2026},
author = {Ji, Y and Liu, X and Zhao, S and Zhou, S and Yang, Y and Zhang, P and Shi, Y and Qin, W and Zhu, G and Zhu, Y and Gao, Y and Jiang, J and Wang, B},
title = {Unveiling Global Diversity of Patescibacteriota and Functional Interactions with Host Microbes.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {11},
pages = {e09416},
doi = {10.1002/advs.202509416},
pmid = {41387121},
issn = {2198-3844},
support = {U22A20590//National Natural Science Foundation of China/ ; 42277304//National Natural Science Foundation of China/ ; 42477318//National Natural Science Foundation of China/ ; 42407399//National Natural Science Foundation of China/ ; 2025YFE0103900//National Key R&D Program of China/ ; BK20241558//Natural Science Foundation of Jiangsu Province/ ; BX20240168//China National Postdoctoral Program for Innovative Talents/ ; 2024ZB624//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
mesh = {Phylogeny ; *Host Microbial Interactions/genetics/physiology ; *Bacteria/genetics/classification ; Metagenome/genetics ; Ecosystem ; Biodiversity ; Metagenomics/methods ; },
abstract = {Patescibacteriota, also known as Candidate Phyla Radiation (CPR), is a diverse clade of ultra-small bacteria with an epibiotic lifestyle. Despite their ubiquity across diverse ecosystems and ecological importance in microbial networks, the global distribution of Patescibacteriota and functional interactions with their host organisms remain largely unknown. Here, by leveraging comprehensive Patescibacteriota genomic resources and global multi-habitat metagenomic datasets, it is demonstrated that ribosomal protein S3 (rpS3) as a reliable phylogenetic marker, enabling accurate recovery of Patescibacteriota diversity from short-read metagenomes. Using this framework, extensive taxonomic diversity and pronounced community heterogeneity are uncovered across eight ecosystems. Through network analysis and genome-wide functional screening, habitat-specific co-occurrence patterns are also revealed between Patescibacteriota and host-associated bacteria, especially potential functional synergies mediated by metabolic pathway cascades. Notably, Patescibacteriota-encoded NirK may assist sulfate-reducing bacteria in resisting nitrite stress, while NorB can mitigate nitric oxide toxicity for complete ammonia-oxidizing bacteria. Taken together, this study highlights the underappreciated diversity of Patescibacteriota and elucidates its important role in supporting host metabolism through complementary biochemical functions, offering new insights into its ecological significance and evolutionary adaptations in the global ecosystem.},
}

Phylogeny
*Host Microbial Interactions/genetics/physiology
*Bacteria/genetics/classification
Metagenome/genetics
Ecosystem
Biodiversity
Metagenomics/methods

@article {pmid41721873,
year = {2026},
author = {Sankar, SA and Girijan, SK and Shambhugowda, YB and Busala, SKK and Narayanane, S},
title = {Decoding the biotic networks and functional potential of seamount sediments in the Arabian sea.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41721873},
issn = {1573-4978},
mesh = {*Geologic Sediments/microbiology ; Metagenomics/methods ; Biodiversity ; Nitrogen/metabolism ; Seawater/microbiology ; Oceans and Seas ; Metagenome/genetics ; Fungi/genetics ; Microbiota/genetics ; Bacteria/genetics ; Phylogeny ; },
abstract = {BACKGROUND: The Arabian Sea is ecologically and environmentally significant due to its high biotic diversity and its potential role as a reservoir of emerging resistance determinants. However, molecular-level insights into the taxonomic composition, functional potential, and resistome of sediment associated communities from deep-sea seamount sediments remain limited.

METHODS AND RESULTS: A metagenomic approach was employed to investigate the biotic composition, metabolic potential, resistome profiles, and physicochemical characteristics of two seamount sediment samples (SM1 and SM7) collected from the Arabian Sea. Distinct environmental conditions were observed, with SM1 enriched in inorganic nitrogen, whereas SM7 exhibited higher organic carbon content and pigment concentrations, indicating differences in substrate availability. These variations were consistent with differences in the community structure, with SM1 harbouring a less diverse assemblage dominated by Actinomycetota and fungi, while SM7 supported a broader community comprising Actinomycetota, diverse fungi, protists, metazoans, and a richer viral component. Functional annotation revealed enrichment of nitrogen metabolism pathways in SM1, whereas SM7 showed increased representation of carbohydrate metabolism and a higher proportion of novel gene content. Both sediment samples encoded antibiotic and heavy metal resistance genes; however, SM7 exhibited greater abundance and diversity of putative resistance-associated genes, including resistance to mupirocin, triclosan, and sulfonamides, along with broader metal resistance and stress response genes.

CONCLUSIONS: The results based on two samples demonstrate pronounced sample specific variation in community structure, metabolic potential, and resistome profiles across Arabian Sea seamount sediments. These findings highlight Arabian Sea deep-sea sediments as important molecular reservoirs of microbial diversity and adaptive potential shaped by local environmental conditions.},
}

*Geologic Sediments/microbiology
Metagenomics/methods
Biodiversity
Nitrogen/metabolism
Seawater/microbiology
Oceans and Seas
Metagenome/genetics
Fungi/genetics
Microbiota/genetics
Bacteria/genetics
Phylogeny

@article {pmid41715233,
year = {2026},
author = {Choi, Y and Zhou, M and Oba, M and Romero-Pérez, A and Beauchemin, KA and Duval, S and Kindermann, M and Guan, LL},
title = {Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {72},
pmid = {41715233},
issn = {2049-2618},
support = {Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food & Agriculture Research Greener Cattle Initiative/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; },
mesh = {Metagenome ; *Rumen/enzymology/microbiology ; Animals ; *Cattle/microbiology ; Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Fatty Acids, Volatile/biosynthesis ; *Methane/biosynthesis ; Hydrogen/metabolism ; Metabolic Networks and Pathways/drug effects ; },
abstract = {BACKGROUND: The compound 3-nitrooxypropanol (3-NOP), an inhibitor of methyl-coenzyme M reductase (MCR), reduces enteric methane production in both beef and dairy cattle. Although the proposed mechanisms of 3-NOP involve on inhibiting the activity of MCR in vivo, it is unknown how this process could affect rumen microbiome as a whole and if it differs between beef and dairy cattle. This study conducted a comparative analysis of the rumen microbiome and its functional shifts in four different cattle studies (two beef and two dairy cattle studies) that evaluated 3-NOP supplementation using metataxonomics and metagenomics.

RESULTS: Comparative analysis of 281 rumen metataxonomic datasets (143 beef and 138 dairy cattle) revealed that dietary supplementation with 3-NOP affected rumen bacteria and methanogens. Further, comparative analysis of 54 metagenomic datasets (24 beef and 30 dairy cattle) revealed that 3-NOP inhibited mcrA, decreased the abundances of Methanobrevibacter gottschalkii and the protozoal species Isotricha prostoma, while increased the abundances of Methanobrevibacter ruminantium and Methanosphaera sp., Prevotella sp. was a significant bacterial taxon in both beef and dairy cattle, contributing to various pathways such as propionate and butyrate production. Its increased abundance after 3-NOP supplementation may also be linked to the decrease in Isotricha prostoma. Hydrogenotrophic methanogenesis decreased after 3-NOP supplementation with the abundance of genes involved in methylenetetrahydromethanopterin dehydrogenase decreased in beef cattle, while that of 4Fe-4S ferredoxin gene decreased in dairy cattle. The abundance of protozoal Polyplastron multivesiculatum increased after long-term 3-NOP supplementation in beef cattle, potentially due to changes in hydrogen (H2) partial pressure. During 3-NOP-mediated methanogenesis reduction, abundance of genes encoding methanogenic hydrogenase and H2 producing hydrogenase were decreased, while those encoding H2 sensory hydrogenase increased. Acyl-CoA dehydrogenase gene involved in propionate and butyrate production pathways increased in both beef and dairy cattle, while nitrite reductase increased specifically in beef cattle, indicating a rise in alternative H2 sinks. Video Abstract CONCLUSION: Our findings revealed broad effects of 3-NOP on rumen microbiome and functions in vivo, with varied effects in beef and dairy cattle, which provide mechanistic insights into the supplementation of 3-NOP in both beef and dairy cattle, supporting its more sustainable and effective use in the future.},
}

Metagenome
*Rumen/enzymology/microbiology
Animals
*Cattle/microbiology
Dietary Supplements
*Gastrointestinal Microbiome/drug effects
*Propanols/pharmacology
Fatty Acids, Volatile/biosynthesis
*Methane/biosynthesis
Hydrogen/metabolism
Metabolic Networks and Pathways/drug effects

@article {pmid41714786,
year = {2026},
author = {Paládi, P and Benmazouz, I and Tóth, M and Kövér, L and Lengyel, S},
title = {Spatial and temporal dynamics in the use of urban habitats by Hooded Crows.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40561-z},
pmid = {41714786},
issn = {2045-2322},
}

@article {pmid41671795,
year = {2026},
author = {Ji, J and Wang, Q and Hu, F and Yang, H and Li, Y and Wu, G and Dong, Y and Du, J and Li, H and Shen, B and Wang, B},
title = {Advantages of partial denitrification-anaerobic ammonium oxidation system under sulfamethoxazole stress: Adaptive mechanisms and synergistic metabolism.},
journal = {Bioresource technology},
volume = {446},
number = {},
pages = {134181},
doi = {10.1016/j.biortech.2026.134181},
pmid = {41671795},
issn = {1873-2976},
mesh = {*Denitrification/drug effects ; *Sulfamethoxazole/pharmacology ; *Ammonium Compounds/metabolism ; Oxidation-Reduction/drug effects ; Anaerobiosis/drug effects ; Nitrogen/metabolism ; Bioreactors/microbiology ; Microbiota ; },
abstract = {The widespread use of antibiotics has led to their persistence in aquatic environments, posing serious challenges to biological treatment systems. This study systematically compared the performance and adaptive mechanisms of partial denitrification (PD)/anaerobic ammonium oxidation (anammox) and single anammox systems under long-term sulfamethoxazole (SMX) stress over 193 days. At an influent SMX concentration of 3 mg/L, the PD/anammox system retained 75% of its initial total inorganic nitrogen (TIN) removal efficiency, significantly higher than that of the single anammox system (49%). The PD/anammox achieved an SMX degradation efficiency of 80%, substantially exceeding that of the single system (39%). Metagenomic analyses revealed higher abundances of key nitrogen metabolism genes (hzs, hdh, narG/H/I, napA/B, nirK/S) and SMX degradation genes (sadA, sadC, tmoABCDEF, dmpB/D) in the PD/anammox system. The enhanced performance was closely associated with the enrichment of the denitrifying microbiome (e.g., Thauera, Zoogloea, unclassified_f_Rhodocyclaceae), which provided a stable nitrite supply and carried SMX degradation genes. Both systems relied on extracellular polymeric substances (EPS) as a protective barrier under low SMX stress (1 mg/L). Under higher SMX concentrations (>1 mg/L), the PD/anammox system exhibited dynamic enrichment of sulfonamide resistance genes (sul1). These results demonstrated the superiority of the PD/anammox system over the single anammox system. The combined effects of a diverse microbiome, multi-level stress-response mechanisms involving EPS and antibiotic resistance genes, and efficient functional gene expression make PD/anammox a robust and promising technology for the treatment of antibiotic-containing wastewater.},
}

*Denitrification/drug effects
*Sulfamethoxazole/pharmacology
*Ammonium Compounds/metabolism
Oxidation-Reduction/drug effects
Anaerobiosis/drug effects
Nitrogen/metabolism
Bioreactors/microbiology
Microbiota

@article {pmid41651079,
year = {2026},
author = {Xin, Y and Ma, H and Li, X and Sun, R and Fang, L and Pan, L},
title = {Multi-omics reveal the key role of gut microbiota metabolism in adenine-induced chronic kidney disease.},
journal = {Toxicology and applied pharmacology},
volume = {509},
number = {},
pages = {117754},
doi = {10.1016/j.taap.2026.117754},
pmid = {41651079},
issn = {1096-0333},
mesh = {*Gastrointestinal Microbiome/drug effects/physiology ; Animals ; *Adenine/toxicity ; *Renal Insufficiency, Chronic/chemically induced/metabolism/microbiology ; *Metabolomics/methods ; Male ; Mice ; Mice, Inbred C57BL ; Disease Models, Animal ; Kidney/metabolism ; Metagenomics ; Bile Acids and Salts/metabolism ; Multiomics ; },
abstract = {The gut microbiota plays a crucial role in the progression of chronic kidney disease (CKD). The adenine-induced CKD mouse model is widely employed in preclinical research, yet the effects of adenine on the composition and metabolic function of the gut microbiota remain to be elucidated. This study aimed to test the hypothesis that adenine-induced alterations in the structure and function of the gut microbiota are significantly associated with the onset and progression of CKD. To this end, a mouse CKD model was established by alternating feeding with 0.15% and 0.20% adenine for 7 weeks. Multi-omics analysis (untargeted metabolomics, metagenomics, and spatial metabolomics) was performed to compare the adenine-induced CKD group with a standard diet-fed normal control group. Integrated analysis of plasma metabolomics and intestinal content metabolomics identified 94 differentially co-regulated metabolites: among these, indolelactic acid was significantly upregulated, while indole-3-propionic acid was significantly downregulated. The bile acid metabolic pathway also underwent marked perturbations: taurochenodeoxycholic acid and tauro-β-muricholic acid (two taurine-conjugated bile acids) were significantly elevated, whereas nordeoxycholic acid and norcholic acid were notably reduced. Integrated metabolomics-metagenomics analysis further demonstrated that Lactobacillus exhibited a significant positive correlation with a subset of upregulated metabolites (including indolelactic acid), while Taurinivorans muris showed a strong negative correlation with the taurine-conjugated bile acids. Additionally, renal spatial metabolomics revealed that phospholipid metabolic disorders in the adenine-induced CKD group directly contributed to the aggravation of renal inflammatory responses. Collectively, these findings reveal a gut microbiota-metabolite-kidney axis perturbed by adenine, providing novel insights into the pathogenesis of CKD and potential targets for metabolic intervention.},
}

*Gastrointestinal Microbiome/drug effects/physiology
Animals
*Adenine/toxicity
*Renal Insufficiency, Chronic/chemically induced/metabolism/microbiology
*Metabolomics/methods
Male
Mice
Mice, Inbred C57BL
Disease Models, Animal
Kidney/metabolism
Metagenomics
Bile Acids and Salts/metabolism
Multiomics

@article {pmid41455576,
year = {2026},
author = {Kitagawa, H and Kajihara, T and Yahara, K and Kitamura, N and Shigemoto, N and Doi, H and Shimbara, K and Yoshimura, K and Nakashima, I and Uegami, S and Watadani, Y and Kawada-Matsuo, M and Komatsuzawa, H and Ohge, H and Sugai, M},
title = {Impact of antimicrobial prophylaxis in colorectal cancer surgery on the gut and oral microbiome and resistome: A prospective observational cohort study.},
journal = {Journal of global antimicrobial resistance},
volume = {46},
number = {},
pages = {227-234},
doi = {10.1016/j.jgar.2025.12.014},
pmid = {41455576},
issn = {2213-7173},
mesh = {Humans ; Prospective Studies ; Male ; Female ; *Colorectal Neoplasms/surgery/microbiology ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; Feces/microbiology ; Aged ; *Antibiotic Prophylaxis ; *Anti-Bacterial Agents/therapeutic use ; *Mouth/microbiology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Microbiota/drug effects ; Metagenomics ; Drug Resistance, Bacterial ; },
abstract = {BACKGROUND: The use of antibiotics may facilitate the colonisation of antimicrobial-resistant organisms and genes within the host microbiome. However, studies on the effects of antibiotics on microbiomes and resistomes in clinical settings are limited.

AIM: The aim of this study was to determine the effects of antibiotic prophylaxis during colorectal cancer surgery on the oral and gut microbiomes and resistomes of patients.

METHODS: We conducted a single-centre prospective observational cohort study on patients who underwent colorectal cancer surgery with antibiotic prophylaxis. DNA was extracted from oral and stool samples 1 day prior to the procedure and on postoperative days 1, 7, and 28. Subsequently, metagenomic sequencing was performed.

FINDINGS: Among the eight patients with colorectal cancer, α-diversity in the oral and stool samples significantly decreased from baseline to each of the three post-administration time points. The abundance of anaerobic genera significantly decreased from baseline to Day 7. In the stool samples, Enterococcus, Limosilactobacillus, and Lacticaseibacillus abundances were markedly increased. Total antibiotic resistance gene (ARG) abundance significantly increased from the baseline to Day 7 in both oral and stool samples. The impact of the increase observed on Day 7 decreased but still persisted until Day 28 for diversity and total abundance of ARGs.

CONCLUSIONS: Oral and gut microbiomes and resistomes exhibited marked alterations that gradually reversed over time. Changes in the microbiome were associated with the spectrum of antibiotics used.},
}

Humans
Prospective Studies
Male
Female
*Colorectal Neoplasms/surgery/microbiology
*Gastrointestinal Microbiome/drug effects
Middle Aged
Feces/microbiology
Aged
*Antibiotic Prophylaxis
*Anti-Bacterial Agents/therapeutic use
*Mouth/microbiology
*Bacteria/genetics/classification/drug effects/isolation & purification
*Microbiota/drug effects
Metagenomics
Drug Resistance, Bacterial

@article {pmid41712566,
year = {2026},
author = {Bedoya-Urrego, K and Peñuela-Martínez, AE and Alzate, JF},
title = {Uncovering the hidden yeast diversity in fermented coffee: Insights from a shotgun metagenomic approach.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0332370},
pmid = {41712566},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; Fermentation ; *Coffee/microbiology ; Phylogeny ; *Yeasts/genetics/classification ; Metagenome ; Biodiversity ; Genome, Fungal ; },
abstract = {Yeasts play a pivotal role in coffee fermentation, shaping microbial succession and contributing to the development of final flavor profiles. Despite their importance, yeast taxonomy in this context remains poorly resolved. Traditional classification methods often result in misidentifications due to the limited resolution of classical microbiological techniques and the rapidly evolving taxonomic framework driven by advances in phylogenomic. Moreover, the diversity of budding yeasts in coffee fermentations remains underexplored using high-resolution approaches such as metagenomics. To address this gap, we applied a shotgun metagenomic strategy and reconstructed metagenome-assembled genomes (MAGs) from multiple coffee fermentation samples and, using a robust phylogenomic framework based on 832 conserved single-copy genes. We confidently classified 22 yeast MAGs within the subphylum Saccharomycotina. These included well-known taxa such as Pichia kluyveri, Hanseniaspora spp., Torulaspora delbrueckii, and members of the Kurtzmaniella clade. Most MAGs were placed in strongly supported monophyletic groups (ultrafast bootstrap = 100), with short intra-clade branch lengths indicative of intraspecific variation. Pichia kluyveri emerged as the most abundant and widespread species, detected in all analyzed metagenomes, followed by Hanseniaspora spp. Our results underscore the power of high-resolution phylogenomic for classifying yeast MAGs and highlight the ecological importance of Pichia, Hanseniaspora, Torulaspora, and Kurtzmaniella in spontaneous coffee fermentations.},
}

*Metagenomics/methods
Fermentation
*Coffee/microbiology
Phylogeny
*Yeasts/genetics/classification
Metagenome
Biodiversity
Genome, Fungal

@article {pmid41671864,
year = {2026},
author = {Cui, W and Cui, Y and Hao, Y and Li, Y and Wang, Y and Liu, F and Long, J and Jin, Y and Chen, S and Duan, G and Yang, H},
title = {The effect of pet dog exposure on gut antibiotic resistome and microbiome of their owners.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141429},
doi = {10.1016/j.jhazmat.2026.141429},
pmid = {41671864},
issn = {1873-3336},
mesh = {Dogs ; Animals ; Humans ; *Gastrointestinal Microbiome/genetics ; *Pets/microbiology ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Adult ; Male ; Female ; Acinetobacter baumannii/genetics/drug effects ; Enterococcus faecium/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Pet dogs provide well-documented physical and mental health benefits to humans through close interactions. However, the potential role of pet dogs as reservoirs of antibiotic resistance genes (ARGs) and the impact on shaping the gut microbiomes of their owners remains poorly characterized. The growing dual challenges of global antimicrobial resistance and widespread pet ownership underscore the importance of understanding human-animal resistome interactions crucial for One Health solutions. Consequently, this study conducted a metagenomic analysis of pet dogs, dog owners, and non-dog owners to investigate the effects of dogs on the microbiota composition, ARGs profiles, and mobile genetic elements (MGEs) of the human gut. The results indicated that pet dogs exhibited significantly higher gut abundance of both ARGs and ESKAPE pathogens (Enterococcus faecium and Acinetobacter baumannii) compared to humans. Moreover, the abundance of aminoglycoside resistance genes aac(6')-Im and aac(6')-Ie-aph(2'')-Ia, tetracycline resistance genes tetO and tet40 were was significantly higher in dog owners than in non-dog owners. Enterobacteriaceae were identified as shared core ARG hosts in both dog and human guts. Collectively, our results indicate that cohabitation with pet dogs is associated with a shared gut resistome, reflecting correlated patterns of ARGs and resistant microbes. These findings emphasize the necessity of monitoring antibiotic resistance in companion animals, while maintaining the benefits of human-dog relationships.},
}

Dogs
Animals
Humans
*Gastrointestinal Microbiome/genetics
*Pets/microbiology
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Adult
Male
Female
Acinetobacter baumannii/genetics/drug effects
Enterococcus faecium/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid41666549,
year = {2026},
author = {Kang, X and Zhao, Z and Zhu, X and Ju, F},
title = {Uncovering plasticizer-degrading potential in landfill microbiomes with curated PzDE-HMM database and multi-scale validation from isolates to synthetic consortia.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141398},
doi = {10.1016/j.jhazmat.2026.141398},
pmid = {41666549},
issn = {1873-3336},
mesh = {*Plasticizers/metabolism ; *Microbiota ; Biodegradation, Environmental ; Waste Disposal Facilities ; *Bacteria/genetics/metabolism ; Phthalic Acids/metabolism ; },
abstract = {Plasticizers are widely used additives that leach from plastic products and accumulate in landfills, yet the microbial functions supporting their degradation remain poorly resolved. Here, we combined curated functional annotation, substrate-driven enrichment, and isolate-level validation to dissect plasticizer degradation in landfill microbiomes. A plasticizer-degrading enzyme (PzDE) hidden Markov model database (PzDE-HMM) was assembled from 49 experimentally validated enzyme families. It was applied to metagenomes from five landfill niches, identifying 2219 candidate plasticizer-degrading genes, which is 3.6- and 19-fold more than those identified by KofamScan- and BLASTp-based annotation methods, respectively. Enrichment with three legacy phthalates (DEHP, DIDP, DBP) and three non-phthalate plasticizers (DOTP, DOA, ATBC) drove pronounced shifts in landfill microbial communities and functional gene repertoires, revealing coexisting broad-spectrum and substrate-specific degraders. Culture-based isolation from enriched media yielded 51 strains, and three representative isolates showed concordance between PzDE-HMM-predicted gene repertoires, substrate breadth, and degradation ability. Synthetic consortia assembled from these strains exhibited complementary degradation capacities and achieved higher removal of several plasticizers than the best single strains, illustrating how complementary gene sets can be combined to enhance multi-substrate degradation. Together, PzDE-HMM annotation workflow and this multilevel prediction-enrichment-isolate-consortium framework uncover the plasticizer-degrading and bioremediation potential of landfill microbiomes and provide a reusable resource and workflow for future plasticizer-focused microbiome studies.},
}

*Plasticizers/metabolism
*Microbiota
Biodegradation, Environmental
Waste Disposal Facilities
*Bacteria/genetics/metabolism
Phthalic Acids/metabolism

@article {pmid41612472,
year = {2026},
author = {Wang, Y and Shen, Y and Shen, J and Bi, J and Xu, J and Wei, T and Wang, R and Wu, X and Li, F and Bai, J and Jie, Z and Hou, D and Song, Y},
title = {Airway microbiome dysbiosis in severe pneumonia: metagenomic evidence of pathogen expansion and commensal depletion.},
journal = {European journal of medical research},
volume = {31},
number = {1},
pages = {},
pmid = {41612472},
issn = {2047-783X},
support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-18//Shanghai Three-year Action Plan to Strengthen the Construction of Public Health System/ ; 82130001//National Natural Science Foundation of China/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; GZNL2024A02003//R&D Program of Guangzhou National Laboratory/ ; W2020-013//The Construction of Multi-Disciplinary Treatment System for Severe Pneumonia/ ; 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Male ; Female ; Middle Aged ; *Microbiota/genetics ; Prospective Studies ; Aged ; Metagenomics ; *Pneumonia/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {BACKGROUND: The pulmonary microbiome is increasingly recognized as a key determinant of pneumonia severity, yet its clinical implications remain incompletely understood. Disruption of microbial ecology, or dysbiosis, may impair host immune responses and exacerbate disease progression. This study aimed to characterize microbiome alterations associated with severe pneumonia and their correlation with host inflammatory and coagulative parameters.

METHODS: In this multicenter, prospective observational cohort study conducted across nine hospitals in Shanghai (2021-2025), bronchoalveolar lavage fluid (BALF) samples from 306 patients with clinically diagnosed pulmonary infections were analyzed using metagenomic next-generation sequencing (mNGS). Patients were stratified into severe (n = 196) and non-severe (n = 110) groups using WHO-derived severe pneumonia criteria at the time of bronchoalveolar lavage (BAL). Microbial taxonomic profiles, diversity indices, co-occurrence networks, and correlations with clinical markers were comprehensively assessed using standard bioinformatic and statistical approaches.

RESULTS: Severe pneumonia was associated with marked microbial dysbiosis, including reorganization of co-occurrence network topology with centrality shifting away from commensals toward opportunistic taxa in severe disease, characterized by reduced α-diversity, altered β-diversity, and enrichment of opportunistic Gram-negative pathogens including Acinetobacter and Klebsiella. In contrast, commensals such as Rothia and Prevotella were depleted. Co-occurrence network analysis revealed fragmentation of microbial interactions in severe cases, with centrality shifting from commensals to opportunists like Corynebacterium striatum. Shannon diversity negatively correlated with SOFA scores, and specific taxa positively associated with systemic inflammation (CRP, PCT) and coagulation abnormalities. Nearly all samples demonstrated polymicrobial infection, with distinct microbial patterns observed across monomicrobial and polymicrobial subgroups.

CONCLUSION: Our multicenter observational analysis suggests that severe pneumonia is associated with marked ecological disruption of the lower-airway microbiome, characterized by commensal loss, opportunist expansion, and fragmented interspecies networks, and with concurrent inflammatory and coagulative abnormalities. These hypothesis-generating findings warrant external validation in independent, multi-region cohorts and longitudinal sampling to test directionality and causality before informing clinical decision-making.},
}

Humans
*Dysbiosis/microbiology
Male
Female
Middle Aged
*Microbiota/genetics
Prospective Studies
Aged
Metagenomics
*Pneumonia/microbiology
Bronchoalveolar Lavage Fluid/microbiology

@article {pmid41593438,
year = {2026},
author = {Wang, X and Tian, D and Han, B and Zhao, K and Hao, W and Du, K and Li, X and Duan, Z},
title = {Exploring the impact of rumen microbiome on ovine flavor-related compounds and comparing flavor profiles between Tibetan sheep and Small-tail Han sheep.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41593438},
issn = {1471-2180},
support = {2024YFF0728800//National Key Research and Development Program of China/ ; 2024-ZJ-949//the Natural Science Foundation of Qinghai Province/ ; XDA26040305//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {Animals ; *Rumen/microbiology ; Sheep/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Gastrointestinal Microbiome ; Fatty Acids, Volatile/analysis/metabolism ; Metagenomics ; Tibet ; *Flavoring Agents/metabolism/analysis ; Taste ; Tandem Mass Spectrometry ; },
abstract = {The characteristic 'mutton flavor', primarily attributed to branched-chain fatty acids (BCFAs), is influenced by various factors including rumen microbes. This study aims to elucidate the disparities in meat flavor compounds and their underlying regulatory mechanisms mediated by rumen microbes between two important sheep breeds on the Qinghai-Tibetan Plateau. We used LC-MS/MS to analyze BCFAs and rumen short-chain fatty acids (SCFAs), along with metagenomic sequencing to characterize the rumen microbiome. Compared to Tibetan sheep, Small Tail Han sheep exhibited significantly higher concentrations of BCFAs, including 4-ethyloctanoic acid (EOA) and 4-methyloctanoic acid (MOA), as well as SCFAs such as pentanoate, glutarate, and propionate. In contrast, acetate levels were inversely correlated with these fatty acids. Metagenomics revealed a predominance of Bacteroidota (formerly Bacteroidetes) and Bacillota (formerly Firmicutes) in sheep. Furthermore, random forest and LEfSe analyses identified seven bacterial biomarkers, including Lactobacillus, Ligilactobacillus, Blautia, Anaerovibrio, Selenomonas, Phocaeicola, Sodaliphilus. Functional analysis indicated differences in carbohydrate degradation capabilities of two breeds. Likewise, strong positive correlations of propionate with MOA, and glutarate with EOA were observed, respectively. The findings are expected to provide critical insights into the potential for modulating meat flavor through nutritional strategies targeting rumen microbes.},
}

Animals
*Rumen/microbiology
Sheep/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Gastrointestinal Microbiome
Fatty Acids, Volatile/analysis/metabolism
Metagenomics
Tibet
*Flavoring Agents/metabolism/analysis
Taste
Tandem Mass Spectrometry

@article {pmid41581489,
year = {2026},
author = {Liu, Z and Zhao, F and Li, Q and Shang, Q and Fang, D and Li, X and Li, H and He, Q and Zhang, D and Cheng, J and Zhu, Y and Li, Z and Silva, AS and Chen, J},
title = {Multi-omics chemical and biochemical profiling reveals ellagic acid enhances insulin sensitivity via gut microbiota-tryptophan-indole signaling mechanism.},
journal = {Food chemistry},
volume = {505},
number = {},
pages = {147984},
doi = {10.1016/j.foodchem.2026.147984},
pmid = {41581489},
issn = {1873-7072},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Insulin Resistance ; *Indoles/metabolism ; *Tryptophan/metabolism ; Mice ; *Ellagic Acid/metabolism/pharmacology ; Male ; Bacteria/classification/genetics/isolation & purification/metabolism ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Humans ; Multiomics ; },
abstract = {Ellagic acid (EA) is a dietary polyphenol with limited systemic bioavailability, resulting in substantial intestinal exposure. However, the biochemical mechanisms by which EA modulates gut microbiota and metabolism remain unclear. Here, EA improved glucose tolerance and enhanced insulin sensitivity, with histology confirming reduced lipid accumulation and restored tissue architecture in liver, skeletal muscle, brown adipose tissue, and mesenteric fat. Consistently, metagenomic analysis showed that EA enriched Akkermansia muciniphila, Muribaculum intestinale, and Duncaniella dubosii, while reducing Lachnoclostridium phocaeense. These microbial shifts were accompanied by elevated levels of tryptophan-derived metabolites-indole-3-propionic acid, indole, and indole-3-acrylic acid-known to enhance insulin sensitivity. Lipidomics revealed EA decreased triacylglycerols and ceramides, along with restored phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine levels. Transcriptomics revealed EA suppressed hepatic lipogenesis, inhibited MAPK signaling in skeletal muscle, activated thermogenic and oxidative phosphorylation in adipose tissues. Our findings highlight EA, a food-derived polyphenol, might alleviate insulin resistance through a gut microbiota-indole metabolite-multi-tissue axis.},
}

*Gastrointestinal Microbiome/drug effects
Animals
*Insulin Resistance
*Indoles/metabolism
*Tryptophan/metabolism
Mice
*Ellagic Acid/metabolism/pharmacology
Male
Bacteria/classification/genetics/isolation & purification/metabolism
Signal Transduction/drug effects
Mice, Inbred C57BL
Humans
Multiomics

@article {pmid41708187,
year = {2026},
author = {Fang, M and He, J and Zhou, S and Hong, P and Ke, L and Wu, H and Shu, Y},
title = {Pleurotus ostreatus polysaccharides improve microcystin-LR-induced intestinal damage in tadpoles by regulating the interaction between microbiota and intestine.},
journal = {Harmful algae},
volume = {153},
number = {},
pages = {103056},
doi = {10.1016/j.hal.2026.103056},
pmid = {41708187},
issn = {1878-1470},
mesh = {Animals ; *Intestines/drug effects/microbiology ; *Microcystins/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Pleurotus/chemistry ; *Polysaccharides/pharmacology ; Larva/drug effects/microbiology ; *Ranidae ; Marine Toxins ; Oxidative Stress/drug effects ; },
abstract = {Exposure to microcystins (MCs) can cause severe intestinal damage. This study aimed to assess the efficacy of Pleurotus ostreatus polysaccharide in alleviating intestinal damage induced by microcystin-leucine-arginine (MC-LR) in tadpoles. Over a 30-day period, tadpoles (Pelophylax nigromaculatus) received daily exposures to MC-LR and were provided with diets either supplemented with or devoid of P. ostreatus polysaccharide. Results revealed that feeding P. ostreatus polysaccharide conferred protection against MC-LR-induced intestinal damage by mitigating barrier damage, lowering intestinal permeability, and reducing the tissue burden of MC-LR. The LPS/TLR4 pathway response was attenuated, reducing inflammation, and oxidative stress-mediated apoptosis response was also diminished. Gram-negative bacteria (e.g., Bacteroides) in the intestine show a positive correlation with LPS content and the transcription of key genes in the LPS/TLR4 pathway. Metagenomic and metabolite analysis of intestinal contents revealed increased abundance of the alanine-glyoxylate aminotransferase gene (agxt)-the key enzyme converting glyoxylic acid to glycine-and elevated glycine content in the MC-LR-exposed group fed polysaccharide. Results from the corresponding fecal microbiota transplantation experiment aligned with the trends observed in the exposure experiment. Therefore, polysaccharide alleviates MC-LR-induced intestinal damage by enhancing intestinal microbiota-mediated glycine synthesis, supplying raw materials for intestinal GSH production, reducing oxidative stress levels, and simultaneously dampening the LPS/TLR4 pathway response. Moreover, feeding polysaccharides might also regulate the intestine's defense against pathogens after MC-LR exposure by enhancing lysozyme activity. There is no evidence of intestinal damage in the P. ostreatus exopolysaccharide group. This study highlights for the first time the role of P. ostreatus polysaccharides in mitigating MC-LR-induced intestinal tissue damage, potentially offering novel insights for their application in aquaculture.},
}

Animals
*Intestines/drug effects/microbiology
*Microcystins/toxicity
*Gastrointestinal Microbiome/drug effects
*Pleurotus/chemistry
*Polysaccharides/pharmacology
Larva/drug effects/microbiology
*Ranidae
Marine Toxins
Oxidative Stress/drug effects

@article {pmid41691253,
year = {2026},
author = {Daryani, NE and Jazayeri, SM and Izadi, N and Ahmadi, H and Baghi, HB and Shirmohammadi, M and Sabbaghian, M and Shekarchi, AA and Marvi, SS and Azadi, A and Poortahmasebi, V},
title = {Characterizing the gut virome in ulcerative colitis and crohn's disease: signatures of disease severity.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {46},
pmid = {41691253},
issn = {1743-422X},
support = {979157//National Institute for Medical Research Development/ ; },
mesh = {Humans ; *Virome ; *Crohn Disease/virology/pathology ; Cross-Sectional Studies ; Male ; *Colitis, Ulcerative/virology/pathology ; Adult ; Female ; Severity of Illness Index ; Middle Aged ; Feces/virology ; *Viruses/classification/genetics/isolation & purification ; Iran ; Metagenomics ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Young Adult ; Bacteriophages/genetics/classification ; Computational Biology ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is a chronic disorder marked by intestinal inflammation and immune dysregulation. While bacterial dysbiosis has been widely investigated, the gut virome remains less explored. Altered viral communities, particularly bacteriophages, may destabilize microbial balance and amplify host inflammation.

METHODS: To characterize virome alterations, we conducted a cross-sectional observational study in Tabriz, Iran, involving fifty participants divided into five groups: mild UC, severe UC, mild CD, severe CD, and healthy controls. Stool samples were processed for viral nucleic acid extraction and analyzed using metagenomic next-generation sequencing. Bioinformatics pipelines included diversity assessment, taxonomic profiling, functional annotation, and discriminant analysis (LEfSe). Predictive modeling was performed with random forest classifiers.

RESULTS: Virome richness and diversity were reduced in severe UC and CD compared with controls, whereas mild cases showed values closer to healthy individuals. Taxonomic profiling revealed depletion of crAss-like phages and microviridae in IBD, along with enrichment of Caudovirales families such as siphoviridae and myoviridae. Among eukaryotic viruses, anelloviridae were prominent in severe IBD, and herpesviridae were enriched specifically in severe UC. Functional annotation highlighted enrichment of structural and lytic phage proteins in severe groups, whereas lysogeny-associated domains were more abundant in healthy controls. Random forest models based on viral features achieved appropriate accuracy, with an AUC of 0.89 for distinguishing IBD from controls and 0.83 for classifying mild versus severe disease.

CONCLUSION: Thus, IBD is associated with reduced virome diversity, loss of core protective phages, and selective enrichment of bacteriophages and eukaryotic viruses. These findings suggest that virome features may have potential as biomarkers for non-invasive diagnosis and severity stratification in IBD, requiring validation in larger and longitudinal cohorts.},
}

Humans
*Virome
*Crohn Disease/virology/pathology
Cross-Sectional Studies
Male
*Colitis, Ulcerative/virology/pathology
Adult
Female
Severity of Illness Index
Middle Aged
Feces/virology
*Viruses/classification/genetics/isolation & purification
Iran
Metagenomics
*Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing
Young Adult
Bacteriophages/genetics/classification
Computational Biology

@article {pmid41644585,
year = {2026},
author = {Zhou, Y and Liu, K and Gong, P and Wu, J and Ren, Z and Jin, E},
title = {Integrated metagenomic and 16S rRNA analysis reveals temporal associations between resistance genes and microbial communities during dairy manure composting.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41644585},
issn = {2045-2322},
mesh = {*Manure/microbiology ; *Composting/methods ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Animals ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Dairying ; Metagenome ; *Drug Resistance, Bacterial/genetics ; Soil Microbiology ; Cattle ; Genes, Bacterial ; },
abstract = {Dairy manure composting is widely applied to stabilize organic waste and reduce environmental pollution, yet the behavior of resistance determinants during this process remains insufficiently resolved. In this study, shotgun metagenomic sequencing was used to characterize temporal changes in antibiotic resistance genes (ARGs), metal resistance genes (MRGs), biocide resistance genes (BRGs), mobile genetic elements (MGEs), and microbial community composition during dairy manure composting. Rather than inferring direct mechanistic causation, our analyses focused on identifying statistically supported trends, associations, and co-occurrence patterns across composting stages. We observed a rapid decline in the relative abundance of ARGs compared with MRGs and BRGs during the thermophilic phase, coinciding with increasing temperature, while specific genes such as sul2 persisted throughout the process. Shifts in microbial community composition, particularly changes in the relative dominance of Actinobacteria and Proteobacteria, were significantly associated with variations in resistome profiles. Correlation and network analyses further revealed strong associations among ARGs, MRGs, BRGs, and MGEs, suggesting potential co-selection and horizontal gene transfer linkages without implying direct causal mechanisms. In addition, several opportunistic bacterial genera showed positive associations with aminoglycoside- and macrolide-lincosamide-streptogramin-type ARGs, indicating possible dissemination risks following compost application. Overall, this study provides an integrated, association-based overview of resistome and microbial community dynamics during dairy manure composting and highlights the importance of considering multiple resistance determinants when evaluating composting as a manure management strategy.},
}

*Manure/microbiology
*Composting/methods
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Animals
*Microbiota/genetics
*Drug Resistance, Microbial/genetics
Bacteria/genetics
Dairying
Metagenome
*Drug Resistance, Bacterial/genetics
Soil Microbiology
Cattle
Genes, Bacterial

@article {pmid41639568,
year = {2026},
author = {Zeng, Y and Qi, H and Guo, W and Tan, X and Huang, B and Hu, R and Ouyang, X},
title = {Multi-omics insights into Shenling Baizhu Powder's amelioration of murine asthma through gut microbiota and Glutamine-GLS1 pathway.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41639568},
issn = {2045-2322},
support = {2023BSQD002//Doctoral Scientific Initiate Project of Shunde Women and Children's Hospital of Guangdong Medical University (Maternity & Child Healthcare Hospital of Shunde Foshan)/ ; 20241090//The Project of Administration of Traditional Chinese Medicine of Guangdong Province/ ; 2023A04J0550//Guangzhou Municipal Science and Technology Project/ ; 20250403//Medical Research Project of Foshan Municipal Health Bureau/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Asthma/drug therapy/metabolism/pathology/microbiology ; Mice ; *Glutamine/metabolism ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Metabolomics ; Disease Models, Animal ; Mice, Inbred BALB C ; Th17 Cells/immunology/drug effects ; Powders ; Cytokines/metabolism ; Female ; Lung/pathology/drug effects ; Ovalbumin ; Th2 Cells/immunology/drug effects ; Multiomics ; },
abstract = {Shenling Baizhu Powder (SLBZP) is a prominent formulation widely used in the treatment of pulmonary diseases. However, studies examining the mechanisms of SLBZP for treating asthma are limited. This study aimed to clarify the efficacy and possible mechanisms of SLBZP in the context of asthma from the perspective of gut microbiota-metabolism-immune crosstalk. Key parameters including airway hyperresponsiveness, lung pathological features and the expression of inflammatory mediators from Th2 and Th17 cells were employed to validate the anti-inflammatory properties of SLBZP. The anti-asthma mechanism of SLBZP was investigated using metagenomic sequencing, metabolomics, flow cytometry, RT-qPCR, immunohistochemistry (IHC) and immunofluorescence (IF). SLBZP demonstrated significant capacity to mitigate histopathological alterations associated with ovalbumin-induced asthma and suppress the secretion of inflammatory mediators (IL-4, IL-5, IL-13 and IL-17A) in BALF. Metagenomic results demonstrated that the protective effects of SLBZP were primarily associated with Ligilactobacillus, Eubacterium and Clostridium. Additionally, metabolomics results identified that three vital metabolic pathways were substantially regulated by SLBZP in asthmatic mice, especially D-glutamine and -glutamate metabolism. Furthermore, IHC and IF results showed that SLBZP significantly inhibited the expression of GLS1 and GOT1, which inhibited the conversion of L-glutamine to α-ketoglutarate and regulated the imbalance of Th1/Th2 and Treg/Th17. RT-qPCR results showed that SLBZP promoted the expressions of T-bet, IFN-γ, IL-10 and Foxp3 mRNA, and inhibited the expression of GATA3, IL-4, IL-5, IL-13, IL-17A and RORγt mRNA. The findings from flow cytometry provided additional evidence. Thus, this modulated the imbalance of Th1/Th2 and Treg/Th17 and exerted the immunomodulatory properties of SLBZP. SLBZP exerted protective effects against OVA-induced asthma and modified the structure and functional characteristics of the gut microbiota, and serum metabolite profiles in asthmatic mice. The anti-asthma mechanism of SLBZP may be associated with the modulation of the gut microbiota and Glutamine-GLS1 pathway.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Asthma/drug therapy/metabolism/pathology/microbiology
Mice
*Glutamine/metabolism
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Metabolomics
Disease Models, Animal
Mice, Inbred BALB C
Th17 Cells/immunology/drug effects
Powders
Cytokines/metabolism
Female
Lung/pathology/drug effects
Ovalbumin
Th2 Cells/immunology/drug effects
Multiomics

@article {pmid41634308,
year = {2026},
author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A},
title = {Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {7016},
pmid = {41634308},
issn = {2045-2322},
support = {192514//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Humans ; Africa ; Feces/microbiology ; Nanopores ; Switzerland ; Anti-Bacterial Agents/pharmacology ; Metagenome ; *Bacteria/genetics/classification/drug effects ; Nanopore Sequencing ; Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The gut microbiota and resistome may change upon exposure to environments with high prevalence of multidrug-resistant pathogens, potentially impacting health and contributing to the spread of antimicrobial resistance genes (ARGs). In this context, expatriates may acquire endemic microbial communities and ARGs while living abroad. In this work, we investigated the microbiota and resistome of Swiss expatriates living in African countries using Nanopore shotgun metagenomics (SMS).Stool samples from expatriates residing in African and European countries (n = 33 and n = 39, respectively) were sequenced using Nanopore V14 chemistry. Taxonomic and resistome profiling was performed with Kraken2 and ResFinder, respectively. Diversity metrics (e.g., Shannon, Simpson) assessed microbial composition. ARG and bacteria associations were determined using GTDB-Tk on metagenome-assembled genomes (MAGs). Plasmid-borne ARGs were characterized with PlasmidFinder.Our results indicated that microbiota composition did not differ between expatriates in African and European countries. However, resistome analysis revealed a higher prevalence of tetracycline (tet) and folate pathway antagonist (dfr, sul) ARGs in those residing in Africa, suggesting adaptation to the local microbial environment or antibiotic policy. Unique plasmid families were also identified in Gram-negative (IncF) and -positive (repUS43) bacteria across African and European cohorts, indicating the potential for ARG dissemination via mobile genetic elements. Overall, Nanopore-based SMS may provide an alternative approach to monitor microbiota and resistome dynamics, and thus assisting early epidemiological surveys.},
}

*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Humans
Africa
Feces/microbiology
Nanopores
Switzerland
Anti-Bacterial Agents/pharmacology
Metagenome
*Bacteria/genetics/classification/drug effects
Nanopore Sequencing
Plasmids/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid41704501,
year = {2026},
author = {Yoshioka, Y and Ando, C and Yamashita, H and Kawamitsu, M and Kawachi, M and Tsunematsu, Y and Shoguchi, E},
title = {A dataset for forty complete bacterial genome sequences in cultures of the toxic dinoflagellate Ostreopsis cf. ovata.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112499},
pmid = {41704501},
issn = {2352-3409},
abstract = {Increasing occurrences of toxic dinoflagellate blooms are a growing concern under climate change. The benthic dinoflagellate Ostreopsis blooms through mechanisms that remain poorly understood and is assumed to produce palytoxin-like compounds such as ovatoxins. Recent studies have highlighted the diversity of bacterial communities associated with Ostreopsis and suggested a possible role for these bacteria in toxin biosynthesis. However, genome information on potential bacterial toxin producers remains limited. Here, we report a dataset of bacterial metagenome-assembled genomes (MAGs) obtained from the culture of the toxic dinoflagellate Ostreopsis cf. ovata strain (NIES-3351). HiFi long reads from PacBio Revio system were assembled with hifiasm-meta. We identified forty complete bacterial MAGs, each with an estimated completeness of 93-100%. These MAGs span a wide range of genome sizes (1.5 Mb to 6.7 Mb) and GC contents (36% to 67%). The dataset is available at DDBJ/ENA/GenBank under accession number PRJDB37958.},
}

@article {pmid41703832,
year = {2026},
author = {Yao, X and Chen, X and Niu, J and Li, J and Li, W and Zhu, H and Li, X and Sun, B},
title = {Storage time drives divergent microbial functions and flavor metabolism in high-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118363},
doi = {10.1016/j.foodres.2026.118363},
pmid = {41703832},
issn = {1873-7145},
mesh = {*Food Storage/methods ; *Taste ; *Hot Temperature ; *Alcoholic Beverages/microbiology/analysis ; *Microbiota ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Metagenomics ; Metabolomics ; Time Factors ; Bacteria/metabolism/classification ; *Flavoring Agents/metabolism ; },
abstract = {Baijiu is a traditional Chinese distilled liquor, whose unique flavor highly relies on the synergistic metabolism of diverse microbial communities during the brewing process. The high-temperature Daqu (HTD) used in sauce-flavor Baijiu plays a crucial role in flavor synthesis due to its enrichment of heat-resistant functional microbiota. However, traditional techniques have limited understanding of microbial community succession and functional dynamics during Daqu storage, hindering precise quality and flavor regulation. This study systematically investigated the dynamic evolution of physicochemical indexes, microbial community structure, metabolic functions, and flavor compounds in HTD during different storage periods (1st, 3rd, and 6th months) through integrated metagenomics and GC-MS metabolomics. Results showed continuous decreases in moisture, starch, and pH during storage, while aminopeptide nitrogen and acidity peaked at the 3rd month. Esters reached their highest levels at the 1st month (YQ), alcohols peaked at the 3rd month (EQ), and aldehydes dominated at the 6th month (SQ). LEfSe analysis identified Kroppenstedtia eburnea and Paecilomyces variotii as biomarkers for YQ, Saccharopolyspora rectivirgula and Aspergillus chevalieri for EQ, and Rasamsonia emersonii for SQ. Metagenomic analysis revealed differential carbohydrate and amino acid metabolism pathways: YQ showed highest enzyme abundance for phenethyl alcohol metabolism, EQ exhibited peak enzymes for pyrazine synthesis and ethanol metabolism, while SQ demonstrated superior glucoamylase activity. In addition, maximum tetramethylpyrazine at the 3rd month and highest microbial diversity in later storage (6th month).},
}

*Food Storage/methods
*Taste
*Hot Temperature
*Alcoholic Beverages/microbiology/analysis
*Microbiota
*Food Microbiology
Gas Chromatography-Mass Spectrometry
Metagenomics
Metabolomics
Time Factors
Bacteria/metabolism/classification
*Flavoring Agents/metabolism

@article {pmid41651389,
year = {2026},
author = {Shi, B and Zhang, L and Jia, X and Tao, Y and Wang, M},
title = {Profiles of gut microbiome in Litopenaeus vannamei artificially infected with Vibrio parahaemolyticus causing translucent post-larva disease.},
journal = {Developmental and comparative immunology},
volume = {176},
number = {},
pages = {105565},
doi = {10.1016/j.dci.2026.105565},
pmid = {41651389},
issn = {1879-0089},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Vibrio parahaemolyticus/physiology ; *Penaeidae/microbiology/immunology ; *Vibrio Infections/immunology/microbiology ; Virulence ; Host-Pathogen Interactions ; },
abstract = {As the primary defense against pathogen invasion, the dynamic equilibrium of the shrimp gut microbiome is recognized as a critical factor influencing pathogen colonization. In recent years, translucent post-larva disease (TPD) outbreaks during the early stages of shrimp farming have become a serious threat to the sustainable development of the shrimp industry. Compared with other vibriosis, TPD caused by certain Vibrio strains possessing drug resistance and high-virulence genes exhibits greater virulence in shrimp tissues, with mortality rates reaching up to 90%. However, no studies have yet explored the association between this pathogen and the gut microbiome. This study employed metagenomic sequencing technology to analyze differences in the axial distribution of the gut microbiome in shrimp at varying degrees of TPD infection. Histopathological sections revealed that multiple tissue lesions induced by TPD infection in shrimp were primarily concentrated in the midgut. Alpha diversity analysis indicated that the alpha diversity index of the shrimp gut microbiome showed an upward trend as pathogen load increased. Beta diversity analysis revealed the intestinal segment with the most significant microbial community changes during pathogen colonization. Within this region, the abundance of probiotics decreased, while that of pathogenic bacteria increased. Functional prediction results indicate that under TPD stress, the gut microbiome activates a multi-layered, synergistic defense adaptation program through nutritional metabolism shifts, biofilm reinforcement, and toxin efflux. This study elucidates the pathogenic mechanism of TPD from the perspective of pathogen-gut microbiome interactions, suggesting that controlling pathogen load and restoring targeted probiotics may serve as effective strategies for preventing and controlling TPD.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Vibrio parahaemolyticus/physiology
*Penaeidae/microbiology/immunology
*Vibrio Infections/immunology/microbiology
Virulence
Host-Pathogen Interactions

@article {pmid41629580,
year = {2026},
author = {Khurajog, B and Saenkankam, I and Apiwatsiri, P and Supimon, N and Kamwa, R and Niyomtham, W and Yindee, J and Phupolphan, C and Hampson, DJ and Prapasarakul, N},
title = {Effectiveness of probiotic supplementation on growth performance, gut microbiota, and Salmonella reduction in broiler chicks challenged with Salmonella Typhimurium.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6983},
pmid = {41629580},
issn = {2045-2322},
support = {FOOD66310012//the 2022-Fundamental Fund, Thailand Science Research and Innovation (TSRI), Chulalongkorn University/ ; },
mesh = {Animals ; *Probiotics/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Chickens/microbiology/growth & development ; *Salmonella typhimurium ; *Salmonella Infections, Animal/microbiology/prevention & control ; *Poultry Diseases/microbiology/prevention & control ; Dietary Supplements ; Animal Feed ; Ligilactobacillus salivarius ; },
abstract = {Salmonella infection poses a major threat to poultry production, affecting both animal health and food safety. With rising concerns over antimicrobial resistance, probiotics have gained attention as effective non-antibiotic interventions to control enteric pathogens while supporting gut health. This study evaluated the efficacy of a locally isolated probiotic blend comprising Ligilactobacillus salivarius BF12, and Pediococcus acidilactici strains BF9 and BYF20 (ProCU) in comparison with a commercial Clostridium butyricum-based probiotic (TOP GUT) in broiler chicks challenged with Salmonella Typhimurium (ST). A total of 196 chicks were assigned to seven groups receiving different treatments with or without Salmonella challenge. Parameters assessed included growth performance, intestinal histomorphometry, cecal Salmonella load, and microbiota composition and function. Before challenge, ProCU increased fecal lactic acid bacteria (LAB) and enriched amino acid and carbohydrate metabolism pathways. Post-challenge, TOP GUT significantly reduced Salmonella load and maintained growth, while ProCU showed a limited effect on pathogen reduction. Both probiotics improved intestinal morphology, increased Lactobacillus and Akkermansia abundance, and upregulated oxidative stress defense genes. Notably, TOP GUT also enriched Parabacteroides and other Bacteroidetes members and prolonged microbial metabolic activity. These findings emphasize strain-specific probiotic effects and suggest that continuous supplementation, particularly with spore-forming strains, may enhance gut health and reduce the Salmonella burden in poultry.},
}

Animals
*Probiotics/administration & dosage/pharmacology
*Gastrointestinal Microbiome/drug effects
*Chickens/microbiology/growth & development
*Salmonella typhimurium
*Salmonella Infections, Animal/microbiology/prevention & control
*Poultry Diseases/microbiology/prevention & control
Dietary Supplements
Animal Feed
Ligilactobacillus salivarius

@article {pmid41577947,
year = {2026},
author = {Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Henry, AR and Davis, RL and Laboune, F and Longtine, ER and Godbole, S and Horigan, S and Ruhs, EC and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Heraud, JM and Dussart, P and Douek, DC and Brook, CE},
title = {Co-speciation and host-switching drives diversity of picornaviruses and sapoviruses in Malagasy fruit bats.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6583},
pmid = {41577947},
issn = {2045-2322},
support = {P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; OPP1211841//Bill and Melinda Gates Foundation/ ; D18AC00031//Defense Sciences Office, DARPA/ ; P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; },
abstract = {UNLABELLED: Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses that cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Picornaviridae and Caliciviridae (families within Picornavirales) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Prior work in Madagascar has described numerous bat viruses, some with zoonotic potential, that demonstrate both high identity to and extreme divergence from viruses found in sister bat species in Africa. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats (Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis), we identify and describe 13 full-length and 38 partial-length genomic sequences within the Picornaviridae and Caliciviridae families (36 picornavirus and 15 Sapovirus sequences). We find evidence that host-switching between Madagascar and mainland African bat picornaviruses and sapoviruses, followed by host-parasite co-speciation, likely shaped the diversification pattens of these novel sequences, with little evidence for cross-species transmission among Malagasy bat species in close contact.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34969-2.},
}

@article {pmid41575223,
year = {2026},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Hidden reservoir of highly adaptable multi-host plasmids that propagate antibiotic genes in healthy human populations.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag004},
pmid = {41575223},
issn = {1751-7370},
support = {//The National Key Research and Development Program of China/ ; Project32098//National Science and Technology Major Project/ ; },
mesh = {Humans ; *Plasmids/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome ; *Bacteria/genetics/drug effects/classification ; Healthy Volunteers ; Genome, Bacterial ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; },
abstract = {Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters that were detected in >30% of individuals. Among these, the plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a "plug-and-play" module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes such as cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples- validated by single-cell and long-read Nanopore sequencing. Screening of 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This pattern suggests potential repeated cross-species transmission events, equipping diverse pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat by fueling the emergence of multidrug-resistant pathogens.},
}

Humans
*Plasmids/genetics
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Anti-Bacterial Agents/pharmacology
Metagenome
*Bacteria/genetics/drug effects/classification
Healthy Volunteers
Genome, Bacterial
Gene Transfer, Horizontal
*Drug Resistance, Bacterial/genetics
Genes, Bacterial

@article {pmid41540059,
year = {2026},
author = {St John, E and Reysenbach, AL},
title = {Global deep-sea hydrothermal deposit metagenomes and metagenome-assembled genomes over time and space.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {283},
pmid = {41540059},
issn = {2052-4463},
support = {DEB-2409507//National Science Foundation/ ; },
mesh = {*Metagenome ; *Hydrothermal Vents/microbiology ; *Archaea/genetics ; Bacteria/genetics/classification ; Microbiota ; *Genome, Archaeal ; },
abstract = {Actively venting high temperature deep-sea hydrothermal vent deposits along tectonic spreading centers and in backarc basins harbor a rich diversity of thermophilic Bacteria and Archaea, many of which have no representatives in cultivation nor any genomic representation in databases. Here, in order to produce a global-scale time series metagenomic resource for studying the microbial functional and genomic diversity in these high temperature ecosystems, we obtained 70 metagenomes from collections across spatial and temporal gradients from 21 different vent fields spanning 16 years (1993-2009). The dataset (Deep-Sea Hydrothermal Vent dataset (DSV70)) includes 3.56 Tbp of raw DNA sequence reads, that have been assembled to produce 7,422 medium- to high-quality (based on CheckM2) metagenome-assembled genomes (MAGs) of Bacteria (6,063 MAGs) and Archaea (1,359 MAGs). Collectively, this DSV70 dataset and the published 40 metagenomes from more recent deep-sea collections (2004 to 2018), represent a valuable resource for exploring the functional and phylogenomic diversity of the deep-sea hydrothermal microbiomes, and provide many reference genomes for studies in the taxonomy and systematics of poorly studied microbial lineages. Further, with the interest in mining the mineral resources at deep-sea vents, the DSV70 provides a genomic legacy for monitoring impacts on the microbial communities in these systems.},
}

*Metagenome
*Hydrothermal Vents/microbiology
*Archaea/genetics
Bacteria/genetics/classification
Microbiota
*Genome, Archaeal

@article {pmid40908532,
year = {2026},
author = {Wei, M and Mehravar, S and Leite, G and Naji, P and Barlow, GM and Hosseini, A and Rashid, M and Sanchez, M and Fajardo, CM and Pimentel, M and Mathur, R},
title = {Relationship Between Hypothyroidism, Risk of Small Intestinal Bacterial Overgrowth, and Duodenal Microbiome Alterations.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {111},
number = {3},
pages = {707-720},
doi = {10.1210/clinem/dgaf495},
pmid = {40908532},
issn = {1945-7197},
mesh = {Humans ; *Hypothyroidism/microbiology/complications/epidemiology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Intestine, Small/microbiology ; *Duodenum/microbiology ; Incidence ; Case-Control Studies ; *Blind Loop Syndrome/epidemiology/microbiology/etiology ; Thyroiditis, Autoimmune/microbiology/complications/epidemiology ; Risk Factors ; RNA, Ribosomal, 16S/genetics ; Aged ; Prevalence ; Bacteria/growth & development ; },
abstract = {CONTEXT: There is an association between hypothyroidism and small intestinal bacterial overgrowth (SIBO), but the exact mechanistic link between these 2 conditions is not fully elucidated.

OBJECTIVE: We evaluate the incidence and risks of subsequently developing SIBO, and changes in small bowel microbial populations, in subjects with hypothyroidism or autoimmune thyroiditis.

DESIGN AND OUTCOME MEASURES: Duodenal aspirates from REIMAGINE study subjects with a history of hypothyroidism (hypothyroid group, N = 49) and controls (N = 323) underwent 16S rRNA sequencing (MiSeq, Illumina); a subset also underwent metagenomic sequencing (NovaSeq6000, Illumina). Separately, the TriNetX Analytics platform was used to evaluate 10-year cumulative incidences and relative risk (RR) of developing SIBO in subjects with hypothyroidism (unspecified etiology [HUE]), and a subset with autoimmune thyroiditis, vs propensity score matched control groups.

RESULTS: Among REIMAGINE subjects, SIBO prevalence was higher in the hypothyroid group (32.65%) vs controls (15.17%). In the TriNetX analysis, 10-year cumulative incidences of SIBO were higher in HUE (RR = 2.20) and autoimmune thyroiditis (RR = 2.40) subjects vs matched controls. However, these risks appeared to be mitigated both in HUE (RR = 0.33) and autoimmune thyroiditis (RR = 0.78) subjects taking levothyroxine. Analyzing the duodenal microbiome, genus Neisseria was part of the core microbiome in the hypothyroid group (Hypo+/SIBO-, Hypo+/SIBO+) but not in nonhypothyroid subjects (Hypo-/SIBO-, Hypo-/SIBO+). Increased prevalence of Gram-negative coliforms occurred in both SIBO+ groups, but Escherichia/Shigella formed part of the core in nonhypothyroid subjects (Hypo-/SIBO+), whereas Klebsiella species were prevalent in hypothyroid group subjects with SIBO (Hypo+/SIBO+).

CONCLUSION: These findings suggest there is an increased risk for development of SIBO in individuals with a history of hypothyroidism that may be ameliorated by treatment, and may involve specific Gram-negative coliforms.},
}

Humans
*Hypothyroidism/microbiology/complications/epidemiology
Male
Female
*Gastrointestinal Microbiome
Middle Aged
Adult
*Intestine, Small/microbiology
*Duodenum/microbiology
Incidence
Case-Control Studies
*Blind Loop Syndrome/epidemiology/microbiology/etiology
Thyroiditis, Autoimmune/microbiology/complications/epidemiology
Risk Factors
RNA, Ribosomal, 16S/genetics
Aged
Prevalence
Bacteria/growth & development

@article {pmid40810199,
year = {2026},
author = {Lin, YT and Sayols-Baixeras, S and Graells, T and Dekkers, KF and Baldanzi, G and Nguyen, D and Larsson, A and Feldreich, TR and Nielsen, N and Eklund, AC and Holm, JB and Nielsen, HB and Bergström, G and Smith, JG and Malinovschi, A and Engström, G and Orho-Melander, M and Fall, T and Ärnlöv, J},
title = {Identification of Gut Microbiome Signatures and Metabolites Associated With Albuminuria in Type 2 Diabetes.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {111},
number = {3},
pages = {e927-e936},
doi = {10.1210/clinem/dgaf453},
pmid = {40810199},
issn = {1945-7197},
support = {ERC- STG-2018-801965 (T.F.)/ERC_/European Research Council/International ; ERC-CoG-2014-649021/ERC_/European Research Council/International ; ERC-STG-2015-679242/ERC_/European Research Council/International ; VR 2019-01471//Swedish Research Council/ ; 2018-02784//Swedish Research Council/ ; 2018-02837//Swedish Research Council/ ; 2021-03291//Swedish Research Council/ ; EXODIAB 2009-1039//Swedish Research Council/ ; 2019-01015//Swedish Research Council/ ; 2020-00243//Swedish Research Council/ ; 2019-01236//Swedish Research Council/ ; 2021-02273//Swedish Research Council/ ; 20200711//Swedish Heart-Lung Foundation/ ; 20180343//Swedish Heart-Lung Foundation/ ; 20210357//Swedish Heart-Lung Foundation/ ; 20200173//Swedish Heart-Lung Foundation/ ; 20190526//Swedish Heart-Lung Foundation/ ; NNF20OC0063886//Novo Nordic Foundation/ ; DIA 2018-375//Swedish Diabetes Foundation/ ; //Swedish Foundation for Strategic Research/ ; //Center for Clinical Research, Region Dalarna Sweden/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 2/complications/microbiology/metabolism ; *Albuminuria/microbiology/metabolism/etiology ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; *Diabetic Nephropathies/microbiology/metabolism ; Sweden/epidemiology ; },
abstract = {CONTEXT: Type 2 diabetes is a growing global concern with serious complications, including kidney damage and cardiovascular morbidity and mortality. Monitoring albuminuria, which is associated with these complications, is crucial in optimal diabetes management. Gut microbiota composition has been suggested to impact albuminuria, but large studies with granular data are lacking.

METHODS: We investigated the relationship between 1002 gut microbial species, 1308 plasma metabolites, and albuminuria in 752 participants with type 2 diabetes from the Swedish CArdioPulmonary BioImage Study (SCAPIS). To determine the relative abundance of species, we employed deep shotgun metagenomic sequencing of fecal samples. Plasma metabolites were analyzed using mass spectrometry-based methods.

RESULTS: We identified 3 species that were associated with albuminuria, including Sellimonas intestinalis, Eggerthellales sp., and Ellagibacter isourolithinifaciens. Two of these species were replicated in an independent prediabetic population (n = 3423) in SCAPIS. In total, 36 annotated metabolites were associated with the 3 albuminuria-signature species. Functional mapping of the signature species suggests a role in the regulation of the metabolites of imidazole propionate and trigonelline, which have previously been reported to play roles in the progression of albuminuria.

CONCLUSION: These findings provide additional evidence of the potential impact of microbial species and contribute to our understanding of the complex relationship between the gut microbiome, plasma metabolites, and albuminuria in individuals with diabetes.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Diabetes Mellitus, Type 2/complications/microbiology/metabolism
*Albuminuria/microbiology/metabolism/etiology
Male
Female
Middle Aged
Aged
Feces/microbiology
*Diabetic Nephropathies/microbiology/metabolism
Sweden/epidemiology

@article {pmid41703795,
year = {2026},
author = {Pais, ACS and Ribeiro, TB and Coscueta, ER and Salsinha, AS and Pintado, MM and Silvestre, AJD and Santos, SAO},
title = {Phenolic compounds' impact on gut microbiota: Insights from in vitro batch fecal fermentation for composition modulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118167},
doi = {10.1016/j.foodres.2025.118167},
pmid = {41703795},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Feces/microbiology ; *Fermentation ; Fatty Acids, Volatile/metabolism/analysis ; *Phenols/pharmacology/metabolism ; Prebiotics ; Flavanones/pharmacology/metabolism ; Ellagic Acid/pharmacology/metabolism ; Bacteria/drug effects/genetics/metabolism ; Male ; Adult ; Female ; },
abstract = {The relationship between phenolic compounds and gut microbiota (has been widely studied to explore the health benefits of these bioactive dietary compounds. Phenolic compounds are metabolized by gut microbiota, while also modulating its composition. However, the individual effects of these compounds on human gut microbiota remain underexplored. To address this, three phenolic compouds-ellagic acid, naringenin, and phloroglucinol-underwent in vitro batch fermentation with fecal samples from healthy donors. Samples were analyzed through 16S metagenomics sequencing, and short-chain fatty acids (SCFAs) were measured using gas chromatography. Results showed that ellagic acid and phloroglucinol had prebiotic properties, producing SCFAs like acetic, propanoic, and butyric acids and promoting the growth of beneficial bacteria such as Lactobacillus and Bifidobacterium. In contrast, naringenin was linked to the growth of pathogenic genera like Escherichia and Salmonella. This study provides valuable insights into how specific phenolic compounds influence gut microbiota composition, contributing to potential pharmaceutical or nutraceutical developments.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Feces/microbiology
*Fermentation
Fatty Acids, Volatile/metabolism/analysis
*Phenols/pharmacology/metabolism
Prebiotics
Flavanones/pharmacology/metabolism
Ellagic Acid/pharmacology/metabolism
Bacteria/drug effects/genetics/metabolism
Male
Adult
Female

@article {pmid41702408,
year = {2026},
author = {Hernández-Vázquez, A and Garcia-Arellano, H and González-Cervantes, RM and López-Pérez, M and Soto, LMH and Meza, JAC and Aguirre-Garrido, JF},
title = {Study of Microbial Communities in the Soda Lake of Isabel Island: Identification of Polyhydroxybutyrate (PHB) Degrading Enzymes.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70279},
doi = {10.1111/1758-2229.70279},
pmid = {41702408},
issn = {1758-2229},
mesh = {*Lakes/microbiology ; Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation & purification/metabolism ; *Hydroxybutyrates/metabolism ; Mexico ; Metagenome ; Bacterial Proteins/genetics/metabolism ; *Polyesters/metabolism ; *Microbiota ; Geologic Sediments/microbiology ; *Carboxylic Ester Hydrolases/genetics/metabolism ; Polyhydroxybutyrates ; },
abstract = {Crater Lake (Isabel Island, Mexico) is a meromictic, stratified, haloalkaline system. To identify and characterise PHB depolymerases across the vertical physicochemical gradients of the lake, we analysed seven metagenomes from the water column (0-23 m), one sediment metagenome, and the genomes of two organisms (HB105m and VN105m) isolated from 5 m. Taxonomic profiles revealed vertical stratification: Actinobacteriota and Cyanobacteriota dominated surface waters, while Pseudomonadota, Bacillota, and Bacteroidota prevailed in deeper layers and sediments. Alpha-diversity indices peaked at 5 and 20 m and declined at 23 m. We identified 16 putative PHB depolymerases spanning a broader phylogenetic range than previously documented for haloalkaline ecosystems. These included homologues affiliated with Vreelandella, Thiomicrorhabdus, Chloroflexota, Candidatus Cloacimonadota, and Desulfobacterales. The structural variation observed in lipase-box motifs and signal peptides suggests functional differentiation linked to redox and oxygen gradients across depths. Phylogenetic analysis of predicted and reference enzymes showed depth-specific clustering, with extracellular depolymerases predominant in oxic layers and intracellular forms more common in microoxic-anoxic zones. Overall, our results expand the known diversity of PHB-degrading lineages in extreme environments and highlight several candidate enzymes with potential biotechnological relevance for future experimental characterisation.},
}

*Lakes/microbiology
Phylogeny
*Bacteria/genetics/classification/enzymology/isolation & purification/metabolism
*Hydroxybutyrates/metabolism
Mexico
Metagenome
Bacterial Proteins/genetics/metabolism
*Polyesters/metabolism
*Microbiota
Geologic Sediments/microbiology
*Carboxylic Ester Hydrolases/genetics/metabolism
Polyhydroxybutyrates

@article {pmid41700136,
year = {2026},
author = {Hubot, N and Giering, SLC and Orel, N and Klun, K and Herndl, GJ and Hohaus, F and Lucas, CH and Tinta, T},
title = {Jellyfish mucus-derived organic matter as a source of labile nutrients for the ambient microbial community.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20784},
pmid = {41700136},
issn = {2167-8359},
mesh = {*Scyphozoa/chemistry/metabolism ; Animals ; *Microbiota ; *Mucus/chemistry/metabolism ; Seawater/microbiology/chemistry ; Nitrogen/metabolism/analysis ; *Nutrients/metabolism ; Ecosystem ; Amino Acids/metabolism ; },
abstract = {Jellyfish are increasingly recognized as a significant contributor to marine organic matter (OM) on a global scale, with implications for ecosystem dynamics. While the role of jellyfish detritus in microbial nutrient cycling has been explored, the contribution of OM released by live jellyfish-primarily as mucus (hereinafter referred to as mucus-associated OM, or MAOM)-remains understudied. This study investigates the release of organic and inorganic nutrients through MAOM from live jellyfish and their effects on ambient microbial communities in the northern Adriatic Sea using a series of leaching and short-term microcosm experiments. Our results show that per gram of MAOM dry weight from the jellyfish Aurelia spp, approximatively 2 µmol of phosphate, 4 µmol of dissolved inorganic nitrogen, 18 µmol dissolved organic nitrogen, 134 µmol of dissolved organic carbon and 15 µmol of dissolved free amino acids can be released in the ambient seawater in 24 h. Almost half of the OM is released as dissolved OM (DOM), of which a substantial part is low molecular weight (<1 kDa) molecules. During the first 20 h, the DOM fraction of MAOM was rapidly consumed by the ambient microbial community without a corresponding increase in biomass, likely due to nitrogen limitation. In the subsequent 22 h, microbial growth accelerated to 0.19 ± 0.03 h[-1] until phosphate became limiting, leading to a sharp decline in microbial production. Our metagenomics analysis revealed that the MAOM-degrading microbial community, dominated by Gammaproteobacteria opportunistic copiotrophs, exhibited increased functional capacity for nutrient assimilation and OM degradation, particularly in the transport and metabolism of amino acids (particularly glycine and taurine) and phosphorus. These traits mirror those found in detritus-degrading microbial communities, suggesting that jellyfish blooms promote the emergence of specialized microbial consortia with shared metabolic capabilities. Taken together, our findings highlight that live jellyfish, through the release of OM, play an active and previously underappreciated role in shaping ambient microbial community dynamics and nutrient fluxes in marine systems affected by jellyfish blooms.},
}

*Scyphozoa/chemistry/metabolism
Animals
*Microbiota
*Mucus/chemistry/metabolism
Seawater/microbiology/chemistry
Nitrogen/metabolism/analysis
*Nutrients/metabolism
Ecosystem
Amino Acids/metabolism

@article {pmid41697419,
year = {2026},
author = {Ni, W and Huang, H and Wang, X and Yu, A and Ren, J and Li, H},
title = {Metagenomic Analysis Reveals Alterations in the Gut Microbiome of Preterm Infants with Extrauterine Growth Restriction.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {177},
pmid = {41697419},
issn = {1432-0991},
support = {No. 82101811//National Natural Science Foundation of China/ ; No. RCJC20231211085923029//Shenzhen Science and Technology Program/ ; No. SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; Guangdong High-level Hospital Construction Fund//Guangdong High-level Hospital Construction Fund/ ; Clinical key specialty construction project of Guangdong Province//Clinical key specialty construction project of Guangdong Province/ ; No. 20232011//Project of Guangdong Provincial Administration of Traditional Chinese Medicine/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature/growth & development ; Infant, Newborn ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; Female ; Feces/microbiology ; Male ; },
abstract = {Extrauterine growth restriction (EUGR) is a pervasive clinical issue in preterm infants, affecting neonatal development and their long-term health. This study aimed to characterize the gut microbiome and its derived genes in preterm neonates with EUGR using metagenomic sequencing. Sixty-two preterm infants hospitalized in the neonatal intensive care unit at Guangdong Women and Children Hospital were enrolled in this study. Participants were divided into two groups: the EUGR group (n = 34) and the normal growth group (AGA, n = 28). Fecal samples were collected at one month postnatally. Total bacterial DNA was extracted and sequenced using the Illumina HiSeq X Ten system. Significant differences in the gut microbial community between the EUGR and AGA groups were observed, as evidenced by the Bray-Curtis dissimilarity index. The EUGR group exhibited a notable increase in Klebsiella pneumoniae and Enterococcus faecalis, along with a significant decrease in Streptococcus raffinosi, Rothia mucilaginosa, Parabacteroides merdae and Eggerthella lenta compared to the AGA group. Functional annotation of metagenomic genes identified 415 genes with significantly different relative abundances between the groups. A classification model incorporating five discriminatory genes achieved effective separation of EUGR from AGA infants. Additionally, the EUGR group exhibited a higher relative abundance of antibiotic resistance genes. This study elucidates the alterations in the gut microbiome and its derived genes in preterm neonates with EUGR. These findings provide new insights into the potential microbial signatures associated with impaired growth, although further mechanistic studies are needed to clarify causal relationships.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Infant, Premature/growth & development
Infant, Newborn
Metagenomics
*Bacteria/genetics/classification/isolation & purification
Female
Feces/microbiology
Male

@article {pmid41638014,
year = {2026},
author = {Song, Y and Song, X and Liu, X and Jiang, L and Chai, L},
title = {Metagenomics and targeted metabolomics uncover concomitant gut microbiota dysbiosis and bile acid metabolism alteration in norfloxacin-exposed Bufo gargarizans tadpoles.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {292},
number = {},
pages = {107742},
doi = {10.1016/j.aquatox.2026.107742},
pmid = {41638014},
issn = {1879-1514},
mesh = {Animals ; Larva/drug effects/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; Metagenomics ; *Norfloxacin/toxicity ; *Bile Acids and Salts/metabolism ; *Anti-Bacterial Agents/toxicity ; Metabolomics ; *Dysbiosis/chemically induced/veterinary ; *Bufonidae/microbiology ; },
abstract = {Norfloxacin (NOR) is a fluoroquinolone antibiotic widely detected in aquatic environments, yet little is known about its toxic effects on amphibians. Bile acids (BAs) are crucial metabolites derived from gut microbiota-host co-metabolism and play vital roles in maintaining host health. BA composition is regulated by the gut microbiota through specific enzymes: bile salt hydrolases (BSHs) deconjugate primary BAs; bile acid-inducible enzymes (BAIs) and hydroxysteroid dehydrogenases (HSDHs) then convert them into secondary BAs. This study investigated the effects of NOR on Bufo gargarizans tadpoles using a combination of intestinal-targeted BA metabolomics, metagenomics, and histopathological analysis. Tadpoles were exposed to 10 and 100 μg/L NOR from Gs26 to Gs36, with 4 independent biological replicates per group. Our results showed that NOR exposure significantly increased the relative abundance of gut microbiota encoding BAIs, HSDHs, and/or BSHs, which was accompanied by a decrease in the ratios of primary/secondary BAs and conjugated/deconjugated BAs. Meanwhile, NOR treatment elevated antibiotic resistance gene abundance and induced intestinal histopathological alterations in tadpoles, characterized by reduced epithelial cell height and hypertrophy of smooth muscle cells (SMCs). In summary, environmentally relevant concentrations (10 and 100 μg/L) of NOR affected the intestinal microbiota, thereby disrupting BAs biotrasformation, ultimately potentially compromising intestinal health in tadpoles. This highlighted the potential ecological risks posed by NOR pollution in aquatic ecosystems.},
}

Animals
Larva/drug effects/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
*Water Pollutants, Chemical/toxicity
Metagenomics
*Norfloxacin/toxicity
*Bile Acids and Salts/metabolism
*Anti-Bacterial Agents/toxicity
Metabolomics
*Dysbiosis/chemically induced/veterinary
*Bufonidae/microbiology

@article {pmid41576942,
year = {2026},
author = {Masi, D and Watanabe, M and Clément, K},
title = {Gut microbiome and obesity care: Bridging dietary, surgical, and pharmacological interventions.},
journal = {Cell reports. Medicine},
volume = {7},
number = {2},
pages = {102573},
doi = {10.1016/j.xcrm.2025.102573},
pmid = {41576942},
issn = {2666-3791},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/therapy/diet therapy ; Animals ; *Diet ; Mice ; },
abstract = {In the mid-2000s, mouse studies suggested that the gut microbiome might influence energy harvest, fat storage, appetite, insulin sensitivity, and inflammation. Since then, our understanding of the gut microbiome's role in obesity has advanced significantly. Mechanistic studies identified microbial metabolites, such as short-chain fatty acids, bile acids, branched-chain amino acids, tryptophan catabolites, and imidazole propionate, as key modulators of metabolism, inflammation, and gut-brain communication. Metagenomic and multi-omics technologies now provide deeper insights into the intricate interactions between microbes, metabolites, and host factors, reshaping obesity research and reinforcing the need for phenotype stratification by recognizing microbiome-driven metabolic profiles. Integrating gut microbiome data into clinical strategies may enable targeted interventions for specific obesity subtypes, advancing prevention and personalized care. However, as new anti-obesity medications emerge, it is imperative to determine how microbiome-based therapies can complement them, considering efficacy, cost, and patient-specific variability.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Obesity/microbiology/therapy/diet therapy
Animals
*Diet
Mice

@article {pmid41535683,
year = {2026},
author = {Chen, S and Yuan, Y and Wang, Y and Peng, Y and Tun, HM and Jiang, Z and Miao, Y and Lee, S and Yin, X and Shen, X and DeLeon, O and Chang, EB and Chan, FKL and Sun, Y and Ng, SC and Su, Q},
title = {Identification of antimicrobial peptides from ancient gut microbiomes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {1788},
pmid = {41535683},
issn = {2041-1723},
support = {2025 Youth Science and Technology Talent Development Program//China Association for Science and Technology (China Association for Science & Technology)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Antimicrobial Peptides/pharmacology/isolation & purification/chemistry ; Feces/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Metagenomics/methods ; Mice ; Bacteria/drug effects ; },
abstract = {Fecal coprolites preserve ancient microbiomes and are a potential source of extinct but highly efficacious antimicrobial peptides (AMPs). Here, we develop AMPLiT (AMP Lightweight Identification Tool), an efficient tool deployable to portable hardware for AMP screening in metagenomic datasets. AMPLiT demonstrates AUPRC performances of 0.9486 ± 0.0003 and reasonable overall training time of 3200 ± 53 s. By computationally utilizing AMPLiT, we analyze seven ancient human coprolite metagenomes, identifying 160 AMP candidates. Of 40 representative peptides synthesized, 36 (90%) peptides demonstrate measurable antimicrobial activity at 100 μM or less in vitro. Strikingly, approximately two-thirds of these peptides are sourced from Segatella copri, a dominant ancient gut commensal that is conspicuously underrepresented in modern populations, particularly those with Westernized lifestyles. Representative S. copri-derived AMPs exhibit disruptions against membranes of pathogenic bacteria, coupled with low cytotoxicity and hemolytic risk. In vivo, lead peptides demonstrate potent antibacterial and wound-healing efficacy comparable to traditional antibiotics, especially in combating gram-positive pathogens. Our findings highlight the ancient gut microbiomes as sources of novel AMPs, offering valuable insights into the historical role of S. copri in human health and its decline in contemporary populations.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Antimicrobial Peptides/pharmacology/isolation & purification/chemistry
Feces/microbiology
Animals
Anti-Bacterial Agents/pharmacology
Metagenome
Metagenomics/methods
Mice
Bacteria/drug effects

@article {pmid41507798,
year = {2026},
author = {Zhao, J and Cai, W and Zhang, X and Fang, H and Zhuge, J and Zhang, L and Wang, J and Sun, L and Hua, Z and Fu, J},
title = {Exploring lung microbiota and clinical application of BALF-mNGS in patients with pulmonary mycobacterial diseases: a multicenter retrospective study.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {130},
pmid = {41507798},
issn = {1471-2180},
support = {2020ZZ002,2021ZZ003//Project of Zhejiang Administration of Traditional Chinese Medicine/ ; LZ22H150001//Natural Science Foundation of Zhejiang Province/ ; 82072161//National Natural Science Foundation of China/ ; 2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; },
mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Lung/microbiology ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Nontuberculous Mycobacteria/genetics/isolation & purification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Adult ; },
abstract = {BACKGROUND: Pulmonary mycobacterial diseases (PMDs) remain a leading cause of infectious disease-related mortality worldwide, with the majority of cases attributed to the Mycobacterium tuberculosis complex (MTBC). However, non-tuberculous mycobacteria (NTM) can also cause PMDs, and the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has been increasing in recent years.

OBJECTIVES: This study aimed to explore the lung microbiota and assess the clinical application of bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) in patients with PMDs caused by MTBC or NTM.

METHODS: This multicenter, retrospective study included patients with suspected PMDs between July 2021 to June 2025. mNGS and conventional diagnostic methods (CDTs), including GeneXpert, BALF culture, acid-fast bacillus (AFB) staining, and T-SPOT, were performed. Based on the microbiological diagnosis, patients were classified into TB and NTM-PD groups. We further analyzed the clinical impact of different MTBC/NTM abundance levels. The relative abundance of MTBC/NTM was represented by reads ten per million (RTPM). Patient clinical characteristics, length of hospital stay (LOHS), laboratory results, and treatment effectiveness were collected from the electronic medical record system.

RESULTS: Compared with the TB group, patients with NTM-PD exhibited a higher prevalence of immunosuppression (34.96% vs. 53.85%, P = 0.013), particularly prolonged corticosteroid or immunosuppressant therapy (8.94% vs. 21.54%, P = 0.016). In the TB group, higher MTBC abundance was associated with increased positivity of CDTs and alterations in pulmonary microbiota, including enrichment of Candida albicans and other opportunistic pathogens. In the NTM-PD group, although CDTs positivity did not significantly differ between high- and low-abundance subgroups (21.21% vs. 20.00%, P = 0.906), higher NTM abundance was linked to distinct microbial community patterns and a markedly higher ineffective treatment rate (66.67% vs. 39.39%, P = 0.043). Notably, in both TB and NTM-PD groups, elevated MTBC or NTM abundance was associated with longer hospital stays and lower treatment effectiveness, indicating that pathogen abundance is significantly associated with clinical outcomes in pulmonary mycobacterial diseases.

CONCLUSION: BALF-mNGS not only provides superior pathogen detection in patients with PMDs but also shows that lower MTBC/NTM abundance is associated with better clinical prognosis, including shorter hospital stay and better treatment effectiveness, highlighting its potential role as a prognostic indicator.},
}

Humans
Retrospective Studies
Male
Female
Middle Aged
*Bronchoalveolar Lavage Fluid/microbiology
Aged
*Lung/microbiology
*Mycobacterium Infections, Nontuberculous/microbiology/diagnosis
Nontuberculous Mycobacteria/genetics/isolation & purification
*Microbiota/genetics
High-Throughput Nucleotide Sequencing
Adult

@article {pmid41696869,
year = {2026},
author = {Ju, Y and Lin, S and Hu, S and Jin, X and Xiao, L and Zhang, T and Zhang, Y and Zhang, L and Ma, X and Zhu, F and Guo, R},
title = {GutMIND: A multi-cohort machine learning framework for integrative characteristics of the microbiota-gut-brain axis in neuropsychiatric disorders.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2630563},
doi = {10.1080/19490976.2026.2630563},
pmid = {41696869},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Machine Learning ; *Mental Disorders/microbiology ; *Brain ; Cohort Studies ; Bacteria/classification/genetics/isolation & purification ; Male ; Metagenomics ; Female ; *Brain-Gut Axis ; Biomarkers ; },
abstract = {Emerging evidence underscores bidirectional communication along the microbiota-gut-brain axis in neuropsychiatric disorders. However, the field lacks dedicated metagenomic resources with standardized phenotyping for these conditions. Existing single-cohort studies face inherent limitations due to restricted sample sizes, confounding heterogeneity, and methodological fragmentation, compromising reproducibility and mechanistic insights. To overcome these challenges, we constructed the Gut Microbiome in Multinational Integrated Neuropsychiatric Disorders (GutMIND) database, a comprehensive resource integrating shotgun metagenomic data with harmonized metadata. Adhering to a standardized preprocessing protocol and rigorous quality control workflow, this dataset represents the largest gut-brain microbiome repository to date, encompassing 31 studies across 12 countries (n = 3,492) spanning 14 neuropsychiatric conditions. Utilizing this dataset, we characterized microbial community heterogeneity, which was significantly elevated in patients compared to healthy controls. Subsequently, we developed a computational framework, MetaClassifier, enabling the diagnosis of neuropsychiatric disorders and the identification of microbial biomarkers. Employing a comprehensive two-stage validation strategy, we first assessed the model utilizing taxonomic abundance profiles via nested cross-validation in the high-quality discovery cohort (n = 2,734), achieving a mean AUROC of 0.69 (range: 0.55-0.78) across 8 disorders. Its robustness was further confirmed in an independent platform-extended validation cohort (n = 400), yielding a mean AUROC of 0.71 (range: 0.60-0.76). We also developed the Microbial Gut-Brain Axis Health Index (MGBA-HI), which effectively distinguished neuropsychiatric status in both the high-quality cohort and the platform-extended cohort. Furthermore, integrative analysis of health-abundant species, index-derived biomarkers, and ecological prevalence, we identified 9 core neuropsychiatric-protective microbiota. These species predominantly exhibited metabolic capacities linked to glutamate synthesis and acetate production. Building upon this, the GutMIND framework ensures robust cross-cohort comparability while minimizing technical heterogeneity, thereby enhancing inferential rigor in gut microbiome-neuropsychiatry research. Notably, the MetaClassifier, MGBA-HI, and core microbiota hold translational potential for developing microbiome-based prognostic tools and personalized therapeutic strategies in neuropsychiatric disorders. The source code and usage instructions for MetaClassifier are accessible at https://github.com/juyanmei/MetaClassifier.},
}

Humans
*Gastrointestinal Microbiome
*Machine Learning
*Mental Disorders/microbiology
*Brain
Cohort Studies
Bacteria/classification/genetics/isolation & purification
Male
Metagenomics
Female
*Brain-Gut Axis
Biomarkers

@article {pmid41696361,
year = {2026},
author = {Yin, L and Xu, L and Shan, YN and He, Z and Li, Y and Chen, W},
title = {Microbiota-driven therapeutic efficacy of Hyperoside in ulcerative colitis and associated anxiety.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1734356},
pmid = {41696361},
issn = {2235-2988},
mesh = {Animals ; *Colitis, Ulcerative/drug therapy/microbiology/complications ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Anxiety/drug therapy ; Disease Models, Animal ; *Quercetin/analogs & derivatives/pharmacology/therapeutic use ; Male ; Cytokines/metabolism ; Colon/pathology/drug effects ; Mice, Inbred C57BL ; Molecular Docking Simulation ; Signal Transduction/drug effects ; Metabolomics ; Brain-Derived Neurotrophic Factor/metabolism ; Anti-Inflammatory Agents/pharmacology ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is subtype of inflammatory bowel disease that is frequently comorbid with anxiety disorders. However, effective dual-targeting therapies are still lacking. Hyperoside (HYP), a natural flavonoid, exhibits anti-inflammatory and neuroprotective properties, yet its potential therapeutic effects on UC and associated anxiety, as well as the underlying mechanisms, remain largely unexplored.

METHODS: A murine model of DSS-induced colitis was established and treated with HYP. Disease activity was assessed through body weight, colon length, and histopathology. Anxiety-like behaviors were evaluated using open field and elevated plus maze tests. Neuroinflammation was examined through immunohistochemistry of BDNF expression and microglial activation. Gut microbiota composition was profiled by metagenomic sequencing, and metabolomic profiling was conducted using the Q300 Kit. Network pharmacology and molecular docking were employed to predict signaling pathways, which were further validated by Western blotting. Additionally, antibiotic depletion experiments were conducted to determine microbiota dependency.

RESULTS: HYP administration significantly ameliorated DSS-induced colitis, as evidenced by attenuated weight loss, restored colon length, and improved histopathology. It suppressed pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) and restored intestinal barrier integrity by upregulating Mucin-2 and ZO-1. Furthermore, HYP also alleviated anxiety-like behaviors and mitigated neuroinflammation by increasing BDNF levels and suppressing microglial activation. HYP treatment also restored gut microbial homeostasis, enriching beneficial bacteria such as Enterobacter ludwigii while reducing the abundance of Enterobacter hormaechei, Escherichia coli, and Acinetobacter baumannii. Metabolomic analysis revealed that HYP significantly promoted arginine biosynthesis. Network pharmacology and molecular docking identified the MAPK, PI3K-Akt, and NF-κB pathways as potential targets, with HYP showing strong binding affinity to MAPK3, AKT1, and NFκB1. Importantly, the therapeutic effects of HYP were abolished in microbiota-depleted mice.

CONCLUSION: Our findings demonstrate that HYP effectively alleviates DSS-induced colitis and comorbid anxiety-like behaviors. Its efficacy is dependent on the gut microbiota and is associated with the restoration of microbial homeostasis, enhancement of arginine metabolism, and modulation of the MAPK/PI3K-Akt/NF-κB signaling pathways. HYP represents a promising microbiota-targeting therapeutic candidate for UC and its neuropsychiatric comorbidities.},
}

Animals
*Colitis, Ulcerative/drug therapy/microbiology/complications
Mice
*Gastrointestinal Microbiome/drug effects
*Anxiety/drug therapy
Disease Models, Animal
*Quercetin/analogs & derivatives/pharmacology/therapeutic use
Male
Cytokines/metabolism
Colon/pathology/drug effects
Mice, Inbred C57BL
Molecular Docking Simulation
Signal Transduction/drug effects
Metabolomics
Brain-Derived Neurotrophic Factor/metabolism
Anti-Inflammatory Agents/pharmacology