@article {pmid42617567,
year = {2026},
author = {Zhou, Q and Xu, X and Mi, K and Huo, M and Kou, Z and Li, G and Huang, L},
title = {Investigating AHL-associated quorum sensing impact on antibiotic-driven resistome expansion in anaerobic fermentation microbiomes: Metagenomic insights.},
journal = {Journal of environmental management},
volume = {416},
number = {},
pages = {130711},
doi = {10.1016/j.jenvman.2026.130711},
pmid = {42617567},
issn = {1095-8630},
mesh = {*Quorum Sensing ; *Anti-Bacterial Agents/pharmacology ; Fermentation ; *Microbiota/drug effects ; Anaerobiosis ; *Acyl-Butyrolactones/pharmacology ; Metagenomics ; Metagenome ; },
abstract = {Previous studies have demonstrated that quorum sensing (QS) can mitigate the impact of antibiotics on environmental microbial communities. Metagenomic analysis was used to examine AHL effects on the resistome in anaerobic fermentation microbiomes under antibiotic stress in this research. AHLs reduced ARGs, MGEs, and phage abundance compared to antibiotic-only samples following the addition of high concentrations (500 nmol/L) of AHLs. Phages and integrons played pivotal roles in shaping the resistome. Escherichia coli, Vibrio cholerae, and Pseudomonas aeruginosa were key targets affected by AHLs. Both the assembled environmental metagenomes and the complete genomes of isolated bacteria consistently support the broad potential of quorum-sensing systems in mediating the dissemination or regulation of resistome spreading. Quorum sensing systems are very likely to affect microbial community resistomes by regulating the phageome. These insights are valuable for refining fermentation and waste management processes, offering potential in environmental restoration and possibly curbing the spread of resistance genes.},
}

*Quorum Sensing
*Anti-Bacterial Agents/pharmacology
Fermentation
*Microbiota/drug effects
Anaerobiosis
*Acyl-Butyrolactones/pharmacology
Metagenomics
Metagenome

@article {pmid42695976,
year = {2026},
author = {de Kreek, F and Hertzberger, R and van Eeden, F and Illidge, S and Teunis, EJ and Hanemaaijer, M and Lievens, E and Rienstra, F and Wiedhaup, DE and Lisotto, P and Butler, D and Molenaar, D and Kort, R},
title = {Intra-individual genetic diversity of vaginal Lactobacillus crispatus revealed through citizen science-driven isolation and pangenome analysis.},
journal = {Journal of applied microbiology},
volume = {137},
number = {9},
pages = {},
doi = {10.1093/jambio/lxag218},
pmid = {42695976},
issn = {1365-2672},
support = {404270598028//Netherlands Organisation for Health Research and Development/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology ; *Lactobacillus crispatus/genetics/isolation & purification/classification ; *Genetic Variation ; Citizen Science ; Microbiota ; Metagenome ; Adult ; Probiotics ; },
abstract = {AIMS: A vaginal microbiome dominated by Lactobacillus crispatus is associated with positive reproductive and sexual health outcomes, yet intra-individual genetic diversity within this species remains largely unexplored. This study characterized inter- and intra-individual genomic variation in L. crispatus strains isolated through a citizen science initiative and assessed implications for multi-strain probiotic development.

METHODS AND RESULTS: Fifty-three women participated in this citizen science project. Self-sampling resulted in 48 shotgun metagenomes. Twenty-two participants isolated their own L. crispatus strains using selective enrichment and LAMP-based species confirmation, resulting in 53 whole-genome-sequenced isolates. Lactobacillus crispatus dominated 20 of 48 metagenomes (50.1%-99.6% relative abundance). Pangenome analysis revealed 3456 gene families, of which 43.7% were core and 56.3% accessory. A 14-kb plasmid harbouring a Fic-domain toxin-antitoxin protein, but devoid of antimicrobial resistance genes, was present in 44 of 53 strains. Strains from the same individual clustered closely together yet harboured 1-123 gene differences. Intra-individual variation was observed in the pullulanase type I gene required for glycogen degradation: 40 strains were predicted to grow on glycogen, six showed genetic disruptions with unknown consequences, and seven were predicted to lack this ability entirely. Variation within individuals was also found for bacteriocin classes and CRISPR-Cas genes.

CONCLUSIONS: Substantial functional diversity exists within L. crispatus, even among strains from the same individual, supporting the rationale for multi-strain vaginal probiotics. This citizen science approach enabled discovery of host-specific adaptations while ensuring participant ownership of their strains.},
}

Female
Humans
*Vagina/microbiology
*Lactobacillus crispatus/genetics/isolation & purification/classification
*Genetic Variation
Citizen Science
Microbiota
Metagenome
Adult
Probiotics

@article {pmid42747315,
year = {2026},
author = {Sun, W and Li, Y and Liu, X and Yu, S and Li, W and Wang, H and Geng, H and Li, L and Hu, J and Huo, J and Zhang, W and Fu, J and Jin, X and Li, H and Zhou, X and Zhu, X},
title = {Gut microbiota functional remodeling and butyrate depletion amplify anti-Ro/La antibody-driven type I interferon activation in neonatal lupus.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2728464},
doi = {10.1080/19490976.2026.2728464},
pmid = {42747315},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Interferon Type I/immunology ; Infant, Newborn ; *Autoantibodies/immunology/blood ; *Lupus Erythematosus, Systemic/immunology/microbiology ; *Butyrates/metabolism ; Female ; Bacteria/classification/genetics/isolation & purification/metabolism ; Male ; },
abstract = {The early-life gut microbiome may influence susceptibility to antibody-mediated neonatal autoimmunity, but the underlying mechanisms remain poorly understood. We investigated whether gut microbial functional capacity and metabolites influence autoantibody-dependent immune activation in 90 neonates, including healthy controls, anti-Ro/La-exposed neonates without neonatal lupus erythematosus (No-NLE), and neonates with NLE (n = 30 per group). Shotgun metagenomic profiling demonstrated progressive remodeling of the neonatal gut microbiome across the three groups, with anti-Ro/La exposure associated with depletion of early-life commensal-associated taxa, including Bifidobacterium, Rothia, and Clostridium, and enrichment of taxa with opportunistic potential, including Klebsiella and Enterococcus, with greatest ecological divergence in neonates with NLE. Functional profiling identified altered microbial carbohydrate-processing capacity, marked by enrichment of glycosyltransferase family 4 (GT4) and depletion of GT2 in NLE. These alterations coincided with broad reductions in plasma short-chain fatty acid metabolites, most prominently butyrate, together with increased serum immunoglobulin G (IgG) and interferon-α (IFN-α) and decreased complement component 4 (C4). A GT4-Klebsiella-Rothia-IFN-α signature distinguished NLE from No-NLE (AUC = 0.883; 95% CI, 0.799-0.967). In functional assays, pooled bacteria-depleted fecal filtrates from neonates with NLE potentiated IFN-α production by neonatal peripheral blood mononuclear cells in the presence of anti-Ro/La-positive plasma. Conversely, sodium butyrate suppressed anti-Ro/La-associated IFN-α production and reduced 28 inflammation-related proteins, including CXCL10, ADA, and PD-L1, involved in cytokine, IL-17, and TNF signaling. Together, these findings provide functional evidence supporting a microbiota-associated butyrate-type I interferon pathway that may amplify maternal autoantibody-dependent immune activation and contribute to the clinical manifestation of NLE.},
}

Humans
*Gastrointestinal Microbiome
*Interferon Type I/immunology
Infant, Newborn
*Autoantibodies/immunology/blood
*Lupus Erythematosus, Systemic/immunology/microbiology
*Butyrates/metabolism
Female
Bacteria/classification/genetics/isolation & purification/metabolism
Male

@article {pmid42747640,
year = {2026},
author = {Redding, LE and Hu, W and Daniel, S and Okumura, M and Hiehle, ME and David, MZ and Hunter, L and Cole, SD},
title = {Antimicrobial-resistant organism carriage and metagenomic characterization of the microbiome and resistome in veterinary workers.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42747640},
issn = {1573-7446},
support = {NI25AHDRXXXXG042 Formula Funds//U.S. Department of Agriculture/ ; },
mesh = {Humans ; *Microbiota ; *Drug Resistance, Bacterial ; Hospitals, Animal ; Methicillin-Resistant Staphylococcus aureus/isolation & purification/drug effects/genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; Male ; Escherichia coli/drug effects/isolation & purification/genetics ; Female ; *Animal Technicians ; *Carrier State/microbiology/epidemiology ; *Veterinarians ; Feces/microbiology ; Metagenome ; RNA, Ribosomal, 16S ; Adult ; },
abstract = {BACKGROUND: Veterinary personnel work in environments with high exposure to antimicrobials and antimicrobial-resistant pathogens. However, the extent to which these occupational exposures influence their carriage of antimicrobial-resistant (AMR) organisms and the composition of their microbiome and resistome remains poorly understood. The objective of this study was to characterize AMR pathogen carriage and microbiome/resistome composition in veterinary personnel and to assess whether workplace setting and patient-related exposures were associated with detectable differences in these outcomes.

METHODS: Personnel from a large academic veterinary hospital and a convenience sample of private-practice small-animal veterinary hospitals provided nasal swabs, stool samples, and exposure survey data; environmental samples were also collected from the academic hospital. Nasal swabs were cultured for methicillin-resistant Staphylococcus aureus, and stool samples were cultured for extended spectrum cephalosporin resistance (ESCR) Escherichia coli. Samples also underwent shotgun metagenomic sequencing or 16S rRNA gene sequencing for taxonomic and antimicrobial resistance gene profiling. Alpha/beta diversity were compared across groups, beta diversity by Permutational Multivariate Analysis of Variance, linear models tested differential abundance, and logistic regression was used to assess covariates associated with MRSA and ESCR carriage. A subset of academic-hospital participants also submitted additional samples after time away (1-2 weeks) from the hospital.

RESULTS: Among academic-hospital personnel (n = 38), MRSA and ESCR-E. coli carriage prevalence were 18.4% and 11.1%, respectively. In private-practice personnel (n = 8), carriage was 12.5% and 25%, respectively. Within the academic hospital, MRSA carriage was associated with administering antibiotics to patients. Microbial composition differed modestly by worksite (R[2] = 0.02) when assessed using unweighted UniFrac metrics only, suggesting subtle site-related differences in low-abundance phylogenetically distinct taxa. Global resistome composition did not differ significantly by site or clinical exposure, although a small number of individual AMR ontologies and broad AMR gene families varied across groups, including those associated with commonly-administered oral antibiotics at the hospital. Paired on/off-clinic analyses did not show a clear directional shift after time away from the hospital.

CONCLUSIONS: Veterinary personnel carried MRSA at a notable frequency, while workplace effects on the microbiome and resistome were subtle, with limited evidence for large-scale shifts in community structure by site or patient exposure.},
}

Humans
*Microbiota
*Drug Resistance, Bacterial
Hospitals, Animal
Methicillin-Resistant Staphylococcus aureus/isolation & purification/drug effects/genetics
Animals
Anti-Bacterial Agents/pharmacology
Male
Escherichia coli/drug effects/isolation & purification/genetics
Female
*Animal Technicians
*Carrier State/microbiology/epidemiology
*Veterinarians
Feces/microbiology
Metagenome
RNA, Ribosomal, 16S
Adult

@article {pmid42299860,
year = {2026},
author = {Barandouzi, ZA and Eng, T and Khanna, N and Shelton, J and Scott, I and Patel, P and Remick, J and Jin, R and Meador, R and Bruner, DW},
title = {Gut Microbiome Associations With Depressive Symptoms in Women With Gynecologic Cancer: A Longitudinal Study.},
journal = {Biological research for nursing},
volume = {28},
number = {4},
pages = {560-571},
doi = {10.1177/10998004261461549},
pmid = {42299860},
issn = {1552-4175},
mesh = {Humans ; Female ; Longitudinal Studies ; *Genital Neoplasms, Female/psychology/complications/microbiology ; *Depression/microbiology ; Middle Aged ; *Gastrointestinal Microbiome/physiology ; Aged ; Cross-Sectional Studies ; RNA, Ribosomal, 16S ; },
abstract = {About one-quarter of women diagnosed with gynecologic cancer experience depressive symptoms. While the precise mechanism remains unclear, little is known about the association between gut microbiota and depressive symptoms in gynecologic cancer. Thus, this study aimed to evaluate the associations between gut microbiota and depressive symptoms in women with gynecologic cancer over cancer treatment. Thirty-seven women with cervical or endometrial cancer were followed at pre-treatment (T0), 6-8 weeks (T1), and 6 months post-radiation (T2). Depressive symptoms were assessed using the Patient Health Questionnaire-9 (PHQ-9). Rectal swabs were collected at each visit and sequenced for the V4 region of the 16S rRNA gene. MaAsLin2 models evaluated cross-sectional associations between gut microbial taxa and depressive symptoms at each time point, whereas GEE models assessed longitudinal associations over the course of cancer treatment. The patients had an average age of 60 years, and 43% were Black. At baseline (T0), 24% of patients exhibited depressive symptoms, which decreased to 21% at T1 and further to 13% at T2. GEE models showed that lower α-diversity (Shannon index, p = 0.05), dissimilar β-diversity (Bray-Curtis distance, p = 0.02), and reduced abundance of the genus Ruminococcus (p = 0.02) were predictive factors associated with depressive symptoms throughout cancer treatment. Higher depressive symptoms were longitudinally associated with lower gut microbial Shannon diversity, dissimilar microbial community composition, and lower abundance of the genus Ruminococcus. Larger longitudinal studies using shotgun metagenomic sequencing are needed to validate these findings and further elucidate the microbial mechanisms underlying depressive symptoms in women with gynecologic cancers.},
}

Humans
Female
Longitudinal Studies
*Genital Neoplasms, Female/psychology/complications/microbiology
*Depression/microbiology
Middle Aged
*Gastrointestinal Microbiome/physiology
Aged
Cross-Sectional Studies
RNA, Ribosomal, 16S

@article {pmid42492757,
year = {2026},
author = {Demirci, M},
title = {Metabolic reprogramming and taxonomic drivers in bacterial vaginosis: A large-scale metagenomic meta-analysis.},
journal = {Anaerobe},
volume = {99},
number = {},
pages = {103067},
doi = {10.1016/j.anaerobe.2026.103067},
pmid = {42492757},
issn = {1095-8274},
mesh = {Humans ; *Vaginosis, Bacterial/microbiology/metabolism ; Female ; *Metagenomics ; Microbiota ; *Metagenome ; Vagina/microbiology ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/metabolism ; },
abstract = {OBJECTIVE: Bacterial vaginosis (BV) represents a profound ecological shift from a Lactobacillus-dominated microbiota to a diverse polymicrobial biofilm associated with adverse outcomes. While taxonomic signatures are well-documented, the functional mechanisms driving this transition remain obscured. This study elucidates the genomic potential for metabolic reprogramming and the putative "functional handover" underpinning the stability of the dysbiotic state.

METHODS: A computational meta-analysis of 3557 vaginal microbiomes from diverse global cohorts was performed using the standardized MGnify pipeline. A high-resolution subset of 187 whole-genome shotgun (WGS) metagenomes was stratified to compare functional potential across demographic groups. Taxon-function interaction networks were constructed, utilizing a dual-filter statistical approach (p < 0.05 and effect size ranking), to map the shift from homeostatic maintenance to dysbiotic metabolic potential.

RESULTS: BV was characterized by a fundamental shift from "maintenance" pathways to high-turnover "growth-oriented" genomic repertoires. While ABC transporter-like domains were present in healthy communities, dysbiosis was marked by a quantitative expansion and diversification of these systems alongside P-loop NTPases. Network analysis revealed a putative "functional handover": while Gardnerella serves as the adherent structural scaffold, the metabolic burden appears to be associated with secondary anaerobes, specifically BVAB1 and Sneathia, which exhibit strong genomic correlations with nutrient transport and stress response pathways. Crucially, microbiomes from women of African ancestry (Black cohort) exhibited a distinct functional profile with genomic signatures consistent with functions previously associated with resistome expansion (e.g., tetracycline/macrolide resistance), contrasting with Asian cohorts.

CONCLUSION: BV is a state of metabolic reprogramming where genomic functional dominance is transferred from Lactobacillus to a cooperative network of anaerobic opportunists. Identifying BVAB1 and Sneathia as candidate metabolic engines, supported by a Gardnerella scaffold, challenges current therapeutic paradigms and highlights the potential for precision medicine targeting specific functional drivers and resistome profiles across diverse populations.},
}

Humans
*Vaginosis, Bacterial/microbiology/metabolism
Female
*Metagenomics
Microbiota
*Metagenome
Vagina/microbiology
Dysbiosis/microbiology
*Bacteria/classification/genetics/metabolism

@article {pmid42580006,
year = {2026},
author = {Zhang, L and Xu, W and Wang, Y and Liu, Y and Feng, X and Liu, Q},
title = {Metagenomic profiling of tick-borne viromes across four ecologically diverse provinces in China.},
journal = {Ticks and tick-borne diseases},
volume = {17},
number = {5},
pages = {102693},
doi = {10.1016/j.ttbdis.2026.102693},
pmid = {42580006},
issn = {1877-9603},
mesh = {Animals ; China ; *Virome ; Phylogeny ; Metagenomics ; *Viruses/isolation & purification/classification/genetics ; *Ticks/virology ; },
abstract = {Ticks are important vectors of emerging viruses, and China's ecological landscapes may influence the transmission dynamics of tick-borne viruses (TBV). In 2021, a total of 2867 ticks collected from Inner Mongolia, Hebei, Hunan, and Hainan provinces were subjected to metagenomic sequencing to characterize TBV diversity. A total of eleven TBVs were identified, comprising three members of the family Phenuiviridae (severe fever with thrombocytopenia syndrome virus, Lihan tick virus, Dabieshan tick virus), three belonging to Nairoviridae (Huangpi tick virus 1, Shanxi tick virus 2, Henan tick virus), one in Chuviridae (Wuhan tick virus 2), one in Rhabdoviridaes (Wuhan tick virus 1), and three unclassified viruses (Hubei tick virus 2, Bole tick virus 4, and Tacheng tick virus 7). Viral composition varied significantly across tick species and geographic regions, with phylogenetic analysis revealing distinct regional clustering patterns. Notably, Lihan tick virus was detected for the first time in Hunan Province, Bole tick virus 4 was identified in argasid ticks from Inner Mongolia for the first time, and a novel lineage of severe fever with thrombocytopenia syndrome virus was discovered in Shijiazhuang, Hubei Province. These findings underscore substantial TBV diversity shaped by tick species and geographic origin, emphasizing the necessity for ongoing surveillance to guide the development of targeted prevention and control strategies.},
}

Animals
China
*Virome
Phylogeny
Metagenomics
*Viruses/isolation & purification/classification/genetics
*Ticks/virology

@article {pmid42714425,
year = {2026},
author = {Yang, H and Feng, L and Jiang, Z and Weng, J and Qiu, J and Deng, R and Wu, X and Zeng, K},
title = {Gut Microbiota and Aldosterone Regulate Natriuretic Peptide B Expression to Drive Mitophagy and Metabolic Reprogramming in Sepsis-Like Model of Myocardial Injury.},
journal = {Journal of the American Heart Association},
volume = {15},
number = {18},
pages = {e046120},
doi = {10.1161/JAHA.125.046120},
pmid = {42714425},
issn = {2047-9980},
mesh = {Animals ; *Mitophagy/physiology ; *Sepsis/metabolism/complications/microbiology ; *Aldosterone/metabolism/pharmacology ; Disease Models, Animal ; *Gastrointestinal Microbiome/physiology ; *Natriuretic Peptide, Brain/genetics/metabolism ; *Myocytes, Cardiac/metabolism/pathology ; Mice, Knockout ; Mice ; Metabolic Reprogramming ; Male ; Mice, Inbred C57BL ; *Mitochondria, Heart/metabolism/pathology ; Lipopolysaccharides ; *Cardiomyopathies/metabolism/microbiology/pathology ; Fecal Microbiota Transplantation ; Energy Metabolism ; },
abstract = {BACKGROUND: Myocardial injury is a major contributor to mortality in sepsis, yet the mechanisms underlying gut-heart communication in sepsis-induced myocardial injury remain insufficiently defined. Natriuretic peptide B (NPPB) is a cardiac stress-responsive gene, but its involvement in mitochondrial homeostasis and metabolic regulation is unclear. This study investigated how gut microbiota and aldosterone influence myocardial mitophagy and metabolic reprogramming through NPPB in sepsis-induced myocardial injury.

METHODS: A sepsis-like myocardial injury model was induced in mice by intraperitoneal lipopolysaccharide (LPS). Fecal microbiota transplantation from septic mice into pseudo-germ-free recipients assessed microbial contributions. Metagenomic, metabolomic, and transcriptomic analyses identified disrupted metabolites and cardiac gene signatures. Heart-specific NPPB-knockout mice were used to determine its in vivo role. Mitochondrial function and metabolic alterations were evaluated by energy metabolism assays. In vitro, aldosterone-treated AC16 cardiomyocytes were used to examine NPPB-mediated mitophagy and metabolic changes. Molecular docking, dynamics simulation, and machine-learning screening identified Lestaurtinib, whose therapeutic effects were validated pharmacologically.

RESULTS: Sepsis caused pronounced microbial dysbiosis and elevated aldosterone levels. Multi-omics analysis identified NPPB as a central regulator of mitophagy and metabolic remodeling. NPPB deficiency mitigated mitochondrial impairment and metabolic disturbances in vivo. Aldosterone upregulated NPPB in cardiomyocytes, promoting mitophagy and metabolic reprogramming. Lestaurtinib, identified as a candidate targeting the aldosterone-NPPB axis, improved cardiac structure and function while partially restoring microbial and metabolic homeostasis.

CONCLUSIONS: This study uncovers a novel gut microbiota-aldosterone-NPPB axis driving LPS-induced myocardial injury through dysregulated mitophagy and metabolism and highlights Lestaurtinib as a potential therapeutic strategy for sepsis-induced myocardial injury.},
}

Animals
*Mitophagy/physiology
*Sepsis/metabolism/complications/microbiology
*Aldosterone/metabolism/pharmacology
Disease Models, Animal
*Gastrointestinal Microbiome/physiology
*Natriuretic Peptide, Brain/genetics/metabolism
*Myocytes, Cardiac/metabolism/pathology
Mice, Knockout
Mice
Metabolic Reprogramming
Male
Mice, Inbred C57BL
*Mitochondria, Heart/metabolism/pathology
Lipopolysaccharides
*Cardiomyopathies/metabolism/microbiology/pathology
Fecal Microbiota Transplantation
Energy Metabolism

@article {pmid42742736,
year = {2026},
author = {Sheoran, N and Gogoi, R and Venkadasamy, G and Vijayan, V and Kumar, N and Jat, SL and Rakshit, S and Kumar, A},
title = {Recurrent and niche-specific functional bacteriome of maize hybrid revealed by integrated metabarcoding and culturomics.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42742736},
issn = {1432-072X},
mesh = {*Zea mays/microbiology ; Soil Microbiology ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Microbiota ; DNA Barcoding, Taxonomic ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Rhizosphere ; },
abstract = {The plant microbiome plays a pivotal role in plant survival in natural habitats by facilitating nutrient acquisition, stress adaptation, and disease suppression, while also offering opportunities to enhance crop productivity and climate resilience. However, the distribution of persistent and culturable bacteriome across maize-associated niches and their functional potential remain poorly resolved. This study integrated metagenomic next-generation sequencing (mNGS-based metabarcoding) and culturomics to characterise the maize-associated bacteriome of bulk soil, rhizoplane, phylloplane, and cob of the maize hybrid PHM-1 under contrasting cropping and tillage systems, and to identify recurrent and agriculturally promising bacteriome components. The bacteriome exhibited pronounced niche-specific structuring, whereas overall bacterial community composition did not differ significantly across cropping and tillage treatments (ANOSIM, R = 0.038, p = 0.306). Proteobacteria predominated in the culturable bacteriome (69-84%; mean, 76.2%) but accounted for only 1% of the total bacteriome, whereas Patescibacteria and Firmicutes were relatively enriched. Niche-specific dominance was evident, with Pantoea accounting for 40.79% of the total and 56.27% of the culturable phylloplane bacteriome under cereal monocropping, while Serratia represented 31.59% and 59.40% of the total and culturable cob bacteriomes, respectively. Across niches, mNGS captured substantially greater bacteriome diversity, particularly uncultured and unidentified taxa in soil-associated compartments, whereas culturomics recovered a narrower but functionally accessible fraction. Culturomics yielded 99 isolates representing 32 species across 12 genera, including six genera shared with the mNGS-derived recurrent bacteriome: Bacillus, Enterobacter, Pantoea, Pseudomonas, Serratia, and Stenotrophomonas. Functional screening identified strong biocontrol and plant-beneficial traits among core-associated isolates. Pseudomonas oryzihabitans ZM-DL-PA10 inhibited Rhizoctonia solani, Macrophomina phaseolina, and Bipolaris maydis by up to 40.6%, 43.9%, and 45.2%, respectively, through secreted and volatile metabolites; exhibited P, K, and Zn solubilisation; and produced IAA and siderophores. It also recorded the lowest B. maydis disease index (ADI) of 1.00. Pantoea ananatis ZM-BH-EA4 showed 52.4% and 68.5% inhibition of R. solani and B. maydis, respectively, through volatile metabolites. Collectively, the integration of mNGS and culturomics revealed a strongly compartmentalised maize bacteriome and identified recurrent, culturable, and functionally promising bacterial taxa, providing a targeted resource for microbiome-based crop protection and climate-resilient maize production.},
}

*Zea mays/microbiology
Soil Microbiology
*Bacteria/classification/isolation & purification/genetics/metabolism
*Microbiota
DNA Barcoding, Taxonomic
Metagenomics
High-Throughput Nucleotide Sequencing
Rhizosphere

@article {pmid42742775,
year = {2026},
author = {Pazdro-Zastawny, K and Kos, M and Leszczyszyn, A and Zawadzki, T and Pietruszka, K and Dorobisz, K},
title = {The Oral Microbiome in Oral Cavity Cancer: Mechanisms of Carcinogenesis, Biomarkers, and Therapeutic Implications.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42742775},
issn = {1534-6269},
support = {SUBK.C250.25.065//Wrocław Medical University/ ; },
mesh = {Humans ; *Mouth Neoplasms/microbiology/therapy/pathology ; *Microbiota ; *Mouth/microbiology/pathology ; Dysbiosis/microbiology/complications ; Biomarkers, Tumor ; Carcinogenesis ; },
abstract = {PURPOSE OF REVIEW: Oral cavity cancer (OCC) is a significant clinical challenge within head and neck oncology. It is characterized by significant morbidity, high recurrence rates, and only modest improvements in long-term survival over recent decades. Recent advances in metagenomics and high-throughput sequencing have revealed that oral microbial dysbiosis contributes to tumorigenesis, highlighting the potential of microbiome-derived biomarkers for early detection and prognosis of OCC. The purpose of the work is to discuss oral microbiome alterations in OCC.

RECENT FINDINGS: The microbiome plays a crucial role in regulating the host's physiological, immunological, and metabolic functions. Changes in the composition of the microbiome can influence our health status of local diseases of the oral cavity and oropharynx, as well as systemic diseases. In recent years, the role of the oral microbiome in oral potentially malignant disorders progression and OCC development has been emphasized. Changes in the oral and gut microbiome can lead to the induction of chronic inflammation, modulation of the immune system, and the production of carcinogenic metabolites. Dysbiosis can lead to critical inflammatory responses and consequently contribute to neoplastic events. Microbiome-modulating therapies tailored to the patient's individual profile and aimed at improving cancer treatment outcomes are being introduced, including the introduction of antibiotics to reduce harmful bacteria. Identification of new biomarkers in oral microbiota communities and development of therapeutic strategies in relation with oral microbiota in the future may be one of the pillars of the oral cancer diagnosis and treatment strategy. Oral cancer prevention protocols should include the improvement of oral hygiene as an element of the prevention and treatment of periodontitis. An introduction of microbiota-targeted interventions, including probiotics, prebiotics, and dietary strategies, may reduce the toxicity of radiotherapy, leading to improved patient outcomes.},
}

Humans
*Mouth Neoplasms/microbiology/therapy/pathology
*Microbiota
*Mouth/microbiology/pathology
Dysbiosis/microbiology/complications
Biomarkers, Tumor
Carcinogenesis

@article {pmid42745851,
year = {2026},
author = {Yue, Z and Sheng, S and Peng, L and Xu, W and Zhang, J and Wu, D and Liu, B and Li, Q and Dong, R and Cheng, H and Zou, Y},
title = {Impact of Chamaecrista rotundifolia cover cropping on soil elemental cycling in karst agroecosystems.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1906173},
pmid = {42745851},
issn = {1664-302X},
abstract = {Karst desertification causes severe soil erosion, hydrological imbalance, and biodiversity loss, thereby threatening ecosystem resilience and agricultural productivity. Soil carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) cycling underpin ecosystem stability, yet how agricultural management practices regulate multi-element cycling in degraded karst agroecosystems remains poorly understood. Here, we conducted a four-year field trial in a karst mango orchard in southwestern China and integrated metagenomic sequencing with comprehensive soil environmental profiling to investigate how C. rotundifolia cover cropping reshapes soil elemental cycling. Compared with conventional tillage (CK), C. rotundifolia cover cropping (Y) significantly (p < 0.05) altered topsoil microbial functional profiles and nutrient availability. Carbon cycling potentials, including gene associated with aerobic respiration (cox1/3), fermentation, and CO2 assimilation-were enriched under C. rotundifolia cover cropping. Nitrogen cycling potentials were enhanced through increased representation of genes involved in denitrification (nirK/S, nosZ), nitrogen acquisition, and nitrate reduction (nirA, narB), while phosphorus cycling was promoted through enrichment of the PhoR-PhoB phosphate regulatory system. Sulfur transformation potentials were also altered, with increased representation of genes involved in sulfate reduction, oxidation, and sulfonate utilization. Cover cropping substantially improved soil fertility, increasing SOC (+35.4%), NH4 [+]-N (+31.8%), TN (+35.1%), and AP (+105.9%), while reducing exchangeable Al[3+] concentration by 60.9%. Microbial community restructuring was characterized by decreased Actinobacteriota and Chloroflexota and increased Bacteroidota and Proteobacteria, which exhibited central roles in elemental cycling networks. Mantel analyses identified exchangeable Al[3+] as a dominant environmental constraint shaping microbial communities involved in C, N, P, and S cycling. Collectively, these findings demonstrate that C. rotundifolia cover cropping enhances karst soil resilience through a coupled microbial-geochemical pathway, in which improved soil chemical conditions and microbial functional reorganization jointly restore elemental cycling capacity.},
}

@article {pmid42746328,
year = {2026},
author = {Kuzuya, K and Maeda, Y and Funakoshi, K and Mizuno, Y and Fujimoto, K},
title = {Autoimmune disease-associated pathobionts: mechanisms and therapeutic potential of phage-based approaches.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1884094},
pmid = {42746328},
issn = {1664-3224},
mesh = {Humans ; *Autoimmune Diseases/therapy/immunology/microbiology ; Animals ; *Phage Therapy/methods ; *Gastrointestinal Microbiome/immunology ; *Bacteriophages/immunology ; Bacteria/immunology/virology ; Host Microbial Interactions/immunology ; },
abstract = {The gut microbiota is a critical regulator of systemic immune homeostasis; accumulating evidence implicates specific commensal bacteria, termed "pathobionts," in autoimmune disease pathogenesis. However, the definition of pathobionts remains context-dependent, as their effects are influenced by host genetics and host-microbe interactions. In this review, we summarize representative pathobionts supported by functional evidence in selected extraintestinal autoimmune diseases and discuss how these mechanisms may inform phage-based microbiome-targeted interventions. Mechanistically, pathobionts contribute to autoimmune disease through multiple pathways, including molecular mimicry, induction of intestinal T helper 17 and T follicular helper cell responses, disruption of regulatory T cell homeostasis, intestinal barrier dysfunction, and bacterial translocation from the gut to extraintestinal sites. These processes highlight the central role of gut-associated lymphoid tissue in initiating systemic autoimmunity, and targeting disease-associated microbes represents a promising therapeutic strategy. Whole-phage therapy, which enables highly specific bacterial elimination, has shown efficacy in preclinical immune-mediated disease models, but may be affected by variable in vivo replication, bacterial receptor-mediated resistance, anti-phage immune responses, and ecological effects on the resident microbiome. Phage-derived enzymes that lyse bacterial cell walls, such as endolysins, represent a complementary therapeutic modality that specifically targets bacterial peptidoglycan through cell wall-binding and catalytic domains. Collectively, these findings support the concept that pathobiont-targeted interventions, particularly phage-based strategies, may provide microbiome-directed, immunosuppression-sparing therapeutic approaches for selected patient subsets.},
}

Humans
*Autoimmune Diseases/therapy/immunology/microbiology
Animals
*Phage Therapy/methods
*Gastrointestinal Microbiome/immunology
*Bacteriophages/immunology
Bacteria/immunology/virology
Host Microbial Interactions/immunology

@article {pmid42365131,
year = {2026},
author = {Zhu, S and Yang, Z and Zhao, H and Ma, Y and Chen, K and Qi, D},
title = {Rainfall Drives Differentiation of Plant Rhizosphere Microbial Communities in Two Different Types of Alpine Wetlands: A Perspective Based on a Carbon-Water Coupling Framework.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42365131},
issn = {1432-184X},
support = {Qing[2025]TG04//Demonstration of Techniques for Wetland Protection, Restoration, and Carbon Sink Capacity Enhancement in the Qinghai Lake Basin - Qinghai Provincial Finance Budget/ ; },
mesh = {*Wetlands ; *Rhizosphere ; *Soil Microbiology ; *Rain ; *Carbon/metabolism/analysis ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Microbiota ; China ; Tibet ; Soil/chemistry ; Proteobacteria/genetics/isolation & purification ; },
abstract = {The alpine wetlands of the Qinghai-Tibet Plateau are confronting significant ecological challenges due to drastic shifts in precipitation patterns. Elucidating the response mechanisms of rhizosphere microbial communities in wetland plants to precipitation events is critical to understanding ecosystem resilience. In this study, sandy wetlands at Niaodao and riverine wetlands at Haergai in the Qinghai Lake basin were selected as study sites. Using Poa alpigena rhizosphere and non-rhizosphere soils as the research subjects, metagenomic DNA sequencing combined with environmental factor analysis was employed to compare the microbial community responses before and after a single pulse precipitation event. The results showed that Proteobacteria and Actinobacteria were the dominant phyla in both wetland types (combined relative abundance > 70%). Rainfall induced a differentiated restructuring of soil microbial community composition across different habitats. In rhizosphere soils, rainfall significantly reduced microbial alpha diversity. Co-occurrence network analysis revealed that the rhizosphere community shifted from a competition-coexistence pattern before rainfall to a cooperative adaptation pattern after rainfall, with significant increases in modular cohesion and the proportion of positive correlations. Metagenomic analysis indicated that the number of differentially abundant metabolic pathways in soil microorganisms increased markedly after rainfall, rising to 46 and 40 pathways in the rhizosphere and non-rhizosphere, respectively (compared to 3 and 31 before rainfall), indicating a shift from carbon reserve metabolism to energy-producing metabolism. Total carbon and water content were identified as the core environmental factors jointly regulating community assembly. This study reveals the mechanism by which regional background, precipitation disturbance, and the rhizosphere effect synergistically drive the succession of microbial communities in alpine wetlands, providing a new paradigm for understanding ecosystem adaptation to climate change.},
}

*Wetlands
*Rhizosphere
*Soil Microbiology
*Rain
*Carbon/metabolism/analysis
*Bacteria/classification/genetics/isolation & purification/metabolism
*Microbiota
China
Tibet
Soil/chemistry
Proteobacteria/genetics/isolation & purification

@article {pmid42374196,
year = {2026},
author = {Ye, J and Mao, P and Li, B and Hao, Y and Chen, Y and Li, K},
title = {Metagenomic profiling of gut microbiome in post-cholecystectomy patients with diarrhea: a nested case-control study.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42374196},
issn = {1471-2180},
mesh = {Humans ; Case-Control Studies ; *Diarrhea/microbiology/etiology ; Female ; *Metagenomics/methods ; *Cholecystectomy/adverse effects ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Male ; Prospective Studies ; Middle Aged ; Dysbiosis/microbiology ; Adult ; },
abstract = {BACKGROUND: Cholecystectomy can cause diarrhea, with an incidence as high as 57.2%, seriously impacting patient prognosis. To investigate the gut dysbiosis following cholecystectomy and identify microbial biomarkers and functional genomics associated with post-cholecystectomy diarrhea (PCD), we conducted a nested case-control study within a prospective cohort.

METHODS: We enrolled a cohort of 160 patients. At follow-up completion, 30 patients who developed PCD were matched with 30 non-PCD (NPCD) controls. 16 S rRNA sequencing was used to analyze gut microbiota structure and diversity (mainly at genus level). Representative fecal samples underwent metagenomic sequencing for species level and genetic differential analysis.

RESULTS: The potentially pathogenic bacterial species Coprococcus comes and Blautia sp. were significantly enriched in the gut microbiota of PCD patients, with their abundance positively correlated with the degree of intestinal inflammation. In contrast, the potentially beneficial bacterial species Bacteroides intestinalis and Prevotella copri, known to contribute to lipid metabolism and play a role in modulating gut immunity and suppressing inflammatory responses, were found to be significantly depleted in PCD patients. Further metagenomic functional analysis revealed significant enrichment of pathways related to cell motility, membrane transport, and sulfur metabolism in PCD patients.

CONCLUSIONS: This work identified potential beneficial and pathogenic bacterial species associated with the onset of PCD, as well as significantly enriched functional pathways within the intestinal microbiota. These findings provide a scientific basis for elucidating the relationship between PCD and gut microbiota, and provide candidate microbial signatures and functional pathways that may inform future microbiota-targeted strategies, pending external and mechanistic validation.},
}

Humans
Case-Control Studies
*Diarrhea/microbiology/etiology
Female
*Metagenomics/methods
*Cholecystectomy/adverse effects
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome/genetics
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Male
Prospective Studies
Middle Aged
Dysbiosis/microbiology
Adult

@article {pmid42392368,
year = {2026},
author = {Cheng, M and Qin, X and Han, Y and Tan, F and She, M and Zhu, X and Yuan, L and Teng, M and Ou, X and Luo, S and Xiang, P and Chen, L and Yang, F},
title = {Genomic and biosynthetic landscape of high-temperature Daqu microbiome.},
journal = {Bioresource technology},
volume = {460},
number = {},
pages = {135297},
doi = {10.1016/j.biortech.2026.135297},
pmid = {42392368},
issn = {1873-2976},
mesh = {*Microbiota/genetics ; *Genomics/methods ; *Hot Temperature ; Fermentation ; Metagenome/genetics ; Genome, Bacterial ; Multigene Family ; },
abstract = {As the core starter for Chinese Baijiu, high-temperature Daqu is produced through open solid-state fermentation with recurrent inoculation by mature Daqu, forming a rich yet largely untapped reservoir of genomes and bioactive compounds. This study constructs the High-temperature Daqu Fermentation Microbiome catalog using 463 metagenomes spanning the full fermentation cycle. The catalog comprises 4,264 metagenome-assembled genomes that are dereplicated into 252 representative genome-based species, 82 % of which are absent from current global food microbiome databases. It further contains 14.3 million non-redundant genes, of which 17.3 % are novel, and 17,031 biosynthetic gene clusters, of which 62.63 % are novel, thereby substantially expanding the known genomic and biosynthetic space of food microbiomes. Genome-resolved analyses revealed a U-shaped ecological trajectory, shifting from early Bacillus velezensis-enriched assemblages to transient dominance of lactic acid bacteria during peak thermogenesis, before returning in late fermentation to thermotolerant, spore-forming Bacillota and Actinomycetota. In parallel, biosynthetic potential was further organized into four recurrent, stage-enriched profiles, from RiPP-rich thermogenic states to mature-state assemblages enriched in PKS-, NRPS-, and terpene-related capacities, with Bacillus, Kroppenstedtia, and Saccharopolyspora constituting the principal biosynthetic reservoir. Together, this work uncovers a largely unexplored genomic and biosynthetic reservoir in high-temperature Daqu fermentation, providing a target resource for mining thermotolerant industrial enzymes, flavor-related genes, and bioactive metabolites with biotechnological potential.},
}

*Microbiota/genetics
*Genomics/methods
*Hot Temperature
Fermentation
Metagenome/genetics
Genome, Bacterial
Multigene Family

@article {pmid42419508,
year = {2026},
author = {Hering-Peter, C and Schulz, R},
title = {Physiological responses of floc-forming microalgae-bacteria consortia to environmental perturbations.},
journal = {Bioresource technology},
volume = {460},
number = {},
pages = {135341},
doi = {10.1016/j.biortech.2026.135341},
pmid = {42419508},
issn = {1873-2976},
mesh = {*Microalgae/physiology ; Flocculation ; Hydrogen-Ion Concentration ; Temperature ; *Bacteria ; *Microbial Consortia/physiology ; Biomass ; *Environment ; Light ; Salinity ; Bioreactors ; },
abstract = {Fast-sedimenting microalgae-bacteria consortia (MBC) offer a cost-efficient pathway for biomass harvesting while remediating polluted water bodies in chemostatic photobioreactors. Understanding how abiotic parameters affect floc morphology, sinking properties and metagenomic species composition remains critical for optimization of these specific bioreactors. This study investigated whether fast-sedimenting MBC maintain structural resilience under moderate stress but lose stability beyond critical physiological tipping points. By investigating the physiological boundaries of five environmental factors, we identified clear operational thresholds. Moderate perturbations including light intensities up to 1500 µmol m[-2] s[-1], salinities from 0 to 35 PSU and low antibiotic concentrations showed no statistically significant impact on settling efficiency. In contrast, extreme pH at 12 and temperatures at 45 °C reduced recovery rates by more than 50 % compared to controls maintaining above 87 % efficiency. The surface charge decreased from -27.94 mV to -4.83 mV under acidic conditions at pH 3, indicating electrostatic destabilization of the floc matrix. Dominance of the cyanobacterium Thermoleptolyngbya spp. persisted above 70 % abundance across all treatments. These findings define a safe operating envelope between pH 6-9 and temperatures from 15 to 35 °C necessary to maintain gravity-driven sedimentation. This work provides quantitative boundaries where biological buffering fails, enabling predictive reactor design that avoids biomass washout in continuous cultivation systems.},
}

*Microalgae/physiology
Flocculation
Hydrogen-Ion Concentration
Temperature
*Bacteria
*Microbial Consortia/physiology
Biomass
*Environment
Light
Salinity
Bioreactors

@article {pmid42435910,
year = {2026},
author = {Almeida, L and Alexandrino, DAM and Lilienthal, T and Karpe, NV and Ribeiro, N and Oliveira, RS and Carvalho, MF and Freitas, M},
title = {Compost microbiomes as reservoirs of cellulolytic microorganisms for cellulosic textile degradation.},
journal = {Bioresource technology},
volume = {460},
number = {},
pages = {135373},
doi = {10.1016/j.biortech.2026.135373},
pmid = {42435910},
issn = {1873-2976},
mesh = {*Cellulose/metabolism ; *Composting/methods ; *Textiles/microbiology ; Biodegradation, Environmental ; *Microbiota ; *Bacteria/metabolism/genetics ; Metagenomics ; Gossypium ; },
abstract = {Cellulosic textiles, constituting over 30% of global fibre production, are biodegradable but remain challenging to recycle at scale owing to their high crystallinity, chemical finishes, and heterogeneous waste streams. Although microorganisms drive cellulose turnover in natural ecosystems, their potential for transforming anthropogenic cellulosic waste remains largely unexplored. In this study, composting was evaluated both as a sustainable approach to textile biodegradation and a reservoir of cellulolytic microorganisms with biotechnological potential. Biodegradation assays of cotton and lyocell were integrated with shotgun metagenomics and targeted cultivation to identify microbial taxa and enzymes involved in cellulose degradation. Composting trials showed that degradation was strongly influenced by both composting system and fibre composition. Community composting achieved near-complete textile disintegration, while shredded textiles exhibited the highest degradation rates, reaching up to 97%. Shotgun metagenomic revealed a bacterial-dominated community enriched in Actinomycetota and Bacillota and characterised by an abundance of glycoside hydrolases. Culture-based screening recovered 62 microbial isolates, of which Neurospora and Aspergillus exhibited the highest cellulolytic activity (>60%). In vitro assays further showed that cotton was more readily degraded than lyocell, with several isolates achieving >70% mass loss. Metagenomic approach revealed a predominantly bacterial composting community at the sampled stage, whereas cultivation preferentially recovered fungi that, despite their low relative abundance in situ, exhibited strong cellulolytic potential. These findings highlight the potential of composting as a sustainable end-of-life strategy for cellulosic textiles and identify compost microbiomes as valuable reservoirs of cellulolytic microorganisms for the development of sustainable bioprocesses for textile waste treatment.},
}

*Cellulose/metabolism
*Composting/methods
*Textiles/microbiology
Biodegradation, Environmental
*Microbiota
*Bacteria/metabolism/genetics
Metagenomics
Gossypium

@article {pmid42575094,
year = {2026},
author = {Zhai, J and Li, Y and Liu, J and Su, X and Cui, R and Zheng, D and Sun, Y and Yu, J and Dai, C},
title = {Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease.},
journal = {Cell reports. Medicine},
volume = {7},
number = {9},
pages = {102974},
doi = {10.1016/j.xcrm.2026.102974},
pmid = {42575094},
issn = {2666-3791},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/epidemiology ; *Gastrointestinal Microbiome/genetics ; Female ; Metagenomics ; Phylogeny ; Male ; Feces/microbiology ; Bacteria/genetics/classification ; },
abstract = {The global rise of inflammatory bowel disease (IBD) reflects environmental shifts, yet how these changes are embedded in the gut microbial ecology remains unclear. We construct a microbiome atlas comprising 245,627 profiles. By classifying countries into three epidemiologic stages, we establish a framework. As the IBD burden increases, the gut microbial alpha diversity declines, and community structures form distinct clusters. This transition is characterized by a gradient of core genera. Integrating six shotgun metagenomic cohorts, we identify the depletion of anabolic pathways in IBD patients. Strain-level analysis reveals that epidemiologic staging shapes genetic architecture within species, identifying an IBD-enriched subclade of Eisenbergiella associated with elevated fecal cholic acid. We develop a microbial inflammatory risk score (MIRS), based on 19 genera, that discriminates IBD from controls (area under the curve [AUC] = 0.92). MIRS correlates with IBD prevalence. Our study provides an atlas linking epidemiology to microbiome ecology and strain evolution, offering a foundation for population-level surveillance and interventions in IBD.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/epidemiology
*Gastrointestinal Microbiome/genetics
Female
Metagenomics
Phylogeny
Male
Feces/microbiology
Bacteria/genetics/classification

@article {pmid42624113,
year = {2026},
author = {Wang, Y and Xie, S and Li, C and Huang, R and Zheng, Z and Chen, S and Wu, Y and Zhang, H and Yang, R and Chan, YL and Sun, Y and Chan, FKL and Chan, NY and Ng, SC and Su, Q},
title = {Faecalibacterium prausnitzii-derived L-arginine ameliorates insomnia by inhibiting POMC-ACTH-cortisol axis.},
journal = {Cell reports. Medicine},
volume = {7},
number = {9},
pages = {102997},
doi = {10.1016/j.xcrm.2026.102997},
pmid = {42624113},
issn = {2666-3791},
mesh = {*Arginine/metabolism/pharmacology/biosynthesis ; *Adrenocorticotropic Hormone/metabolism ; Animals ; *Sleep Initiation and Maintenance Disorders/microbiology/metabolism/drug therapy ; Humans ; *Hydrocortisone/metabolism ; *Faecalibacterium prausnitzii/metabolism ; Mice ; *Pro-Opiomelanocortin/metabolism/genetics ; Male ; Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {Insomnia is associated with gut microbial dysbiosis, but the specific microbial metabolites mediating gut-brain communication remain elusive. Here, we integrate metagenomic sequencing from 171 individuals (primary insomnia, post-COVID insomnia, and controls) with functional pathway analysis and preclinical validation. We identify Faecalibacterium prausnitzii depletion and reduced L-arginine biosynthesis as consistent features in both insomnia subtypes, accompanied by elevated cortisol levels. Genomic and in vitro analyses confirm that F. prausnitzii is a key microbial contributor to L-arginine production. In a chronic mild stress mouse model, administration of either F. prausnitzii or L-arginine restores sleep duration, normalizes corticosterone levels, and reverses stress-induced gut dysbiosis. Mechanistically, L-arginine suppresses POMC gene expression and dampens adrenocorticotropic hormone (ACTH)-stimulated corticosterone release, implicating the POMC-ACTH-cortisol axis as a key target. These findings uncover a gut-brain axis driven by F. prausnitzii-derived L-arginine that modulates sleep through endocrine signaling, positioning this metabolite as a potential therapeutic avenue for insomnia.},
}

*Arginine/metabolism/pharmacology/biosynthesis
*Adrenocorticotropic Hormone/metabolism
Animals
*Sleep Initiation and Maintenance Disorders/microbiology/metabolism/drug therapy
Humans
*Hydrocortisone/metabolism
*Faecalibacterium prausnitzii/metabolism
Mice
*Pro-Opiomelanocortin/metabolism/genetics
Male
Gastrointestinal Microbiome
Mice, Inbred C57BL
Disease Models, Animal

@article {pmid42664954,
year = {2026},
author = {Zhang, B and Zhang, Y and Cai, Y and Cheng, S and Han, Z and Yin, X and Xie, T and Tan, Y and Feng, Y and Wang, Y and Guo, X and Shen, L and Peng, Z},
title = {Lactobacillus salivarius potentiates gastrointestinal cancer immunotherapy through its metabolite chenodeoxycholic acid.},
journal = {Cell reports. Medicine},
volume = {7},
number = {9},
pages = {103009},
doi = {10.1016/j.xcrm.2026.103009},
pmid = {42664954},
issn = {2666-3791},
mesh = {*Chenodeoxycholic Acid/metabolism/pharmacology ; Animals ; Humans ; *Immunotherapy/methods ; *Gastrointestinal Neoplasms/therapy/immunology/microbiology ; Mice ; CD8-Positive T-Lymphocytes/immunology/drug effects ; *Ligilactobacillus salivarius/metabolism ; Macrophages/immunology/drug effects ; Cell Line, Tumor ; Female ; Mice, Inbred C57BL ; Tumor Microenvironment ; Gastrointestinal Microbiome ; },
abstract = {Immune checkpoint inhibitor therapy has improved gastrointestinal (GI) cancer management; however, many patients exhibit resistance. Although gut microbiota influences immunotherapeutic responses, the underlying mechanisms remain unclear. Metagenomic analysis of 278 GI cancer patients reveals that Lactobacillus salivarius (L. salivarius) is enriched in responders and enhances anti-PD-1 efficacy in syngeneic tumor models by increasing the infiltration of antitumor M1-like macrophages and CD8[+] T cells and enhancing CD8[+] T cell effector function. L. salivarius-associated chenodeoxycholic acid (CDCA) is identified as a functional metabolite. CDCA recapitulates the antitumor effects of L. salivarius and significantly improves anti-PD-1 efficacy in vivo, an effect attenuated by depleting macrophages or CD8[+] T cells. Mechanistically, CDCA-induced reactive oxygen species triggers immunogenic cell death in tumor cells and polarizes macrophages toward antitumor M1 phenotype, activating CD8[+] T cell antitumor immunity. These findings identify L. salivarius and its associated metabolite CDCA as a promising adjuvant for potentiating immunotherapy in GI cancers.},
}

*Chenodeoxycholic Acid/metabolism/pharmacology
Animals
Humans
*Immunotherapy/methods
*Gastrointestinal Neoplasms/therapy/immunology/microbiology
Mice
CD8-Positive T-Lymphocytes/immunology/drug effects
*Ligilactobacillus salivarius/metabolism
Macrophages/immunology/drug effects
Cell Line, Tumor
Female
Mice, Inbred C57BL
Tumor Microenvironment
Gastrointestinal Microbiome

@article {pmid42679805,
year = {2026},
author = {Samarra, A and Alcañiz, AJ and Quijada, NM and Renwick, S and George, S and Sinha, T and Martínez-Costa, C and Segata, N and Zhernakova, A and Bode, L and Collado, MC},
title = {Maternal secretor status and human milk oligosaccharides influence the infant gut resistome.},
journal = {Cell reports. Medicine},
volume = {7},
number = {9},
pages = {103007},
doi = {10.1016/j.xcrm.2026.103007},
pmid = {42679805},
issn = {2666-3791},
mesh = {Humans ; *Milk, Human/metabolism/chemistry ; *Oligosaccharides/metabolism ; Female ; Infant ; Breast Feeding ; Feces/microbiology ; Trisaccharides/metabolism ; *Gastrointestinal Microbiome/genetics ; Adult ; Lactose/analogs & derivatives/metabolism ; Cesarean Section ; Drug Resistance, Microbial/genetics ; },
abstract = {The infant gut resistome is established early in life and is shaped by perinatal exposures, yet the mechanisms underlying its modulation remain unclear. We combined shotgun metagenomics of fecal samples from 57 one-month-old infants and paired milk samples from 50 mothers in the MAMI cohort to investigate the influence of maternal secretor status on early-life resistome development. Longitudinal follow-up at 6 and 12 months, and also further validation in the independent Lifelines NEXT (LLNEXT) cohort, support our findings. Cesarean section (C-section) was associated with increased antibiotic resistance gene (ARG) diversity, whereas exclusive breastfeeding reduced ARG abundance and diversity. Maternal secretor status further modified resistome composition among exclusively breastfed infants. Human milk oligosaccharide profiling identified specific glycans underlying these associations, with 2'-fucosyllactose and 6'-sialyllactose showing negative correlations with distinct ARG classes. These findings identify human milk composition as a key determinant of early-life resistome assembly and a potential target for modulating antimicrobial resistance.},
}

Humans
*Milk, Human/metabolism/chemistry
*Oligosaccharides/metabolism
Female
Infant
Breast Feeding
Feces/microbiology
Trisaccharides/metabolism
*Gastrointestinal Microbiome/genetics
Adult
Lactose/analogs & derivatives/metabolism
Cesarean Section
Drug Resistance, Microbial/genetics

@article {pmid42734665,
year = {2026},
author = {Naik, S and Kousar, H},
title = {Synergistic Biodegradation and Detoxification of High Alkaline Textile Effluent by Acinetobacter indicus KUHKSN-02 and Native Microbiome Aided Bioaugmentation.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42734665},
issn = {1432-0991},
mesh = {Biodegradation, Environmental ; *Acinetobacter/metabolism/isolation & purification/genetics ; *Wastewater/microbiology/chemistry ; *Microbiota ; *Water Pollutants, Chemical/metabolism ; Textiles ; Textile Industry ; Azo Compounds/metabolism ; Industrial Waste/analysis ; },
abstract = {Textile effluent is a chemically complex wastewater containing azo dyes, high alkalinity and recalcitrant organic pollutants. Its untreated discharge poses serious ecological risks and requires sustainable management before release. The comparative efficiency of monoculture treatment and native microbiome assisted bioaugmentation in real highly alkaline textile effluent remains insufficiently documented. This study evaluated the biodegradation and detoxification potential of Acinetobacter indicus KUHKSN-02, isolated from effluent-contaminated soil, under sterile monoculture and non-sterile native microbiome aided conditions. Results shown reduced pollution load evidenced by drastic decrease in physicochemical parameters by both monoculture (COD to 391 ± 6 mg/L and BOD to 18.73 ± 0.25 mg/L) and native bacterial community (COD to 194.3 ± 2.51 mg/L, BOD to 13.5 ± 0.36 mg/L, and TDS to 998.3 ± 6.5 mg/L), with a highest decolorization of 97.72%. FTIR analysis confirmed alterations in functional groups, while HR-LCMS Orbitrap detected Acid Red 18, Acid Orange 7, and Acid Yellow 36 in the raw effluent and in degradation intermediates such as aniline, 2-oxindole, anthranilic acid and betaine after treatment. The Oryza sativa phytotoxicity assay confirmed detoxification, with germination increasing from 0% in raw effluent to 73.33-93.33% after treatment. These findings demonstrate that native microbiome-aided bioaugmentation enhanced biodegradation and detoxification efficiency compared with monoculture treatment. Future studies should validate this approach under field conditions using metagenomic and metatranscriptomic analysis.},
}

Biodegradation, Environmental
*Acinetobacter/metabolism/isolation & purification/genetics
*Wastewater/microbiology/chemistry
*Microbiota
*Water Pollutants, Chemical/metabolism
Textiles
Textile Industry
Azo Compounds/metabolism
Industrial Waste/analysis

@article {pmid42737628,
year = {2026},
author = {Ghaffar, A and Abdul-Careem, MF},
title = {Novel Insights into Metagenomic-Assembled Genomes from Layer Chicken Housing Environment.},
journal = {International journal of molecular sciences},
volume = {27},
number = {17},
pages = {},
pmid = {42737628},
issn = {1422-0067},
support = {10036367//Egg Farmers of Alberta/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Metagenomics/methods ; *Housing, Animal ; *Metagenome ; *Bacteria/genetics/classification ; Genome, Bacterial ; Manure/microbiology ; Archaea/genetics ; Microbiota/genetics ; },
abstract = {Culture-independent techniques are playing a major role in exploring unique and novel microbial communities from complex ecosystems, leading to an outstanding impact on our basic understanding of the tree of life. Microbial communities are not extensively studied in layer chicken housing environments, particularly from the point of view of taxa carrying antimicrobial resistance genes, virulence genes and their functional potential. This study aimed to extract metagenomic-assembled genomes (MAGs) from the Illumina short-reads shotgun metagenomics sequenced data that originated from an Alberta poultry barn environment and then to study host tracking of antimicrobial resistance genes (ARGs) and the roles of genes involved in functions related to ammonia production, short-chain fatty acid (SCFA)-related pathways, sulfur metabolism, methane emission, stress and disinfectant-related pathways. A total of 251 high-quality MAGs were extracted, including 249 bacterial and two archaeal genomes from sequencing data of 30 metagenomic sequencing samples comprising 15 air and 15 manure samples collected from 15-layer farms. Interestingly 22 bacterial MAGs were not classified to species levels using GTDB-based classification. ARGs were mainly harbored by the genera Staphylococcus, Alistepes, Romboutsia, and Enterococcus. Bacteroides is a main taxon carrying ARGs in air samples. Ammonia production-related genes were mainly tracked in Staphylococcus, Ruminococcus and Corynebacterium genera. The assimilatory sulfate reduction genes responsible for sulfur metabolism and hydrogenase-related genes responsible for hydrogen cycling were traced from Staphylococcus originated from both air and manure. The current study provides characterizations of MAGs from a poultry housing environment by linking microbial taxa with virulence, resistance, and metabolic functions. The findings emphasize the role of microbiota in shaping gas emissions and AMR, with implications for poultry health and worker's safety and the ultimate aim of sustainable poultry production.},
}

Animals
*Chickens/microbiology
*Metagenomics/methods
*Housing, Animal
*Metagenome
*Bacteria/genetics/classification
Genome, Bacterial
Manure/microbiology
Archaea/genetics
Microbiota/genetics

@article {pmid42737764,
year = {2026},
author = {Kozhakhmetov, S and Vinogradova, E and Sergazy, S and Chulenbayeva, L and Kossumov, A and Kovenskiy, A and Mukhanbetzhanov, N and Ospankulova, G and Saduakhasova, S and Khamitova, D and Kamanova, S and Toimbayeva, D and Shaimenova, B and Kalemshariv, B and Aitmukhanbetov, D and Kushugulova, A},
title = {Enteral Nutrition Is Associated with a Distinct Gut Microbiome Composition and Fermentation Capacity Profile After Acute Colonic Injury in Rats.},
journal = {International journal of molecular sciences},
volume = {27},
number = {17},
pages = {},
pmid = {42737764},
issn = {1422-0067},
support = {BR22883587//Ministry of Agriculture of the Republic of Kazakhstan/ ; },
mesh = {Animals ; Rats ; *Gastrointestinal Microbiome ; *Enteral Nutrition/methods ; *Fermentation ; Male ; *Colon/injuries/microbiology/pathology ; Dextran Sulfate ; Metagenomics ; Disease Models, Animal ; *Colitis/microbiology/therapy/chemically induced ; Rats, Sprague-Dawley ; },
abstract = {Enteral nutrition (EN) is known to promote mucosal healing in inflammatory bowel disease, and multi-omics data suggest that the gut microbiome mediates its therapeutic effects. However, the impact of EN and its components on the gut community during recovery from acute epithelial injury remains incompletely understood. We used whole-genome metagenomic sequencing to investigate the effect of an EN formula based on extruded amaranth flour and pea protein on the gut microbiome in a dextran sulfate sodium (DSS) rat model of acute colonic injury. Three groups were compared, as follows: an unchallenged control (n = 9) with standard chow, a colonic injury (5% DSS; n = 9) group with standard chow, and a colonic injury (5% DSS; n = 9) group with EN. Injury was confirmed histologically (median MCHI score was 2, indicating epithelial damage without inflammation). DSS caused significant weight loss. Animals receiving EN regained baseline weight faster, by day 14, whereas animals on standard chow achieved recovery only by day 21. Differences in energy intake should be further investigated to validate the effect of EN on body weight recovery. At day 21, both injury groups demonstrated higher relative abundances of Bacteroidaceae and Erysipelotrichaceae, including the mucin-degrader Allobaculum mucilyticum, compared with the control group. Conversely, Lactobacillus abundance, notably Lactobacillus acidophilus, was higher in the EN group than in both other groups, as was the inferred capacity for lactate-producing fermentation. These findings suggest that EN is associated with a distinct microbial composition and inferred metabolic profile during the post-injury period, with lactobacilli as one of the potential mediators of its effects.},
}

Animals
Rats
*Gastrointestinal Microbiome
*Enteral Nutrition/methods
*Fermentation
Male
*Colon/injuries/microbiology/pathology
Dextran Sulfate
Metagenomics
Disease Models, Animal
*Colitis/microbiology/therapy/chemically induced
Rats, Sprague-Dawley

@article {pmid42737961,
year = {2026},
author = {Tang, J and Li, N and Zhou, W and Pan, R and Suo, L and Li, B and Zhao, H},
title = {Spatially Specialized Nasopharynx-Rectal Microbiomes in Golden Snub-Nosed Monkeys (Rhinopithecus roxellana).},
journal = {Biology},
volume = {15},
number = {17},
pages = {},
pmid = {42737961},
issn = {2079-7737},
support = {32270536//National Natural Science Foundation of China/ ; 32371563//National Natural Science Foundation of China/ ; //Shaanxi Special Support Plan for High-level Talents/ ; 32672006//National Natural Science Foundation of China/ ; 2024P-02, 2025k-13, 2025K-32, 2026K-32//Special Foundation of Shaanxi Academy of Sciences, China/ ; 2026RS-CXTD-73//Shaanxi Provincial Key Science and Technology Innovation Team/ ; 2024JC-YWGCZ-05, 2024JC-YBQN-0242, 2025JC-YWGCZ-05, 2025JC-GXPT-037//Shaanxi Key Research and Development Program/ ; },
abstract = {BACKGROUND: Understanding the nasopharyngeal (NAS) and rectal (INT) microbiomes is critical to maintain host health. However, their functional roles in shaping microbial network structure and niche differentiation remain unexplored in most animal species, especially endangered primates. Here, we compared the NAS and INT microbiomes of golden snub-nosed monkeys (Rhinopithecus roxellana) using full-length 16S rRNA amplicon sequencing and metagenomics, focusing on taxonomic composition, functional profiles (KEGG, CAZy, PHI), and microbial co-occurrence networks.

RESULTS: Our results indicate that microbial community structure and diversity (Shannon evenness) differ significantly between the two niches. Taxonomically, both sequencing approaches consistently show that, at the relative-abundance level, NAS is dominated by genera such as Dolosigranulum and Vibrio, whereas the INT is characterized by Campylobacter, Helicobacter, and Aerococcus. Notably, metagenomic analysis indicates a relatively high abundance of potential pathogens, including Helicobacter pylori and Chlamydia psittaci. LEfSe analysis shows Dolosigranulum and Campylobacter are key microbial markers for the NAS and INT niches, respectively. KEGG pathway analysis reveals that the NAS microbiome is enriched in valine/leucine/isoleucine degradation and glutathione metabolism, while the INT microbiome is enriched in amino sugar and nucleotide sugar metabolism and ribosome pathways. At the CAZy level, all 29 differentially abundant families (e.g., GH13_29, GH103, AA3_2) were enriched in the NAS. Distinct pathogen-host interaction profiles further reflect niche-specific adaptations. Exploratory Spearman-based co-occurrence networks (in which no genus-CAZy edge survived Benjamini-Hochberg (FDR) correction) linked core commensals to KEGG pathways and CAZy families (e.g., GT35, GH0). In the INT, Campylobacter and Helicobacter form high-connectivity modules associated with pathways such as those involving the two-component system and ABC transporters.

CONCLUSIONS: The nasopharyngeal and rectal microbiomes in golden snub-nosed monkeys differ not only taxonomically but also functionally, exhibiting clear spatially specialized functional differentiation. Given the small sample size (n = 8), these findings provide preliminary evidence for niche-specific microbial and functional partitioning and suggest that the nasopharynx may harbor a relatively high abundance of potential zoonotic pathogens. This study provides a basis for further exploration with a larger sample size.},
}

@article {pmid42738866,
year = {2026},
author = {Jiménez-Ortega, RF and Ortega-Meléndez, AI and Montes-García, JF and Negrete-Abascal, E and Patiño, N and Ramírez-Salazar, EG and Sevilla-Montoya, R and Velázquez-Cruz, R and Hidalgo-Bravo, A},
title = {Genome-Resolved Functional Profiling of Osteoporosis-Associated Gut Bacteria Highlights Putative Metabolic and Immunogenic Signatures of the Gut-Bone Axis.},
journal = {Cells},
volume = {15},
number = {17},
pages = {},
pmid = {42738866},
issn = {2073-4409},
mesh = {*Osteoporosis/microbiology/immunology/genetics/metabolism ; Humans ; *Bone and Bones/metabolism/microbiology ; *Gastrointestinal Microbiome/genetics ; *Genome, Bacterial ; *Bacteria/genetics/metabolism/classification ; },
abstract = {The gut microbiota has emerged as a potential regulator of bone metabolism, but the genome-encoded functional repertoire of osteoporosis-associated gut bacteria remains insufficiently characterized. This study performed in silico functional profiling of gut bacterial taxa associated with osteoporosis, low bone mineral density, or comparator bone-related phenotypes. Twenty candidate taxa were selected from evidence in the human microbiome and represented by 26 curated bacterial reference genomes. Genome-wide annotations were used to map predicted gut-bone axis signatures, carbohydrate-active enzyme (CAZyme) repertoires, selected Kyoto Encyclopedia of Genes and Genomes pathways, and gutSMASH-predicted metabolic gene clusters. Functional burdens were normalized as hits per 1000 annotated proteins and integrated into metabolic, immunogenic, CAZyme, KEGG, and metabolic gene cluster profiles. Twelve predicted gut-bone axis signatures were identified, comprising 3337 primary candidate protein hits and a strict high-confidence subset of 2497 hits. Dominant signatures included vitamin B12/cobalamin metabolism, folate/one-carbon metabolism, peptidoglycan/cell-wall biosynthesis, and short-chain fatty acid-related functions. Dialister invisus, Dialister succinatiphilus, Megamonas funiformis, and Megamonas hypermegale showed the strongest normalized predicted gut-bone axis signal. These hypothesis-generating findings prioritize microbial metabolic and immunogenic features for future metagenomic, metabolomic, and experimental validation studies.},
}

*Osteoporosis/microbiology/immunology/genetics/metabolism
Humans
*Bone and Bones/metabolism/microbiology
*Gastrointestinal Microbiome/genetics
*Genome, Bacterial
*Bacteria/genetics/metabolism/classification

@article {pmid42738945,
year = {2026},
author = {Pawłowski, P and Kościołek, O and Jeżak, M and Jakubik, K and Kościołek, A and Samardakiewicz, M},
title = {The Gut-Brain Axis and Dietary Patterns in Shaping Long-Term Neurocognitive and Psychosocial Outcomes in Adolescent and Young Adult Survivors of Childhood Cancer: A Systematized Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42738945},
issn = {2072-6643},
mesh = {Humans ; Adolescent ; *Cancer Survivors/psychology ; *Gastrointestinal Microbiome/physiology ; Young Adult ; *Diet ; *Brain-Gut Axis/physiology ; *Neoplasms/psychology ; Dysbiosis ; Child ; *Brain ; },
abstract = {Background: The dynamic advancement of pediatric hemato-oncology and intensified therapeutic protocols have significantly increased survival rates while simultaneously highlighting the challenge of long-term treatment complications. Within the cohort of adolescent and young adult (AYA) survivors, delayed neurocognitive deficits, often manifesting as the chemobrain phenotype, and psychosocial disorders constitute a particularly substantial burden. Contemporary neurogastroenterological evidence indicates a fundamental role of persistent dysbiosis and gut-brain axis dysfunction in the pathogenesis of these alterations. This review aims to critically synthesize translational evidence elucidating the impact of iatrogenic gut microbiota damage and modifiable dietary patterns on the development of long-term neurocognitive sequelae in survivors of early childhood cancer. Methods: A systematized narrative review was conducted in accordance with the SANRA guidelines by integrating data from in vivo models and observational studies. A comprehensive literature search across the PubMed, Embase, Cochrane Central, Scopus, and Web of Science databases up to June 2026 was performed utilizing the Population, Exposure, and Outcomes (PEO) framework. Results: Oncological therapies, including myeloablative conditioning and broad-spectrum antibiotic therapy, induce a microbial scar phenomenon characterized by the depletion of commensal Firmicutes in favor of resistant pathobionts. The subsequent decline in the synthesis of neuroprotective short-chain fatty acids (SCFAs) alongside the pathological activation of the kynurenine pathway disrupts central nervous system homeostasis. Translocation of lipopolysaccharides (LPSs) across the compromised intestinal barrier generates systemic inflammation recognized as inflammaging, which, in turn, stimulates neurotoxic microglial hyperreactivity. This pathophysiological cascade is accelerated by a pro-inflammatory Western diet, whereas anti-inflammatory interventions such as the MIND diet and postbiotics demonstrate measurable restorative potential. Conclusions: The pathophysiology of delayed neurotoxicity is largely a consequence of systemic neuroinflammation driven by intestinal dysbiosis. Implementing individualized dietary and microbiome-targeted strategies into survivorship care protocols constitutes a crucial direction for clinical prophylaxis. Validating their clinical efficacy in the AYA population necessitates prospective randomized controlled trials integrated with shotgun metagenomic sequencing.},
}

Humans
Adolescent
*Cancer Survivors/psychology
*Gastrointestinal Microbiome/physiology
Young Adult
*Diet
*Brain-Gut Axis/physiology
*Neoplasms/psychology
Dysbiosis
Child
*Brain

@article {pmid42738989,
year = {2026},
author = {Nyambal, T and Lkhamsuren, K and Hübner, A and Khuygaa, SO and Bromage, S and Stahl, R and Rest, M and Reichhardt, B and Battulga, A and Odonchimed, S and Dambadarjaa, D and Tulgaa, K and Warinner, C and Tsolmon, S},
title = {Distinctive Patterns of Gut Bifidobacterium Diversity in Mongolian Adults: Regional Variation and Dairy Intake Associations.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42738989},
issn = {2072-6643},
support = {804884/ERC_/European Research Council/International ; },
mesh = {Humans ; *Bifidobacterium/classification/genetics/isolation & purification ; Mongolia ; Adult ; Male ; Female ; *Dairy Products ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Diet ; Middle Aged ; Young Adult ; },
abstract = {Background/Objectives: Despite increasing interest in the human gut microbiome, particularly in Bifidobacterium, studies focusing on traditionally living populations with high habitual dairy consumption remain limited. This study investigated species-level diversity, abundance, and regional variation of Bifidobacterium among healthy Mongolian adults and contextualized these findings within a global comparative framework. Methods: A total of 100 healthy adults were recruited from four Mongolian regions. Fecal samples were analyzed using species-resolved shotgun metagenomics, and dietary intake was assessed through a standardized food frequency questionnaire. Alpha- and beta-diversity metrics, differential abundance tests, and diet-microbe correlations were performed on members of the Bifidobacterium species. To assess the broader significance of the Mongolian Bifidobacterium profile, Shannon diversity was further compared against a curated global dataset comprising 1286 healthy adults from 29 countries using harmonized bioinformatic and statistical pipelines. Results: Shannon diversity within the Bifidobacterium genus was significantly higher in nomadic Mongolians, particularly those from Khuvsgul and Dundgobi, and strong geographic structuring was observed in beta-diversity analyses (PERMANOVA, p < 0.001). Nomadic populations showed higher relative abundances of B. adolescentis and B. angulatum, whereas B. pseudocatenulatum predominated in Ulaanbaatar. Although overall Bifidobacterium abundance was lowest in Bulgan, B. longum remained the dominant species in this region. Spearman correlation analysis with false discovery rate correction identified significant associations between dairy intake and specific Bifidobacterium species. Homemade yogurt and traditional dairy intake were positively associated with B. angulatum. B. catenulatum was positively associated with homemade yogurt, traditional dairy, and total fermented dairy intake, whereas factory milk intake was negatively associated with B. angulatum but positively associated with B. pseudocatenulatum. Mongolia ranked among the top eight of 30 countries for Bifidobacterium Shannon diversity though total Bifidobacterium abundance showed substantial inter-individual and regional variation. Conclusions: Mongolian adults exhibit relatively high Bifidobacterium diversity at both national and global scales. Traditional dairy consumption was associated with species-specific variation in Bifidobacterium composition, supporting the contribution of dietary practices to regional gut microbiota patterns.},
}

Humans
*Bifidobacterium/classification/genetics/isolation & purification
Mongolia
Adult
Male
Female
*Dairy Products
Feces/microbiology
*Gastrointestinal Microbiome
*Diet
Middle Aged
Young Adult

@article {pmid42739046,
year = {2026},
author = {Szabó, J and Maróti, G and Solymosi, N and Andrásofszky, E and Tuboly, T and Bersényi, A and Bruckner, G and Fébel, H},
title = {Effects of Dietary Glucose, Fructose, and Monosaccharide-to-Lard Energy Ratios on Cecal Microbiota Composition and Ecological Organization in Rats.},
journal = {Nutrients},
volume = {18},
number = {17},
pages = {},
pmid = {42739046},
issn = {2072-6643},
mesh = {Animals ; *Fructose/administration & dosage/pharmacology ; *Cecum/microbiology ; Male ; *Glucose/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Monosaccharides/administration & dosage/pharmacology ; *Dietary Fats/administration & dosage ; Rats, Sprague-Dawley ; *Dietary Carbohydrates/administration & dosage ; Bacteria/classification ; Diet ; Energy Intake ; },
abstract = {Background: Although dietary fat and carbohydrates are major determinants of gut microbiota composition, their interactive effects across changing dietary monosaccharide-to-lard energy ratios remain incompletely understood. This study descriptively examined treatment-level cecal microbiome profiles across dietary gradients in which lard (L) was progressively replaced with glucose (G) or fructose (F). Methods: A carbohydrate-free, lard-rich control diet was formulated, and lard was progressively replaced with glucose or fructose while maintaining a constant protein-to-energy ratio. Cecal contents from eight rats per dietary group were pooled in equal amounts, yielding one composite microbiome sample per treatment. Pooled samples were characterized by shotgun metagenomic sequencing. Sequencing/classified read counts (CRs) and relative abundance (RA) were treated as complementary sequencing-derived representations rather than measures of absolute bacterial abundance. Microbiome outcomes were interpreted descriptively at the treatment level. Results: Across the pooled treatment profiles, CRs and RA showed non-linear patterns and did not consistently change in parallel, providing complementary descriptions of treatment-level taxonomic responses. CR patterns indicated a combined effect of L and monosaccharide content, with several mixed L-monosaccharide diets showing lower CRs than both the L6.03 reference and the lard-free endpoints. Differences between the G and F series were most apparent at low L and high monosaccharide levels, particularly under lard-free conditions, although their magnitude and direction varied among taxa. Hierarchical clustering and exploratory correlation networks provided complementary descriptions of treatment-level community organization. Conclusions: The pooled treatment-level microbiome profiles revealed non-linear responses to changing dietary L-monosaccharide composition, with CRs and RA providing partly different information on taxonomic patterns. Differences between the G and F series were most apparent at low L and high monosaccharide levels, particularly under lard-free conditions.},
}

Animals
*Fructose/administration & dosage/pharmacology
*Cecum/microbiology
Male
*Glucose/administration & dosage/pharmacology
*Gastrointestinal Microbiome/drug effects
Rats
*Monosaccharides/administration & dosage/pharmacology
*Dietary Fats/administration & dosage
Rats, Sprague-Dawley
*Dietary Carbohydrates/administration & dosage
Bacteria/classification
Diet
Energy Intake

@article {pmid42740607,
year = {2026},
author = {Lee, J and Minot, S and Dey, N},
title = {Pangenome analysis reveals both niche-specific "specialists" and microbial "side hustlers" in colorectal cancer microbiomes.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2728331},
doi = {10.1080/19490976.2026.2728331},
pmid = {42740607},
issn = {1949-0984},
mesh = {*Colorectal Neoplasms/microbiology ; Humans ; Phylogeny ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; },
abstract = {The gut microbiome is reproducibly implicated in colorectal cancer (CRC), yet the inter-study and interpersonal variability of certain species associations suggests that CRC microbiomes may be defined by convergent functional states achievable by phylogenetically diverse organisms. Distinguishing lineage-conserved "specialists" from taxonomically diverse "side hustlers"-organisms whose shared functional traits are dispersed across phylogenetically distant lineages-offers complementary translational insights: "specialists" are primary candidates for lineage-targeted biomarkers and inhibitors, while the shared functional architecture of "side hustlers" may reveal high-priority potential therapeutic targets robust to inter-individual variability. Here, we quantify phylogenetic coherence (monophyly) of 3,711 co-associated gene bins (CAGs) across 13 bacterial species and evaluate CRC associations across three independent cohorts, identifying hundreds of CAGs associated with CRC or health across a spectrum of monophyly scores, indicating that both states harbor a mixture of "specialist" and "side hustler" gene content. Strikingly, in Faecalibacterium prausnitzii-a species with a complex relationship to CRC-health-associated CAGs exhibited significantly higher monophyly scores than CRC-associated CAGs, consistent with health-linked traits being lineage-conserved while CRC-linked traits behave as polyphyletically distributed, potentially mobile "side hustlers." Across multiple CRC-associated species, we observe functional convergence in gene bins encoding Type IV secretion systems (T4SS), TonB-dependent receptors, and RagB/SusD nutrient uptake proteins. Fusobacterium animalis strains encode T4SS elements across bins with variable phylogenetic origins, representing simultaneous "specialist" and "side hustler" strategies within a single species. Pairwise interaction analysis further reveals synergistic interspecies associations, including co-occurrence of F. animalis and Clostridium scindens gene bins associated with a CRC probability of > 90%, suggesting that microbial "side hustlers" may amplify oncogenic risk through ecological interactions invisible to species-level analysis. These findings provide proof-of-principle that an ecological and evolutionary lens on the CRC microbiome can identify shared functional vulnerabilities and lineage-specific targets for microbiome-based cancer prevention.},
}

*Colorectal Neoplasms/microbiology
Humans
Phylogeny
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome/genetics

@article {pmid42741868,
year = {2026},
author = {Dong, X and Hu, X and Hu, K and Li, Z and Wang, W},
title = {Nutrient Transfer Hypothesis for the Fluctuation and Regional Variation of Microbial Diversity in the Pacific Ocean.},
journal = {Environmental microbiology},
volume = {28},
number = {9},
pages = {e70427},
doi = {10.1111/1462-2920.70427},
pmid = {42741868},
issn = {1462-2920},
support = {25FV0CWZ02//Fujian Ocean Innovation Center/ ; 42577318//National Natural Science Foundation of China/ ; T2017002//Fundamental Research Funds for the Central University and 111 Program/ ; },
mesh = {Pacific Ocean ; *Biodiversity ; *Seawater/microbiology/chemistry ; *Nutrients/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Food Chain ; Metagenomics ; },
abstract = {Microbial diversity affects marine biogeochemical cycles and sustainability. However, the processes and feedbacks that control the spatial and temporal trends in species diversity and functional gene diversity remain largely unknown at the global marine scale. We analysed 1582 marine metagenomic samples and 19 variables related to marine climate and microbial community dynamics. Over the past 12 years, marine microbial species diversity has significantly decreased across the surface ocean, especially in the Pacific. The greatest decrease reached 24.29% in the central region of the North Pacific Ocean (NPO). We propose a food chain-based nutrient transfer hypothesis in which a decrease in grazing intensity is associated with a decrease in microbial diversity. This hypothesized relationship was further examined using 27 years of independent time series data from a Pacific site. The Pacific Ocean presented high sensitivity to grazing intensity coupled with environmental fluctuations of < 5%, in which species diversity in the NPO and South Pacific Ocean (SPO) regions changed from -9.62% to 13.02% and from -8.38% to 15.03%, respectively. The incorporation of nutrient transfer concepts to reduce the unpredictable uncertainty in marine biogeochemical cycles and ecological stability related to microbial diversity is urgent, especially in the vulnerable Pacific Ocean.},
}

Pacific Ocean
*Biodiversity
*Seawater/microbiology/chemistry
*Nutrients/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Food Chain
Metagenomics

@article {pmid42742644,
year = {2026},
author = {Dhiman, K and Devi, M and Kumar, A and Pandey, SS and Dkhar, J},
title = {Characterization of culturable endophytes and microbial communities in the rhizosphere and pitcher fluid of the carnivorous plant Nepenthes khasiana.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42742644},
issn = {1432-072X},
support = {MLP-202//Council of Scientific and Industrial Research, India/ ; SRG/2020/001139 (GAP 273) and EEQ/2022/000015 (GAP 318)//Science and Engineering Research Board/ ; },
mesh = {*Rhizosphere ; *Endophytes/isolation & purification/classification/genetics ; *Bacteria/isolation & purification/classification/genetics ; *Fungi/isolation & purification/classification/genetics ; Soil Microbiology ; Plant Roots/microbiology ; *Microbiota ; Phylogeny ; *Carnivorous Plant/microbiology ; Metagenomics ; *Caryophyllales/microbiology ; },
abstract = {Endophytes colonize plant tissues through roots and shoots without causing harm and can move throughout the plant via its vascular system. However, little is known about culturable endophytes, particularly bacteria, in pitcher plants, and their possible entry through pitcher fluid remains unexplored. To address this gap, we isolated endophytes from the pitcher plant Nepenthes khasiana, and performed metagenomic analysis of its rhizospheric soil and pitcher fluid, from which bacteria and fungi were also isolated, to investigate the possible origin of these endophytes. We found that culturable endophytic bacteria were predominantly associated with roots and seeds, whereas endophytic fungi were more abundant across the N. khasiana pitcher. Although most endophytes were restricted to specific tissues, some exhibited a broader distribution across nearly the entire plant. Several OTUs from the rhizospheric soil matched endophytes at the genus level, including some that were also detected in the pitcher fluid. Specifically, three bacterial genera - Enterobacter, Staphylococcus and Bacillus - and one fungal genus, Cladosporium, detected in the pitcher fluid, matched the isolated endophytes. These findings suggest that endophytes in N. khasiana most likely originate from the rhizosphere, with possible migration into the pitcher fluid.},
}

*Rhizosphere
*Endophytes/isolation & purification/classification/genetics
*Bacteria/isolation & purification/classification/genetics
*Fungi/isolation & purification/classification/genetics
Soil Microbiology
Plant Roots/microbiology
*Microbiota
Phylogeny
*Carnivorous Plant/microbiology
Metagenomics
*Caryophyllales/microbiology

@article {pmid41175312,
year = {2026},
author = {Miller, BC and Haggler, JA and Chaudhari, DS and Shukla, R and Kumar, V and Mishra, SP and Masternak, MM and Holland, P and Labyak, C and Golden, A and Dangiolo, M and Arikawa, AY and Kociolek, J and Fraser, A and Williams, C and Agronin, M and Aymat, M and Pledger, W and Yadav, H and Jain, S},
title = {Gut microbiome signatures predict cognitive impairment in older cancer survivors.},
journal = {GeroScience},
volume = {48},
number = {4},
pages = {5575-5596},
pmid = {41175312},
issn = {2509-2723},
support = {22A17//Florida Department of Health/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/physiology ; Aged ; *Cognitive Dysfunction/microbiology/etiology ; Male ; *Cancer Survivors ; *Neoplasms ; Middle Aged ; },
abstract = {Cancer treatments are improving, and the population of cancer survivors is steadily increasing. However, many survivors experience long-term side effects, including chemobrain and other age-related geriatric disorders like cognitive impairment (CI), severely impacting their quality of life. Emerging studies suggest that the gut microbiome plays a central role in cognitive health. However, the long-term effects of cancer treatments on the microbiome, and how these changes impact cognitive health in survivors, remain largely unknown. Shotgun metagenomic data from 150 older adults (≥ 60 years old, including 49 cancer survivors and 101 controls) from the Microbiome in Aging Gut and Brain (MiaGB) consortium revealed that Tyzzerella, Eggerthella lenta, and Bacteroides vulgatus were specific markers of the cancer survivor gut and could differentiate cancer survivorship in this cohort. Microbiome signatures were distinct in cancer survivors with CI compared to those without and differed from those seen in non-cancer individuals with CI. Bacterial taxa including Streptococcus thermophilus and Firmicutes bacterium CAG 114 were significantly reduced in cancer survivors and strongly associated with CI. Importantly, metabolic pathway analysis revealed that microbial neurotransmitter synthesis was significantly depleted in the gut of cancer survivors, suggesting a mechanistic link to CI. Our results suggest that microbiome signatures predict cancer survivorship and the risk of CI in older adults, potentially by depleting neurotransmitter synthesis in the gut. These findings aid in establishing the role of the microbiome in predicting cancer survivorship and CI risk, which is valuable in the development of novel therapies to support the growing population of cancer survivors.},
}

Humans
Female
*Gastrointestinal Microbiome/physiology
Aged
*Cognitive Dysfunction/microbiology/etiology
Male
*Cancer Survivors
*Neoplasms
Middle Aged

@article {pmid42733080,
year = {2026},
author = {Li, C and Wang, Y and Zhou, ASK and Pan, X and Zhu, Y and Zhang, X and Chen, T and Xiong, A and Ho, YW and Liu, J and Zhou, Z and Wang, J and Adyel, TM and Fang, JK and Bank, MS and Rillig, MC and Jin, LN},
title = {Unraveling the coastal marine plastisphere archaeome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42733080},
issn = {2041-1723},
mesh = {*Archaea/genetics/classification ; *Seawater/microbiology ; Crenarchaeota/genetics/classification ; Phylogeny ; Euryarchaeota/genetics/classification ; Metagenomics ; Ecosystem ; Biodiversity ; Methane/metabolism ; },
abstract = {Plastic pollution has created an expanding anthropogenic microbial niche, the plastisphere, raising questions about microbial ecology and associated impacts. Archaea, the third domain of life with fundamental ecological and evolutionary significance, remain poorly understood in this habitat. Here, using paired plastic debris and bulk-water samples from coastal marine ecosystems, key archaeal habitats increasingly threatened by plastic pollution, we characterize the plastisphere archaeome through archaeal amplicon sequencing and metagenomics. We show that the archaeome is significantly reshaped in the plastisphere, exhibiting higher taxonomic diversity, greater community heterogeneity, and selective enrichment of Euryarchaeota and Crenarchaeota. Archaeal genes involved in methane, nitrogen, and sulfur cycling are enriched in the plastisphere. Taxonomic and functional divergence between the plastisphere and bulk water increases with anthropogenic chemical stress. These findings suggest that plastic pollution could alter marine archaeal diversity, biogeography, and biogeochemical potential, extending understanding of plastisphere impacts to the archaeal domain.},
}

*Archaea/genetics/classification
*Seawater/microbiology
Crenarchaeota/genetics/classification
Phylogeny
Euryarchaeota/genetics/classification
Metagenomics
Ecosystem
Biodiversity
Methane/metabolism

@article {pmid42734183,
year = {2026},
author = {Chen, W and Pan, Y and Chen, M and Zhou, S and Liu, X and Sun, M and Yang, Z and Zhi, Y},
title = {Integrated metagenomic and metabolomic analysis identifies severity-specific inflammatory and metabolic signatures in post-stroke depression.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2726620},
doi = {10.1080/19490976.2026.2726620},
pmid = {42734183},
issn = {1949-0984},
mesh = {Humans ; *Stroke/complications/metabolism ; Metabolomics ; Metagenomics ; *Depression/metabolism/etiology/microbiology ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Inflammation/metabolism ; Middle Aged ; Aged ; Cytokines/blood ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; Biomarkers/blood ; },
abstract = {Post-stroke depression (PSD) is a common complication that significantly impacts patient prognosis. This study aimed to systematically characterize the associations among gut microbial ecology, metabolic profiles, and inflammatory responses across different severities of PSD. We conducted metagenomic sequencing, non-targeted metabolomics, and serum cytokine analysis (IL-1β, IL-6, IL-10, IL-18, TNF-α, IFN-γ, and CRP) in 91 patients with varying degrees of PSD and non-PSD controls. Bioinformatics analyzes were employed to construct multi-omics association networks and machine learning models. Results indicated that PSD patients exhibited significantly increased gut microbiota alpha-diversity, suggesting dysbiosis. Mild depression was characterized by compensatory neural signaling activation, whereas the moderate depression group exhibited abnormalities in tryptophan/indole metabolism, oxidative stress-related metabolic imbalances, and functional decompensation. Further analyzes suggested that Alistipes, Blautia_A, Evtepia gabavorous, and Lachnospira were associated with inflammatory features, GABA-related metabolic alterations, aromatic amino acid/indole metabolism, and lipid-amino acid metabolism, respectively. Under a more rigorous 10-fold cross-validation framework, the performance of different multi-omics combination models showed heterogeneity; however, some combinations still demonstrated superior discriminatory ability compared to single-omics approaches. This study provides multi-omics clues suggesting associations between different PSD severity levels and features such as increased Alistipes abundance, reduced antioxidant capacity, and altered tryptophan metabolism. It provides candidate biomarker combinations that may be useful for PSD stratification and suggests that the gut microbiome may represent a potential target for future PSD intervention. In summary, PSD may be associated with dynamic alterations along the "gut-brain-inflammation-metabolism" axis. These findings provide integrated evidence for microbial, metabolic, and inflammatory abnormalities across different PSD severity levels, but still require validation in larger samples, longitudinal cohorts, and mechanistic studies.},
}

Humans
*Stroke/complications/metabolism
Metabolomics
Metagenomics
*Depression/metabolism/etiology/microbiology
Female
Multiomics
Male
*Gastrointestinal Microbiome
Inflammation/metabolism
Middle Aged
Aged
Cytokines/blood
Bacteria/classification/genetics/isolation & purification
Dysbiosis/microbiology
Biomarkers/blood

@article {pmid42250066,
year = {2026},
author = {Fu, Y and Jiang, H and Peng, D and Bai, Z and Wang, S and Liu, H and Zhang, W and Shang, W},
title = {Fecal Microbiome and Serum Metabolome Profiles of the Ovarian Failure Mouse Model.},
journal = {Applied biochemistry and biotechnology},
volume = {198},
number = {9},
pages = {6906-6925},
pmid = {42250066},
issn = {1559-0291},
support = {KFKT-2024-KY-019//the Key Project Program of the 2024 Scientific Research Fund, Chinese Association of Rehabilitation Medicine/ ; },
mesh = {Animals ; Female ; *Metabolome ; *Feces/microbiology ; Mice ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; Disease Models, Animal ; },
abstract = {Ovarian dysfunction is closely associated with reproductive aging and systemic metabolic disturbances; however, the underlying microbial and metabolic mechanisms remain unclear. In this study, we analyzed fecal microbiome and serum metabolome profiles in young (7-week-old) and aged (12-month-old) female C57BL/6J mice using shotgun metagenomic sequencing and untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry. Microbial and metabolic data were processed using QIIME2, HUMAnN, and MetaboAnalyst 5.0. Differential taxa and metabolites were identified using DESeq2 and linear discriminant analysis effect size (LEfSe), and their associations were evaluated using Spearman's correlation analysis. Our results showed that aged mice exhibited significant alterations in gut microbiota composition, including a decreased abundance of Firmicutes and an increased abundance of Bacteroidetes, along with enrichment of the genera Alistipes and Akkermansia. Serum metabolomic profiling identified 246 differential metabolites, primarily involved in amino acid and energy metabolism pathways. Integrated analysis revealed that tryptophan metabolism represents a key pathway linking microbial dysbiosis with systemic metabolic alterations. Notably, enriched microbial taxa, including Akkermansia muciniphila and species within the genus Alistipes, were strongly correlated with tryptophan-related metabolites. These findings indicate that ovarian failure is associated with coordinated alterations in the gut microbiome and serum metabolome, converging on tryptophan metabolism. This study provides new insights into host-microbiome-metabolite interactions in ovarian failure and highlights potential microbial and metabolic targets for therapeutic intervention.},
}

Animals
Female
*Metabolome
*Feces/microbiology
Mice
Mice, Inbred C57BL
*Gastrointestinal Microbiome
Disease Models, Animal

@article {pmid42575184,
year = {2026},
author = {Zha, Y and Wang, Z and Sun, W and Meng, J and Liu, Y and Wang, B},
title = {Metagenomic insights into biogeochemical functional potential and resistome dynamics of PM2.5 microbial communities.},
journal = {Environmental research},
volume = {307},
number = {},
pages = {125444},
doi = {10.1016/j.envres.2026.125444},
pmid = {42575184},
issn = {1096-0953},
mesh = {*Particulate Matter/analysis ; Metagenomics ; *Bacteria/genetics ; *Microbiota ; *Air Pollutants/analysis ; *Air Microbiology ; *Metagenome ; },
abstract = {Atmospheric particulate matter harbors diverse microorganisms, yet their functional potential in biogeochemical cycling and the associated risks of resistome remain poorly understood. Here, we performed metagenomic sequencing on PM2.5 samples collected across four months to unravel the microbial genetic repertoire involved in methane, nitrogen, phosphorus, and sulfur cycling, as well as the resistome, and pathogen composition. A broad range of functional genes was detected for each biogeochemical cycle, with more than 65% of gene subtypes shared across all months, indicating conserved functional signatures. In contrast, more than 80% of the resistome showed temporal variation in abundance, with the lowest richness observed in March. Temporal shifts were also observed in resistome composition, with several resistance determinants reaching higher abundances in April and May. Network analysis indicated frequent co-occurrence among several pathogenic and opportunistic taxa. Contig-based profiling identified 51 potential pathogenic taxa, including 32 human- or animal-associated taxa. In addition, both PM10 and PM2.5 concentrations were associated with pathogen abundance and functional gene richness (e.g., antibiotic resistance genes and virulence factors). Together, this metagenomic survey suggests contrasting temporal patterns between conserved biogeochemical functional potential and more variable resistome-related traits in PM2.5 microbial communities. While constrained by limited temporal coverage and sample size, this study provides preliminary insights into the ecological and potential public health relevance of airborne microbial communities in urban environments.},
}

*Particulate Matter/analysis
Metagenomics
*Bacteria/genetics
*Microbiota
*Air Pollutants/analysis
*Air Microbiology
*Metagenome

@article {pmid42696749,
year = {2026},
author = {Cisneros-Martínez, AM and Flores Varela, MÁ and González-Serrano, F and Rebollar, EA},
title = {Exploring the ecological drivers of bacteriophage diversity and functional viral potential in the skin of the axolotl Ambystoma altamirani.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {9},
pages = {},
doi = {10.1093/femsec/fiag103},
pmid = {42696749},
issn = {1574-6941},
support = {//Secretaría de Ciencia/ ; },
mesh = {Animals ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Skin/microbiology/virology ; Skin Microbiome ; Metagenome ; *Ambystoma/microbiology/virology ; Bacteria/virology/classification/genetics ; Microbiota ; Batrachochytrium ; Metagenomics ; Biodiversity ; },
abstract = {Bacteriophages play important roles in shaping microbial community dynamics across diverse environments. In the amphibian skin, most microbiome studies have focused on bacteria and their interactions with the fungus Batrachochytrium dendrobatidis (Bd), leaving other microbial components, including viruses, largely unexplored. Here, we present the first characterization of the viral community in the amphibian skin microbiome, focusing on ecological drivers of bacteriophage diversity and functional potential in the axolotl Ambystoma altamirani. Using public shotgun metagenomes, we found that the viral fraction was dominated by bacteriophages of the class Caudoviricetes. Bacteriophage diversity was significantly associated with local physicochemical parameters at the time of sampling, and showed a strong positive correlation with bacterial diversity, whereas no significant associations were detected with the presence of Bd. In addition, seasonality influenced the composition and properties of bacteria-bacteriophage co-abundance networks. Functional annotation of assembled bacteriophage sequences revealed a diverse functional potential, including putative auxiliary metabolic genes, superinfection exclusion, toxin-antitoxin, and virulence factors. Overall, these findings highlight the ecological relevance of bacteriophages in amphibian skin microbiomes and underscore the need for further studies on their role in the amphibian host's health.},
}

Animals
*Bacteriophages/genetics/classification/isolation & purification/physiology
*Skin/microbiology/virology
Skin Microbiome
Metagenome
*Ambystoma/microbiology/virology
Bacteria/virology/classification/genetics
Microbiota
Batrachochytrium
Metagenomics
Biodiversity

@article {pmid42729502,
year = {2026},
author = {Tagele, SB and Kassa, AS and Tilahun, S and Zegeye, WA},
title = {Editorial: Harnessing genomics to revolutionize plant disease management and preservation of soil biodiversity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1901274},
doi = {10.3389/fmicb.2026.1901274},
pmid = {42729502},
issn = {1664-302X},
}

@article {pmid42729922,
year = {2026},
author = {Cong, J and Xu, W and Zhang, Y and Ding, X and Cui, S and Chi, X and Yang, X},
title = {Gut microbiota dynamics and metabolic pathways associated with bleomycin-induced pulmonary fibrosis progression.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21693},
doi = {10.7717/peerj.21693},
pmid = {42729922},
issn = {2167-8359},
mesh = {Animals ; *Bleomycin ; *Pulmonary Fibrosis/chemically induced/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome ; Mice ; Disease Progression ; *Metabolic Networks and Pathways ; Disease Models, Animal ; Mice, Inbred C57BL ; Feces/microbiology ; Male ; Lung/pathology ; },
abstract = {BACKGROUND: Pulmonary fibrosis (PF) is a progressive respiratory disease characterized by epithelial injury, aberrant repair and excessive extracellular matrix deposition. Although the gut-lung axis is increasingly implicated in respiratory disorders, stage-resolved characterization of gut microbiota taxonomic and functional potential during PF development is limited.

METHODS: We established a bleomycin-induced murine PF model and performed cross-sectional shotgun metagenomic sequencing of fecal samples from separate cohorts at three defined stages: baseline (control), day 7 (early fibrosis; M7), and day 14 (established fibrosis; M14). Microbial taxonomy, alpha/beta diversity, and predicted functional capacity were inferred using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-Active enZymes (CAZy) annotations; associations were assessed using Procrustes and Spearman correlation analyses.

RESULTS: Histopathology and immunohistochemistry confirmed progressive fibrogenesis with increased TGF-β1 and α-SMA expression. Compared with baseline, bleomycin-treated groups exhibited stage-specific shifts in gut microbial composition, including depletion of mucin-associated taxa (e.g., Prevotella, Akkermansia muciniphila) and expansion of Muribaculaceae- and Clostridiaceae-affiliated taxa. Alpha and beta diversity metrics differed across groups. KEGG/CAZy-based annotations revealed predicted, stage-dependent changes in microbial metabolic potential, including early reductions in pathways related to amino acid and glycan metabolism (M7) and later increases in predicted starch/sucrose catabolism, phosphotransferase system (PTS) representation, and secondary bile acid biosynthesis (M14). Correlation analyses linked compositional shifts to these predicted functional changes.

CONCLUSION: In a stage-resolved, cross-sectional study, bleomycin-associated pulmonary fibrosis was accompanied by compositional and predicted functional alterations in the gut microbiota. These data identify candidate taxa and predicted pathways for follow-up mechanistic testing, but functional (metabolomic) and causality experiments are required to confirm whether and how microbial changes contribute to PF pathogenesis.},
}

Animals
*Bleomycin
*Pulmonary Fibrosis/chemically induced/microbiology/pathology/metabolism
*Gastrointestinal Microbiome
Mice
Disease Progression
*Metabolic Networks and Pathways
Disease Models, Animal
Mice, Inbred C57BL
Feces/microbiology
Male
Lung/pathology

@article {pmid42227352,
year = {2026},
author = {Pérez-Carrasco, V and Uroz-Torres, D and Soriano-Lerma, A and Soriano, M and García-Salcedo, JA and Arias-Moliz, MT},
title = {Association Between the Root Canal Microbiome and Apical Lesion Size: An Observational Shotgun Metagenomic Study.},
journal = {International endodontic journal},
volume = {59},
number = {10},
pages = {2211-2222},
doi = {10.1111/iej.70190},
pmid = {42227352},
issn = {1365-2591},
support = {//European Society of Endodontology/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Dental Pulp Cavity/microbiology ; *Periapical Periodontitis/microbiology/pathology ; *Metagenomics ; Shotgun Sequencing ; DNA, Bacterial ; },
abstract = {AIM: The aim was to characterize the taxonomic and functional composition of the microbiome involved in primary endodontic infections and to evaluate their association with the periapical lesion size using shotgun metagenomic sequencing.

METHODOLOGY: Samples from primary root canal infections diagnosed with apical periodontitis were analysed with shotgun sequencing. Samples were classified according to the lesion size as small (< 3 mm) or large (> 7 mm). The bacterial DNA copies in each group were quantified by qPCR. Taxonomic and functional annotations were made using Bracken/Kraken2 and HUMAnN3 software. Species richness, Shannon, Simpson and Pielou indices were used to measure alpha diversity. The similarity of the bacterial communities between study groups was evaluated by Principal Coordinate Analysis based on Bray-Curtis distances. The ALDEx2 package was used to infer the differences between species, and the edgeR package for KEGG pathways. For all statistical analyses, p < 0.05 was considered as significant.

RESULTS: A total of 49 samples were analysed, 27 with small lesions and 22 with large lesions. Species richness and Shannon indices showed differences between both groups, whereas no differences were seen according to Simpson and Pielou indices. A different community composition (PERMANOVA, p = 0.0019) was observed between the two groups. Three species were significantly enriched in the large lesion samples, Filifactor alocis, Lachnospiraceae bacterium oral taxon 500 and Olsenella uli, while three others were enriched in small lesion samples, Acinetobacter baumannii, Acinetobacter pittii and Cutibacterium acnes. Functionally, benzoate, flavonoid and steroid degradation, the sphingolipid signalling pathway and proteasome function were enriched in samples with large lesions. Monoterpenoid biosynthesis, phospholipase D signalling, the sulphur relay system and staurosporine biosynthesis were enriched in small lesions.

CONCLUSIONS: Teeth with large periapical lesions harbour greater bacterial loads and exhibit a more diverse microbial community than those with small lesions. Differences in species-level taxonomic composition were observed between both groups. Functionally, large lesions are enriched in pathways associated with immune evasion and pro-inflammatory activity, whereas small lesions are characterized by pathways related to apoptosis, metabolic adaptation and anti-inflammatory processes. These findings suggest that lesion severity is also shaped by the functional potential of the microbiome to modulate host inflammation.},
}

Humans
*Microbiota/genetics
*Dental Pulp Cavity/microbiology
*Periapical Periodontitis/microbiology/pathology
*Metagenomics
Shotgun Sequencing
DNA, Bacterial

@article {pmid42723054,
year = {2026},
author = {Zhao, J and Chen, X and Wang, X and Cui, Y and Zhuge, J and Zhang, Y and Zhang, L and Yan, Y and Fang, H and Hua, Z and Li, G},
title = {Metagenomic-based quantification of Pseudomonas aeruginosa burden links microbiome collapse to mortality in severe community-acquired pneumonia.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {25},
number = {1},
pages = {},
pmid = {42723054},
issn = {1476-0711},
support = {2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; },
mesh = {Humans ; *Community-Acquired Pneumonia/mortality/microbiology ; *Pseudomonas aeruginosa/genetics/isolation & purification ; Female ; *Microbiota ; Retrospective Studies ; *Pseudomonas Infections/mortality/microbiology ; Metagenomics ; Male ; Aged ; Middle Aged ; Lung/microbiology ; *Community-Acquired Infections/microbiology/mortality ; ROC Curve ; Metagenome ; High-Throughput Nucleotide Sequencing ; Prognosis ; },
abstract = {BACKGROUND: Severe community-acquired pneumonia (sCAP) remains a major cause of mortality in critically ill patients, Pseudomonas aeruginosa (P. aeruginosa) is a frequent pathogen associated with poor prognosis in this population. While metagenomic next-generation sequencing (mNGS) is widely used for pathogen detection, its value in quantifying pathogen abundance and linking it to lung microbiome alterations remains unclear.

OBJECTIVES: This study investigated the association between P. aeruginosa abundance quantified by mNGS and lung microbiome alterations and clinical outcomes in sCAP patients.

METHODS: This multicenter retrospective study included 130 patients with sCAP caused by P. aeruginosa from five hospitals (September 2021-June 2025). Patients were stratified into low, medium, and high abundance groups according to mNGS-derived reads per ten million (RPTM) values of P. aeruginosa. Lung microbiome diversity and community structure were analyzed, and differences between groups were assessed using appropriate statistical methods. The association between P. aeruginosa abundance and clinical outcomes was evaluated using correlation analysis, sankey diagram, receiver operating characteristic curve, grey zone analysis and logistic regression.

RESULTS: A total of 130 patients with sCAP due to P. aeruginosa were stratified into low, medium, and high abundance groups based on mNGS-derived RPTM value. Microbial diversity decreased progressively with increasing abundance, and community structures differed significantly among groups (all P < 0.05). P. aeruginosa became increasingly dominant, accounting for up to 95.99% of the microbiota in the high abundance group. Higher P. aeruginosa abundance was associated with increased disease severity, including longer mechanical ventilation, prolonged hospital stay, and higher 28-day mortality. Sankey diagram showed a progressive decline in treatment effectiveness and an increase in mortality with increasing P. aeruginosa abundance. P. aeruginosa_RPTM showed moderate predictive value for mortality (AUC = 0.761, Sens = 69.40%, Spec = 75.30%, cutoff: 41122, grey zone: 2287-220339) and remained independently associated with 28-day mortality in multivariable analysis [2.219 (1.509 to 3.262), P < 0.001].

CONCLUSION: In patients with sCAP, higher P. aeruginosa_RPTM measured by mNGS was associated with reduced lung microbiome diversity and unfavorable clinical outcomes. RPTM-based risk stratification may help identify patients at increased risk of poor prognosis.},
}

Humans
*Community-Acquired Pneumonia/mortality/microbiology
*Pseudomonas aeruginosa/genetics/isolation & purification
Female
*Microbiota
Retrospective Studies
*Pseudomonas Infections/mortality/microbiology
Metagenomics
Male
Aged
Middle Aged
Lung/microbiology
*Community-Acquired Infections/microbiology/mortality
ROC Curve
Metagenome
High-Throughput Nucleotide Sequencing
Prognosis

@article {pmid42723112,
year = {2026},
author = {Zhang, S and Zhang, N and Zhang, X and Liu, Y and Feng, Y and Xiang, J and Zhang, J and Ma, H and Lu, Y and Zhang, T},
title = {Integrated landscape of salivary metagenome and multi-biofluid metabolome characterizes a microbial-metabolic axis in upper gastrointestinal cancer progression.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42723112},
issn = {2049-2618},
mesh = {Humans ; *Saliva/microbiology ; *Metabolome ; *Gastrointestinal Neoplasms/microbiology/metabolism/pathology/diagnosis ; *Metagenome ; Disease Progression ; Metagenomics/methods ; Metabolomics/methods ; Female ; Multiomics ; Male ; Middle Aged ; Dysbiosis/microbiology ; Microbiota ; Lysine/metabolism ; },
abstract = {BACKGROUND: Upper gastrointestinal cancer (UGIC) imposes a major global health burden, yet the stage-specific molecular changes along the microbial-metabolic axis remain limited understood. We aimed to delineate this molecular landscape across UGIC progression and evaluate its potential as non-invasive methods for precision screening.

RESULTS: Derived from a multi-center population-based UGIC screening program, we enrolled 420 individuals, stratified into normal, low-grade intraepithelial neoplasia (LGIN), high-grade intraepithelial neoplasia (HGIN), and UGIC (n = 105 per group). Integrated salivary metagenomics and paired salivary/plasma metabolomics were performed to capture local and systemic dysregulation. We uncovered distinct stage-specific divergence during UGIC progression: profound remodeling of the salivary microbiota (104 differential species) and salivary metabolomics (80 differential metabolites) initiated early at the LGIN stage, whereas plasma metabolic dysregulation (40 differential metabolites) peaked significantly later at the HGIN stage. Integrative analysis revealed salivary microbiota related more closely with salivary metabolome than plasma metabolome. Moreover, statistical evidence suggested that dysbiotic salivary microbiota was associated with altered lysine- and tryptophan-related catabolic pathways converging on Acetyl-CoA-related metabolic nodes, supporting a potential metabolic mechanism in precancerous lesions. Finally, the discriminative model integrating metagenomic and metabolomic markers demonstrated promising diagnostic performance in distinguishing these precancerous lesions (LGIN: area under the curve [AUC] = 0.83; HGIN: AUC = 0.77) and UGIC (AUC = 0.76) from normal.

CONCLUSION: This study characterizes a stage-specific microbial-metabolic axis that facilitates the comprehensive understanding of UGIC pathogenesis. These multi-biofluid signatures offer a promising non-invasive triage strategy for detecting precancerous lesions and optimizing endoscopic resource allocation. Video Abstract.},
}

Humans
*Saliva/microbiology
*Metabolome
*Gastrointestinal Neoplasms/microbiology/metabolism/pathology/diagnosis
*Metagenome
Disease Progression
Metagenomics/methods
Metabolomics/methods
Female
Multiomics
Male
Middle Aged
Dysbiosis/microbiology
Microbiota
Lysine/metabolism

@article {pmid42723989,
year = {2026},
author = {Ma, Z and Bai, X and Tian, J and Yao, C and Yan, Z and Ma, X and Zhang, C and Ma, J and Lin, Y and Zhang, X and Wang, H},
title = {Brucellar spondylitis is associated with disturbance in gut microbiota and histamine metabolism associated inflammation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1914654},
pmid = {42723989},
issn = {2235-2988},
mesh = {Humans ; Female ; *Histamine/metabolism/blood ; Adult ; Male ; Cytokines/blood ; *Gastrointestinal Microbiome ; *Inflammation ; *Spondylitis/microbiology/pathology/metabolism ; Dysbiosis/microbiology ; Middle Aged ; Histidine Decarboxylase/blood ; Metagenomics ; Lipopolysaccharides/blood ; Fatty Acids, Volatile ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The pathogenesis of brucellar spondylitis (BLS) has traditionally been considered to be primarily limited to local osteoarticular lesions. With the proposal of the "gut-spine axis" concept, the role of intestinal microecological dysbiosis in inflammatory spinal diseases has attracted in an increase of attention. The overactivated inflammatory cytokine network not only mediates bone destruction and intervertebral disc damage, but also forms a bidirectional interaction with gut microbiota dysbiosis through the "gut-spine axis," collectively driving disease progression. However, the inflammatory mechanism by which gut microbiota participates in the pathological process of BLS remains largely unclear.

METHODS: This study recruited 20 BLS patients and 20 healthy donors. Multi-omics analysis including metagenomics, untargeted metabolomics, and targeted short-chain fatty acids (SCFAs) analysis, were used to compare the structural differences in gut microbiota between the two groups and screen for signature differential bacterial species. Plasma levels of histamine and histidine decarboxylase were measured by ELISA to clarify the role of differential histidine metabolic pathway in the disease. Additionally, plasma levels of lipopolysaccharide (LPS) and inflammatory cytokines (IL-1β, IL-6, IL-10, IL-17A, TNF-α) were detected by ELISA. The correlation between gut microbiota and inflammatory indicators was further analyzed.

RESULTS: Compared to the healthy control group, the α-diversity of the gut microbiota in BLS patients was significantly reduced, with the microbial community structure exhibiting increased homogeneity. Beta diversity analysis revealed significant differences, suggesting that disease progression is associated with an overall imbalance in the gut microbiota and the deterioration of its specific structural composition. At the phylum level, the abundances of Actinomycetota, unclassified_d_Viruses, and Fusobacteriota were significantly increased in the gut microbiota of BLS patients compared to the control group, while the abundances of Bacillota and Pseudomonadota were significantly decreased. Further analysis revealed that, compared to the control group, the generic abundance of Enterococcus was significantly increased, while the proportions of Blautia, Faecalibacterium, Ruminococcus, Agathobacter, Roseburia, Clostridium, Eubacterium, Alistipes and Anaerobutyricum were significantly decreased. At the species level, the abundances of Enterococcus sp and Enterococcus-faecium were increased, whereas Blautia sp, Ruminococcus sp, Faecalibacterium sp, Faecalibacterium prausnitzii, Agathobacter rectalis, Eubacterium sp, Agathobacter sp, and Roseburia sp were decreased. Furthermore, untargeted metabolomics revealed that metabolites were enriched in the histidine metabolic pathway, and the levels of SCFAs including butyrate, isobutyrate, valerate, and 4-methylvalerate in the intestinal contents were reduced in BLS. Functional KEGG profiling revealed that key KOs involved in butyrate synthesis (e.g., K00074, K00172, K01640) and transport were globally downregulated in the patient group, whereas histidine decarboxylase KOs (K01693, K11755, K19787) that convert histidine to pro-inflammatory histamine were significantly enriched. The loss of butyrate-producing symbionts led to SCFAs deficiency and mucosal barrier disruption, creating ecological niches for facultatively anaerobic Enterococcus, which further exacerbated local inflammation via proteolytic fermentation and histamine production. Compared with the control group, BLS patients showed decreased plasma levels of IL-10, while levels of IL-1β, IL-6, IL-17A, and TNF-α were increased, and LPS levels were elevated. In addition, significantly elevated plasma pro-inflammatory LPS levels in patients with BLS suggest disruption of intestinal integrity and permeability. Correlation analysis indicated a close relationship between gut microbiota and inflammation.

CONCLUSION: BLS is associated with gut microbiota dysbiosis and alterations in microbial metabolites, which may be linked to inflammatory responses and histamine metabolism. The differential microbial taxa identified in this study could be developed into a stool-based non-invasive diagnostic panel to facilitate early differentiation of BLS from other spinal disorders. Furthermore, restoring gut microbial balance through probiotic supplementation or dietary modulation may represent a promising adjunctive strategy to enhance the efficacy of standard antibiotic therapy and reduce disease recurrence.},
}

Humans
Female
*Histamine/metabolism/blood
Adult
Male
Cytokines/blood
*Gastrointestinal Microbiome
*Inflammation
*Spondylitis/microbiology/pathology/metabolism
Dysbiosis/microbiology
Middle Aged
Histidine Decarboxylase/blood
Metagenomics
Lipopolysaccharides/blood
Fatty Acids, Volatile
Metabolomics
Bacteria/classification/genetics/isolation & purification

@article {pmid42725663,
year = {2026},
author = {Furneaux, B and Roslin, T and Hardwick, B and Kerdraon, D and Autto, H and Banelyte, G and deWaard, JR and deWaard, SL and Farrell, A and Kalttopää, O and Kristensen, E and Rogers, HMK and Sones, JE and Zakharov, EV and Ovaskainen, O},
title = {Is There a Fly in My Soup? To What Extent Do Metabarcoding and Individual Barcoding Tell the Same Story?.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70195},
doi = {10.1111/1755-0998.70195},
pmid = {42725663},
issn = {1755-0998},
support = {336212//Research Council of Finland/ ; 345110//Research Council of Finland/ ; 101059492//HORIZON-CL6-2021-BIODIV-01/ ; 856506/ERC_/European Research Council/International ; 225-20-002//Naturvårdsverket/ ; NFRFT-2020-00073//New Frontiers in Research Fund/ ; MSI 42450//Canadian Foundation for Innovation/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA ; *Metagenomics/methods ; *Insecta/classification/genetics ; },
abstract = {Metabarcoding has become the method of choice for characterizing complex arthropod communities. The extent to which metabarcoded bulk samples will recover the same community composition as individual sequencing of all individuals in the sample remains poorly quantified. Biases such as unequal extraction of DNA from different taxa, primer mismatches and non-random PCR may cause the selective drop-out of species from metabarcoding data. At the same time, DNA metabarcoding may reveal arthropod taxa present not as individuals, but as DNA residues on the surface or in the gut of insects. To quantify the consistency in sample contents established by different means, we metabarcoded 45 bulk insect samples, then extracted all arthropods and sequenced them individually. Metabarcoding targeted 418 bp at the 3' end of the Folmer barcoding region, while individual barcodes captured the entire 658 bp Folmer region. The metabarcoding workflow, including PCR amplification, sequencing and bioinformatics, was performed in three replicates from three separate lysate aliquots per sample. For the main analyses, sequences were assigned to Barcode Index Numbers (BINs) as identical taxonomic categories across data types, thereby allowing the detection of even rare but biologically true taxa. Since such reference-based validation will be unavailable to any researcher dealing with metabarcoding data alone, we validated our key findings through an alternative workflow, i.e., de novo clustering of sequences. We found that metabarcoding is replicable, as different replicates of the same sample recover similar species richness and composition. Individual barcoding and metabarcoding provide similar impressions of relative differences in community structure: species-rich vs. species-poor samples rank similarly among data types (Spearman's ⍴ = 0.88-0.99) as do differences in relative dissimilarity between sample pairs (Spearman's ⍴ = 0.55-0.90). Dissimilarity between data types varies with BIN richness in the sample, but this relationship reflects nestedness rather than turnover: metabarcoding recovers the same set of core species as individual barcoding but adds hundreds of species on top. Any BIN recovered as an individual occurred with high probability in the metabarcoding data, and any BIN found in high read abundances by metabarcoding was likely found as an individual (p > 0.8). In terms of abundances, the number of individual insects per BIN was well predicted by the number of metabarcoding reads (R[2] > 0.68 for a model including taxonomy as a random effect). Our analysis suggests that metabarcoding data will be informative of the sample contents in terms of arthropod species richness, composition and taxon-specific abundances. Taxa recovered in low copy numbers in metabarcoding sequence data will likely represent DNA left as residues from past biotic interactions. Barring sequencing errors, both types of data yield biologically relevant insights into the taxa present in the source community.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Sequence Analysis, DNA
*Metagenomics/methods
*Insecta/classification/genetics

@article {pmid42725826,
year = {2026},
author = {Chenuil, A and Bouchereau, E and Legrand, T and Calvert, V and Chemin, C and Chenesseau, S and Guillemain, D and Ortega, JMG and Haguenauer, A and Leduc, M and Legendre, F and Marschal, F and Marschal, C and Mirleau, F and Selva, M and Vanbostal, L and Zuberer, F and Mirleau, P and Plaisance, L and Rossi, V and Ruitton, S and Meglécz, E and Dubut, V},
title = {Separating Faces in ARMS Metabarcoding Improves Marine Biodiversity Monitoring: A Comparison Across Protocols, Experimental Designs and Photographic Surveys.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70188},
doi = {10.1111/1755-0998.70188},
pmid = {42725826},
issn = {1755-0998},
support = {OOB_EMBRC FR_AAP2018_n°2179//EMBRC France/ ; ANR-17-MART0001-01//Agence Nationale de la Recherche/ ; ANR-17-MART0001-02//Agence Nationale de la Recherche/ ; ANR-17-MART0001-03//Agence Nationale de la Recherche/ ; 145//ERA-Net Mar-TERA/ ; SERA-20181031//Centro para el Desarrollo Tecnológico e Industrial/ ; 4000141547/23/I-DT//European Space Agency/ ; 1166-39417//European Regional Development Fund/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; Photography/methods ; Electron Transport Complex IV/genetics ; Animals ; Mediterranean Sea ; *Metagenomics/methods ; },
abstract = {Monitoring marine biodiversity requires approaches capable of capturing its spatial and temporal complexity. DNA metabarcoding coupled with Autonomous Reef Monitoring Structures (ARMS) is increasingly used for this purpose, yet most applications still pool all sessile fractions and rarely benchmark molecular outputs against photographic observations. Here, we combined photographic analysis with cytochrome c oxidase I (COI) metabarcoding across 10 north-western Mediterranean sites to compare and refine ARMS-based monitoring protocols. We first optimized laboratory procedures (DNA extraction and polymerase choice) and applied the control-driven, replicate-aware VTAM pipeline to minimize false positives and ensure traceability. We then conducted the first face-by-face comparison of α- and β-diversity between imaging and eDNA, metabarcoding each ARMS face separately rather than pooling samples. Metabarcoding detected ~15× higher site-level richness and revealed stronger correlations with geographic distance and environmental gradients-which stemmed from its finer taxonomic resolution-whereas photography provided complementary information on macro-taxa and surface cover. For metabarcoding, processing each face separately yielded much higher richness and stronger β-diversity-distance correlations than with the NOAA pooling protocol, demonstrating that pooling inflates sampling variance, weakening ecological signal. Grouping the 17 faces into five structural categories offered a more operational alternative while further increasing α-diversity and strengthening β-diversity correlations. Overall, our results show that retaining ARMS microhabitat structure is critical for maximizing metabarcoding performance. Using five structural sessile fractions per ARMS combined with a control-driven bioinformatic workflow provides a reproducible, scalable framework for long-term eDNA monitoring and early detection of biodiversity change.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
*Aquatic Organisms/classification/genetics
Photography/methods
Electron Transport Complex IV/genetics
Animals
Mediterranean Sea
*Metagenomics/methods

@article {pmid42726321,
year = {2026},
author = {Duan, DY and Ran, J and Guo, XL and Liu, L and Liu, GH and Asada, M and Cheng, TY},
title = {Metagenomic analysis of the midgut microbiome in Dermacentor abaensis ticks at different feeding states.},
journal = {Experimental & applied acarology},
volume = {97},
number = {3},
pages = {},
pmid = {42726321},
issn = {1572-9702},
support = {No. 2025JJ50143//Natural Science Foundation of Hunan Province, China/ ; No. kq2502005//Natural Science Foundation of Changsha City, China/ ; No. 31902294//National Science Foundation of China/ ; 2024YFD1800103//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Dermacentor/microbiology/physiology ; Female ; Bacteria/classification/isolation & purification/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; Feeding Behavior ; China ; *Metagenome ; },
abstract = {Ticks are blood-sucking ectoparasites of humans and animals, ranking second only to mosquitoes as vectors of diseases. Dermacentor abaensis is distributed in Sichuan, Qinghai, and Gansu, China. Because D. abaensis harbors several pathogens, it poses a threat to public health and livestock production. However, the midgut microbiota of D. abaensis at distinct feeding states remains poorly characterized. Adult D. abaensis ticks at various feeding states were collected from yaks in Gansu Province, China. Genomic DNA was extracted from midguts and midgut contents of unfed, partially fed, and fully engorged female D. abaensis. A metagenomic sequencing approach was employed to profile the midgut microflora among three groups. A total of 83 phyla, 908 genera, and 1857 species were annotated across the three groups. At the phylum level, Pseudomonadota, Mucoromycota, and Ascomycota were the most abundant. At the species level, common bacterial species such as Klebsiella pneumoniae and Anaplasma phagocytophilum, alongside viruses and eukaryotes, were detected in all three groups. Unique microorganisms were also observed in each group: unfed (n = 305), partially fed (n = 59), and fully engorged (n = 20). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that the D. abaensis microbiome contains a relatively high abundance of functional genes involved in lipid and amino acid metabolism across the three different feeding states. These findings indicate that while core microbial taxa are shared in the midgut of female D. abaensis, observable trends suggest variations in microbial diversity and composition as blood-feeding progresses. The present study provides a descriptive baseline of the midgut microbial composition of D. abaensis, which may inform future studies on tick biology and the ecology of tick-borne pathogens.},
}

Animals
*Dermacentor/microbiology/physiology
Female
Bacteria/classification/isolation & purification/genetics
Metagenomics
*Gastrointestinal Microbiome
Feeding Behavior
China
*Metagenome

@article {pmid42312840,
year = {2026},
author = {Peterson, LF and Wang, J and Gow, NAR and LeibundGut-Landmann, S and Brewer, MG},
title = {Influence of fungi on epithelial homeostasis and role in inflammatory diseases.},
journal = {Clinical microbiology reviews},
volume = {39},
number = {3},
pages = {e0031925},
pmid = {42312840},
issn = {1098-6618},
support = {T32 AI118689/NH/NIH HHS/United States ; LF-OC-22_001060//LEO Fondet/ ; 310030_189255/SNSF_/Swiss National Science Foundation/Switzerland ; 310030E_219182/SNSF_/Swiss National Science Foundation/Switzerland ; MR/V033417/1//Medical Research Council Centre for Medical Mycology/ ; 200208/WT_/Wellcome Trust/United Kingdom ; 215599/WT_/Wellcome Trust/United Kingdom ; 224323/WT_/Wellcome Trust/United Kingdom ; MR/M026663/2/MRC_/Medical Research Council/United Kingdom ; MR/Y002164/1/MRC_/Medical Research Council/United Kingdom ; APP57173- UKRI1405/MRC_/Medical Research Council/United Kingdom ; MR/N006364/2//Medical Research Council Centre for Medical Mycology/ ; NIHR203320//NIHR Exeter Biomedical Research Centre/ ; },
mesh = {Humans ; *Homeostasis ; Skin Microbiome ; *Fungi/pathogenicity/physiology ; *Host-Pathogen Interactions ; Skin/microbiology/immunology ; *Dermatomycoses/microbiology ; *Inflammation/microbiology ; },
abstract = {SUMMARYThe skin harbors a diverse fungal community that contributes to both epidermal homeostasis and inflammatory disease. Historically, studies of cutaneous fungi focused primarily on opportunistic infections in immunocompromised hosts. Advances in sequencing technologies and metagenomic analyses have revealed that commensal yeasts of the skin microbiome likely influence host physiology and cutaneous disease severity. In this review, we summarize the current knowledge of host-fungal interactions at the skin epithelium, with particular emphasis on the yeast genera Malassezia and Candida. We discuss how fungal colonization shapes epidermal biology through direct interactions with keratinocytes and immune cells, highlighting fungal virulence factors such as secreted proteases and candidalysin, as well as host-sensing pathways. We further examine how these interactions contribute to inflammatory skin diseases, particularly atopic dermatitis and psoriasis, and how fungi participate in polymicrobial networks with bacteria and viruses to alter susceptibility to infection. Finally, we discuss how emerging therapeutic strategies change the fungal composition on skin. These advances suggest the importance of fungi as active regulators of skin immunity and emphasize key knowledge gaps that need to be addressed in future studies to better understand how they contribute to cutaneous diseases.},
}

Humans
*Homeostasis
Skin Microbiome
*Fungi/pathogenicity/physiology
*Host-Pathogen Interactions
Skin/microbiology/immunology
*Dermatomycoses/microbiology
*Inflammation/microbiology

@article {pmid42323440,
year = {2026},
author = {Carboni, S and Macfarland, C and Cheves Hernandez, S and Buret, AG and Kutz, S and Melin, AD},
title = {Ecological and methodological insights from genetic and coprological profiling of gastrointestinal communities in wild howler monkeys.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42323440},
issn = {2045-2322},
support = {RGPIN-2017-03782//Natural Sciences and Engineering Research Council of Canada/ ; 950-231257//Canada Foundation for Innovation and Canada Research Chairs/ ; },
mesh = {Animals ; *Alouatta/microbiology/parasitology/genetics ; Helminths/genetics/isolation & purification/classification ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; *Gastrointestinal Tract/microbiology ; Bacteria/genetics/classification/isolation & purification ; Female ; Host-Parasite Interactions ; Male ; },
abstract = {The gastrointestinal tract hosts a complex community of microorganisms and helminth parasites that collectively contribute to host health and fitness. Analysis of these communities provides insight into diverse aspects of host dietary ecology, immunity, nutrition, and host-parasite interactions. However, research methodologies, such as sample preservation and sequencing approach, can influence how we understand and characterize these features. Here, we profiled the gastrointestinal microbial and helminth communities in different groups of wild Costa Rican mantled howler monkeys (Alouatta palliata palliata). We compared samples stored in ethanol versus directly flash frozen, and contrasted conclusions drawn from 16S versus shotgun sequencing approaches. Bacterial, archaeal, and eukaryotic taxa associated with the digestion of plant material dominated the GI communities. Storage and sequencing methods influenced microbial profiles: ethanol-stored samples exhibited higher diversity than frozen samples, and 16S sequencing detected lower diversity than shotgun. Helminths were detected via coprological microscopy in 71% of individuals, whereas metagenomic detection was inconsistent. This study provides new data on the microorganisms and their putative digestive functions in the gut of a folivorous primate, and highlights the pros and cons of different methodological choices when profiling host-microbiome and host-parasite interactions.},
}

Animals
*Alouatta/microbiology/parasitology/genetics
Helminths/genetics/isolation & purification/classification
*Gastrointestinal Microbiome/genetics
*Feces/microbiology/parasitology
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
*Gastrointestinal Tract/microbiology
Bacteria/genetics/classification/isolation & purification
Female
Host-Parasite Interactions
Male

@article {pmid42431299,
year = {2026},
author = {Zhang, X and Cai, M and Lin, J and Feng, Z and Wang, W and Jiao, Y and Lu, L},
title = {Multi-year glyphosate exposure impairs soil fertility, microbial communities, nutrient cycling genes, and tea quality in tea plantations.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {407},
number = {},
pages = {128689},
doi = {10.1016/j.envpol.2026.128689},
pmid = {42431299},
issn = {1873-6424},
mesh = {Glyphosate ; *Glycine/analogs & derivatives/toxicity ; *Soil Microbiology ; *Soil/chemistry ; *Camellia sinensis ; *Herbicides/toxicity ; *Soil Pollutants/toxicity ; Nitrogen ; Agriculture ; *Tea/chemistry ; *Microbiota/drug effects ; },
abstract = {Although glyphosate is highly effective for weed control, its potential risks to tea agroecosystems remain a significant concern. Previous studies have shown inhibitory effects on soil microbial communities in tea plantations, yet the multi-year impacts of glyphosate on microbially mediated nutrient cycling remain poorly understood. To address this gap, we conducted a three-year controlled field experiment, applying glyphosate at 0 kg a.i. ha[-1] (CK), 2.3 kg a.i. ha[-1] (G1), and 6.9 kg a.i. ha[-1] (G2), and used metagenomic sequencing to evaluate its effects on soil fertility, microbial communities, nutrient cycling genes, and tea quality. The results showed that glyphosate application significantly increased soil pH but reduced the contents of total organic carbon, total nitrogen, total potassium, available nutrients, and enzyme activities, leading to marked declines in soil fertility. Relative to CK, G2 reduced microbial alpha diversity, with Chao1, Shannon, and Pielou indices decreasing by 33.22%, 14.97%, and 11.50%, respectively. Tea quality was also affected, with free amino acids and caffeine decreasing by 22.67% and 11.30%, respectively, whereas tea polyphenols and the phenol/ammonia ratio increased by 12.16% and 45.08%, respectively. G2 also restructured bacterial communities, including depletion of Actinobacteria and Planctomycetota and more than 70-fold enrichment of Candidatus Rokubacteria. Metagenomic analysis revealed broad suppression of carbon, nitrogen, and phosphorus cycling genes under G2. Overall, these results suggest that repeated glyphosate exposure over three years may alter soil ecological processes and compromise tea quality, highlighting the need for more sustainable weed management strategies and reduced reliance on glyphosate in tea plantations.},
}

Glyphosate
*Glycine/analogs & derivatives/toxicity
*Soil Microbiology
*Soil/chemistry
*Camellia sinensis
*Herbicides/toxicity
*Soil Pollutants/toxicity
Nitrogen
Agriculture
*Tea/chemistry
*Microbiota/drug effects

@article {pmid42462951,
year = {2026},
author = {Jin, Y and Liu, J and Liu, Z and Yuan, Y and Cui, H and Dong, Z and Zhang, F and Lv, M and Hu, L and Zhang, L and Zhou, D and Yang, W},
title = {Linking oral microbiota to clinic air during ultrasonic scaling: Quantitative sequencing and CFD modeling reveal pathogenic aerosol emissions, infection risk, and control strategies.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {407},
number = {},
pages = {128796},
doi = {10.1016/j.envpol.2026.128796},
pmid = {42462951},
issn = {1873-6424},
mesh = {Aerosols/analysis ; *Microbiota ; *Air Microbiology ; *Mouth/microbiology ; Humans ; Hydrodynamics ; Bacteria/isolation & purification/genetics ; *Dental Scaling ; },
abstract = {Microbial aerosols from dental procedures pose a recognized yet unquantified airborne infection risk. During ultrasonic scaling, we performed multi-site sampling (saliva, air, surfaces) and combined metagenomics with quantitative 16S rRNA and ITS amplicon sequencing to profile viral, bacterial, and fungal communities. Using size-resolved aerosol sampling and absolute quantification, we determined the emission strength and size distribution of pathogenic bacterial aerosols (PBA), which were key inputs for computational fluid dynamics (CFD) simulations performed at ventilation velocities of 0.1, 0.2, and 0.4 m/s, corresponding to air exchange per hour (ACH) of 2.4, 4.7, and 9.4 h[-1], respectively. We first linked patient oral microbiota to clinic aerosols, identifying a shared core of 51 viral, 55 bacterial, and 23 fungal families, of which three bacterial families (Streptococcaceae, Pasteurellaceae, Nocardiaceae) were pathogenic. The emission strength of PBA was ∼3.06 × 10[3] copies/min, with 66.7% concentrated in the 2.1∼4.7 μm fraction, a size associated with higher deposition in the lower respiratory tract. CFD simulations, fed with real pathogen concentrations and aerodynamic size spectra, revealed that increasing ACH from 0.1 to 0.4 m/s reduced PBA suspension (-26.4%) and surface deposition (-12.7%) during scaling, lowering the inhalation infection risk (IIR) at the dentist's position by 80.8% and keeping overall IIR below 25%. After scaling, lower velocity favours particle removal, supporting a dynamic ventilation strategy (high during treatment, low afterwards). This integrated framework provides a direct scientific basis for infection control in dental operatories.},
}

Aerosols/analysis
*Microbiota
*Air Microbiology
*Mouth/microbiology
Humans
Hydrodynamics
Bacteria/isolation & purification/genetics
*Dental Scaling

@article {pmid42476495,
year = {2026},
author = {Chen, M and Cao, J and Fu, S and Han, Y and Zheng, W and Chen, J and Yang, X and Wang, J},
title = {Lambda-cyhalothrin exposure disrupts microbiota-associated bile acid metabolism and enterohepatic feedback in mice.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {407},
number = {},
pages = {128813},
doi = {10.1016/j.envpol.2026.128813},
pmid = {42476495},
issn = {1873-6424},
mesh = {Animals ; *Pyrethrins/toxicity ; *Nitriles/toxicity ; *Bile Acids and Salts/metabolism ; Male ; Mice ; *Insecticides/toxicity ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Enterohepatic Circulation/drug effects ; Microbiota/drug effects ; },
abstract = {Lambda-cyhalothrin (LCT) is a widely used pyrethroid insecticide frequently detected in environmental and food-associated matrices, yet its effects on host bile acid metabolism remain unclear. Male C57BL/6 mice were orally exposed to LCT for 28 days and analyzed using integrated bile acid metabolomics, hepatic and ileal gene-expression profiling, 16S rRNA sequencing, and shotgun metagenomics. LCT reduced hepatic total bile acids but increased plasma and fecal bile acids, indicating compartment-specific bile acid redistribution. This response was accompanied by hepatic Cyp7a1/Cyp27a1 downregulation, selective Cyp8b1 upregulation, altered bile acid transporter expression, and enhanced ileal FXR-FGF15-related feedback responses. LCT also remodeled gut microbial composition and altered bile acid transformation-related functional signatures, particularly those related to 7α-HSDH and 3β-HSDH. Consistently, fecal LCA, 3-ketoLCA, and isoLCA accumulated, consistent with altered microbial LCA oxidation-reduction and epimerization potential. These findings identify microbiota-associated bile acid remodeling as a potential non-neurotoxic metabolic endpoint of pyrethroid-induced gut-liver axis disturbance and provide candidate microbial and host targets for future mechanistic validation.},
}

Animals
*Pyrethrins/toxicity
*Nitriles/toxicity
*Bile Acids and Salts/metabolism
Male
Mice
*Insecticides/toxicity
Mice, Inbred C57BL
Liver/metabolism/drug effects
*Gastrointestinal Microbiome/drug effects
*Enterohepatic Circulation/drug effects
Microbiota/drug effects

@article {pmid42545024,
year = {2026},
author = {Carlson-Jones, JAP and Goddard, TR and Papudeshi, B and Mallawaarachchi, V and Whiteson, KL and Warner, MS and Morton, JM and Jersmann, HPA and Edwards, RA},
title = {DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.},
journal = {Clinical microbiology reviews},
volume = {39},
number = {3},
pages = {e0035225},
pmid = {42545024},
issn = {1098-6618},
support = {FL250100019//Department of Education and Training | Australian Research Council (ARC)/ ; //Women's & Children's Hospital Foundation/ ; DP250103825//Department of Education and Training | Australian Research Council (ARC)/ ; 2046960//National Health and Medical Research Council/ ; //CALHN CEO Clinical Rapid Implementation Project Scheme/ ; },
mesh = {*Cystic Fibrosis/microbiology ; Humans ; *Microbiota/genetics ; *Sequence Analysis, DNA/methods ; Metagenomics/methods ; Sputum/microbiology ; Bacteria/genetics/isolation & purification/classification ; *Respiratory System/microbiology ; },
abstract = {SUMMARYDNA sequencing has revolutionized microbial surveillance in cystic fibrosis (CF), transforming pathogen identification from culture-dependent to total microbial community identification using molecular-based approaches. Techniques such as 16S rRNA gene sequencing have uncovered the complexity of the CF airway microbiome, while shotgun metagenomics, metatranscriptomics, and viromics now provide strain-level, functional, and viral insights beyond bacterial identification. Despite these advances, key technical and logistical challenges remain, including the processing of high-viscosity sputum samples, overwhelming host DNA contamination, managing large data sets, and the integration of complex bioinformatic outputs into clinical workflows. Emerging innovations such as host DNA depletion protocols, targeted enrichment panels, and adaptive sampling on Oxford Nanopore platforms are helping to overcome these barriers, improving microbial recovery and sequencing efficiency. As cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies are changing the lives of people with cystic fibrosis (pwCF), sequencing offers an unprecedented opportunity to track potential microbial adaptation in response. This review investigates current advances, limitations, and translational opportunities in DNA sequencing for CF airway microbiome surveillance, highlighting how these technologies can help reshape research and clinical microbiology in the post-modulator era.},
}

*Cystic Fibrosis/microbiology
Humans
*Microbiota/genetics
*Sequence Analysis, DNA/methods
Metagenomics/methods
Sputum/microbiology
Bacteria/genetics/isolation & purification/classification
*Respiratory System/microbiology

@article {pmid42351291,
year = {2026},
author = {Liu, J and Coker, MO and Osazuwa-Peters, N and Peter, O and Idemudia, NL and Schlecht, NF and Obuekwe, O and Eki-Udoko, FE and Bromberg, Y},
title = {Whole metagenome sequencing: not deep enough for complete microbial function recovery.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42351291},
issn = {2049-2618},
mesh = {Humans ; *Metagenome ; Shotgun Sequencing ; *Microbiota/genetics ; Child ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Molecular Sequence Annotation ; Female ; },
abstract = {BACKGROUND: Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to batch effects, such as differences in sequencing depth and platform and annotation strategies, as well as sample-to-flow-cell assignments. However, the relative effects of these factors on functional inference in such studies have yet to be systematically evaluated. We analyzed oral-rinse WMS data from 671 Nigerian youths aged 9-18, sequenced on two Illumina platforms. Microbial molecular functionality encoded in these data was annotated using the mi-faser/Fusion pipeline, to capture the broad functional repertoire, and HUMAnN 3/EC numbers pipeline to characterize curated enzymatic activities. We then quantified how technical factors and batch effects shaped the recovery of microbial functionality.

RESULTS: Three findings of our work were most salient. First, we observed that the choice of annotation strategy traded off between breadth and specificity of functional coverage. Second, we found that low-prevalence functions were disproportionately lost at shallow sequencing depths, indicating that in, e.g., case-control studies with few representatives of the minor class, sequencing depth could critically impact study resolution. Finally, using our newly developed model relating sequencing depth to functional recovery, we demonstrated that increasing sequencing depth does not directly or proportionally improve functional recall. That is, at as little as 10% of this study's sequencing depth, 30% of the estimated complete microbiome functional repertoire was detectable. However, even at the full depth used in this study, we were only able to recover an estimated 60% of that complete functional repertoire. We further showed that despite biomes differences in functional diversity and host contamination levels (e.g., soil, fecal), incomplete functional recovery at commonly used sequencing depths was consistently observed.

CONCLUSIONS: Together, these findings and our depth-to-function mapping framework provide practical guidelines for the design and interpretation of WMS studies. Coordinating sequencing depth planning with annotation strategy, experimental design, and rigorous batch control is thus essential for robust detection of microbial functions and for ensuring reproducible microbiome insights. Video Abstract.},
}

Humans
*Metagenome
Shotgun Sequencing
*Microbiota/genetics
Child
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Molecular Sequence Annotation
Female

@article {pmid42576026,
year = {2026},
author = {Shiba, S and Yachida, S and Mizutani, S and Totoki, Y and Nakamura, H and Hama, N and Miyoshi, N and Arai, Y and Saito-Adachi, M and Kimura, H and Hayashi, Y and Takamaru, H and Tanaka, K and Hayashi, R and Rokutan, H and Ikuta, S and Kanemitsu, Y and Doki, Y and Eguchi, H and Hattori, S and Saito, Y and Yamada, T and Shibata, T},
title = {Prevalence and chronology of colibactin-associated mutational processes and their microbiome spectra in Japanese colorectal cancer.},
journal = {Nature genetics},
volume = {58},
number = {9},
pages = {2211-2225},
pmid = {42576026},
issn = {1546-1718},
support = {JP25ck0106800//Japan Agency for Medical Research and Development (AMED)/ ; JP26ck0106162//Japan Agency for Medical Research and Development (AMED)/ ; JP23jk0210009//Japan Agency for Medical Research and Development (AMED)/ ; JP21cm0106477//Japan Agency for Medical Research and Development (AMED)/ ; JP25gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP22ck0106546//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106799//Japan Agency for Medical Research and Development (AMED)/ ; JP25ck0106874//Japan Agency for Medical Research and Development (AMED)/ ; JP25ama221430//Japan Agency for Medical Research and Development (AMED)/ ; JP26gm2010009//Japan Agency for Medical Research and Development (AMED)/ ; JP26jf0126022//Japan Agency for Medical Research and Development (AMED)/ ; JP16H06279, 22K16336//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20H03662, 23H02892, 25K21771//MEXT | Japan Science and Technology Agency (JST)/ ; },
mesh = {Humans ; *Colorectal Neoplasms/genetics/microbiology/epidemiology ; Japan/epidemiology ; *Mutation ; *Polyketides/adverse effects ; *Peptides ; Whole Genome Sequencing ; Prevalence ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; Aged ; Feces/microbiology ; Gene Expression Profiling ; Risk Factors ; East Asian People ; },
abstract = {The incidence of colorectal cancer (CRC) has risen in recent decades, with a disproportionate increase observed among younger individuals in Japan and other countries. The etiological contribution of the gut microbiota to CRC pathogenesis is recognized, yet the mechanisms involved remain to be fully clarified. Here we integrated whole-genome sequencing (WGS) and transcriptome profiling of CRC with whole-genome metagenomic sequencing of fecal samples to interrogate host-microbiome interactions at high resolution. Application of interpretable artificial intelligence enabled the stratification of CRC into four distinct microbiome-informed subtypes. WGS analysis identified mutational signatures SBS88 and ID18, linked to colibactin exposure, as early clonal events detected in 44.8% of non-hypermutated patients. Notably, these signatures were significantly more frequent among patients born after the 1960s. Microbiome-based subclassification revealed subtype-specific clinical and molecular features. Collectively, our findings indicate that colibactin exposure constitutes a prevalent and potentially modifiable risk factor for CRC in the Japanese population.},
}

Humans
*Colorectal Neoplasms/genetics/microbiology/epidemiology
Japan/epidemiology
*Mutation
*Polyketides/adverse effects
*Peptides
Whole Genome Sequencing
Prevalence
Female
*Gastrointestinal Microbiome/genetics
Male
Middle Aged
Aged
Feces/microbiology
Gene Expression Profiling
Risk Factors
East Asian People

@article {pmid42580037,
year = {2026},
author = {Kearney, A and Chau, K and Kotay, S and Martin, J and Kirby, A and Mathers, AJ and Stoesser, N},
title = {Hospital sinks and healthcare-associated infection: ecology, transmission, surveillance and mitigation.},
journal = {EBioMedicine},
volume = {131},
number = {},
pages = {106415},
pmid = {42580037},
issn = {2352-3964},
mesh = {Humans ; *Cross Infection/transmission/epidemiology/prevention & control/microbiology ; *Infection Control/methods ; Hospitals ; Microbiota ; },
abstract = {Hospital sinks are recognised polymicrobial reservoirs for multi-drug resistant organisms and have been implicated in patient transmission and outbreaks. Earlier studies on sink-associated microbes predominantly focused on specific species or resistance mechanisms (e.g. carbapenemases) using targeted microbiological methods. More recently, less selective approaches (e.g. metagenomic sequencing) have enabled broader characterisation of these microbial communities. This review summarises current evidence describing hospital sink-trap microbiomes, examining ecological determinants, surveillance strategies and interventions aiming to mitigate transmission from these reservoirs. We discuss biotic and abiotic factors that shape microbial selection/persistence, assess approaches to managing these reservoirs to reduce patient risk, and highlight priorities for future research to inform evidence-based practice in healthcare settings.},
}

Humans
*Cross Infection/transmission/epidemiology/prevention & control/microbiology
*Infection Control/methods
Hospitals
Microbiota

@article {pmid42603474,
year = {2026},
author = {Zhang, C and Chen, J and Yang, W and Du, K and Tao, W and Lu, Q and Jiang, M and Hu, J and Zhu, Q and Elrys, AS and Cai, Z and Meng, L and Müller, C and Dan, X and Zhang, J},
title = {Small-sized biodegradable PLA microplastics inhibit plant nitrogen uptake by reshaping soil microbial communities and stimulating microbial metabolism.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143209},
doi = {10.1016/j.jhazmat.2026.143209},
pmid = {42603474},
issn = {1873-3336},
mesh = {*Polyesters/toxicity ; *Soil Microbiology ; *Nitrogen/metabolism ; *Microplastics/toxicity ; *Microbiota/drug effects ; Bacteria/metabolism/drug effects ; *Soil Pollutants/toxicity ; *Plants/metabolism ; Particle Size ; Biodegradation, Environmental ; },
abstract = {The effects of microplastics (MPs) varying in polymer type and size on soil microbial community composition, metabolic functions, and nutrient cycling remain insufficiently understood. Here, we conducted a pot experiment using MPs differing in polymer type (non-biodegradable polyethylene [PE], and biodegradable polylactic acid [PLA]) and four particle sizes (1200-1400, 600-700, 120-150, and 25-38 μm), with amplicon sequencing, shotgun metagenomics, and nitrogen-15 ([15]N) tracing model. Our results showed that small-sized PLA-MPs (25-38 μm) reduced bacterial diversity, destabilized microbial networks, and shifted community assembly toward deterministic processes, whereas PE-MPs and larger-sized PLA-MPs exerted minimal effects. This shift was associated with enhanced depolymerization-related enzymatic potential, accompanied by greater dissolved organic carbon (DOC) availability. The resulting increase in C availability stimulated central C metabolism, promoting microbial resource acquisition and biomass synthesis. To maintain microbial C:N homeostasis, microbial N assimilation was stimulated through ammonium (NH4[+]) assimilation mediated by the glutamate dehydrogenase (GDH) and glutamine synthetase-glutamate synthase (GS-GOGAT) pathways and nitrate (NO3[-]) assimilation via assimilatory nitrate reduction to ammonium (ANRA). Consistently, the [15]N tracing model revealed that microbial assimilation rates of NH4[+]-N and NO3[-]-N increased by 10.5-fold and 12.7-fold, respectively, exceeding gross N mineralization rates, thereby depleting soil inorganic N pools and suppressing plant N uptake. Overall, our findings provide mechanistic insights into how PLA-MPs reshape soil functioning by reprogramming microbial communities and metabolism, thereby altering plant-microbe competition for N. These results highlight the potential risks of increasing biodegradable plastic inputs for cropland nutrient cycling and plant N acquisition.},
}

*Polyesters/toxicity
*Soil Microbiology
*Nitrogen/metabolism
*Microplastics/toxicity
*Microbiota/drug effects
Bacteria/metabolism/drug effects
*Soil Pollutants/toxicity
*Plants/metabolism
Particle Size
Biodegradation, Environmental

@article {pmid42623872,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG},
title = {A synthetic microbiome drives a multi-omics response to remediate 1,4-dithiane-contaminated soil and simultaneously suppresses antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143337},
doi = {10.1016/j.jhazmat.2026.143337},
pmid = {42623872},
issn = {1873-3336},
mesh = {*Soil Pollutants/metabolism ; *Microbiota ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Biodegradation, Environmental ; Multiomics ; Genes, Bacterial ; },
abstract = {1,4-Dithiane, a degradation product of abandoned Japanese chemical weapons, is a persistent organic pollutant with ecological risks. A synthetic microbiome (SM) was constructed through pollution stress screening and ratio optimization, consisting of Shinella sp., Alcaligenes faecalis, Sphingomonas sp., and Stenotrophomonas sp. at an optimal ratio of 1: 1: 2: 2. The SM achieved a 1,4-dithiane degradation rate of 95.2% and reduced intermediate accumulation. Soil remediation experiments showed complete pollutant removal within 60 days, along with improved soil health: reduced bioavailability of heavy metals (Cu, Zn, Cd), increased pH (6.47-6.95), elevated organic matter and enzyme activities, and decreased salinity and redox potential. Integration of ionomics, 16S sequencing, metagenomics, metabolomics, and HT-qPCR revealed that SM colonization reshaped microbial community structure, suppressed ARG-harboring bacteria (e.g., Pseudomonas), and activated core pathways (oxidative phosphorylation and glutathione metabolism), enhancing metabolic activity and oxidative stress tolerance. Consequently, the diversity, abundance, and diffusion potential of soil ARGs and mobile genetic elements were significantly reduced. These findings provide microbial solutions and a theoretical basis for concurrent organic pollution control and soil ecological risk management.},
}

*Soil Pollutants/metabolism
*Microbiota
*Soil Microbiology
*Drug Resistance, Microbial/genetics
Biodegradation, Environmental
Multiomics
Genes, Bacterial

@article {pmid42623874,
year = {2026},
author = {Zhou, R and Ma, Z and Kou, S and Ni, Y and Huang, X and Wei, H and Jin, Q and Xu, H and Ding, Z},
title = {Microplastics as vectors for microbial pollutants: Biofilm-associated transfer of pathogens and antibiotic resistance genes in zebrafish intestine.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143329},
doi = {10.1016/j.jhazmat.2026.143329},
pmid = {42623874},
issn = {1873-3336},
mesh = {Animals ; *Biofilms ; *Zebrafish/microbiology ; *Microplastics/toxicity ; *Drug Resistance, Microbial/genetics ; *Gastrointestinal Microbiome/drug effects ; *Polyesters/toxicity ; Intestines/microbiology ; Polypropylenes/toxicity ; Genes, Bacterial ; Bacteria/genetics ; Gene Transfer, Horizontal ; *Water Pollutants, Chemical/toxicity ; },
abstract = {As composite carriers of microorganisms and pollutants, biofilm-attached microplastics (MPs) serve as potential vectors for the environmental migration and biotransmission of antibiotic resistance genes (ARGs) and pathogens. In this study, traditional polypropylene (PP) and biodegradable polylactic acid (PLA) MPs were used to investigate the interference effects of biofilms-attached MPs on gut microbiota and ARGs transmission, through a combination of laboratory biofilm cultivation, zebrafish (Danio rerio) exposure simulations, metagenomic sequencing, and metabolomic profiling. Results showed that MP biofilms likely induced gut dysbiosis and were associated with altered diversity and abundance of pathogens and ARGs. At the phylum level, Nitrospira was transferred from PP biofilms to the gut. At the genus level, 23 genera were transferred from MP biofilms, with PLA (23 genera) showing higher transfer capacity than PP (4 genera). Notably, two human pathogens, one opportunistic pathogen, and two ARGs (adeF and oqxB) were specifically transferred from PLA biofilms, highlighting the unique dissemination risk of biodegradable MPs. Mechanistically, MPs may activate mobile genetic elements (e.g., Tn916 transposon) through metabolic remodeling and quorum sensing, thereby promoting horizontal gene transfer and ARGs dissemination within the gut. Our findings highlight the potential role of MPs as carriers of microorganisms and ARGs, underscoring the biotransmission risks of antibiotic resistance caused by composite pollution.},
}

Animals
*Biofilms
*Zebrafish/microbiology
*Microplastics/toxicity
*Drug Resistance, Microbial/genetics
*Gastrointestinal Microbiome/drug effects
*Polyesters/toxicity
Intestines/microbiology
Polypropylenes/toxicity
Genes, Bacterial
Bacteria/genetics
Gene Transfer, Horizontal
*Water Pollutants, Chemical/toxicity

@article {pmid42624114,
year = {2026},
author = {Jang, LG and Huh, JW and Kim, S and Lee, JY and Hwang, HS and Yoon, J and Lee, HG and Kim, TI and Lee, YC and Jee, SH and Kim, JF},
title = {Mouth-to-gut microbial transmission signatures enable robust, non-invasive diagnosis of gastrointestinal cancers.},
journal = {Cell host & microbe},
volume = {34},
number = {9},
pages = {1829-1842.e5},
doi = {10.1016/j.chom.2026.07.007},
pmid = {42624114},
issn = {1934-6069},
mesh = {Humans ; *Mouth/microbiology ; Feces/microbiology ; *Gastrointestinal Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome ; Female ; Bacteria/classification/genetics/isolation & purification ; Male ; Middle Aged ; *Microbiota ; },
abstract = {The human microbiome is spatially compartmentalized, yet oral bacteria can ectopically colonize distal sites such as the gut, potentially influencing disease. By analyzing paired oral and fecal microbiomes from 507 participants across healthy controls and patients with metabolic disorders or gastrointestinal cancers, we established a quantitative mouth-to-feces (MF) index to measure MF microbial transmission. The MF index revealed elevated mouth-to-gut transmission in cancer and a strong association with host metabolic and inflammatory indicators. Using transmitted taxa, we developed a random forest classifier that accurately distinguished gastric/colorectal cancer from healthy controls across seven independent cohorts, even when trained solely on oral microbiome data. When benchmarked against the conventional screening test, the MF-based model achieved markedly higher sensitivity than the fecal occult blood test. These findings uncover disease-specific transmission signatures and highlight MF microbial profiling as a generalizable, non-invasive framework for gastrointestinal cancer diagnosis and risk stratification.},
}

Humans
*Mouth/microbiology
Feces/microbiology
*Gastrointestinal Neoplasms/diagnosis/microbiology
*Gastrointestinal Microbiome
Female
Bacteria/classification/genetics/isolation & purification
Male
Middle Aged
*Microbiota

@article {pmid42648293,
year = {2026},
author = {Oka, A and Bongers, G and Mishima, Y and Baltus, AJ and Gray, SM and Liu, B and Herzog, JW and Benedetto, JR and Fan, TJ and Jang, J and Awoniyi, M and Rousta, E and Hao, LY and Gharaibeh, RZ and Fodor, AA and Ohkusa, T and Atarashi, K and Fukuda, S and Honda, K and San Mateo, LR and Sartor, RB},
title = {Defined human Clostridia consortia reverse colitis via dual effects of tryptophan metabolites on microbiota and immunity.},
journal = {Cell host & microbe},
volume = {34},
number = {9},
pages = {1746-1763.e15},
doi = {10.1016/j.chom.2026.08.003},
pmid = {42648293},
issn = {1934-6069},
support = {K08 DK144596/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Humans ; *Colitis/therapy/microbiology/immunology ; *Tryptophan/metabolism ; Inflammatory Bowel Diseases/therapy/microbiology/immunology ; Mice ; Disease Models, Animal ; Dysbiosis/therapy ; Receptors, Aryl Hydrocarbon/metabolism ; *Clostridium/metabolism ; Interleukin-10/metabolism ; T-Lymphocytes, Regulatory/immunology ; *Microbiota ; Fatty Acids, Volatile/metabolism ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; },
abstract = {Microbial dysbiosis and disrupted mucosal immune homeostasis are integrally involved in the pathogenesis of inflammatory bowel diseases (IBDs). Live biotherapeutic products (LBPs) offer a potential therapeutic strategy to restore beneficial microbes and mitigate disease. We investigated the therapeutic efficacy of 2 LBPs, human Clostridia consortia 17-mix and 11-mix, by treating established colitis in murine models. Both LBPs exhibited therapeutic effects in T cell-mediated chronic colitis models induced by human microbiota and in pathobiont-driven gnotobiotic colitis models established with combinations of IBD-relevant human-derived strains. Metagenomic and metabolomic analyses elucidated mechanisms that go beyond established functions driven by short-chain fatty acids (SCFAs) and interleukin (IL)-10-producing regulatory T cells. Notably, LBPs exerted therapeutic effects by directly inhibiting resident pathobionts and through IL-10-independent activation of host anti-inflammatory aryl hydrocarbon receptor (AhR) pathways by bacterial tryptophan metabolites. These results elucidate SCFA- and IL-10-independent protective mechanisms exerted by defined resident bacterial strains that are depleted in IBD dysbiosis.},
}

Animals
Humans
*Colitis/therapy/microbiology/immunology
*Tryptophan/metabolism
Inflammatory Bowel Diseases/therapy/microbiology/immunology
Mice
Disease Models, Animal
Dysbiosis/therapy
Receptors, Aryl Hydrocarbon/metabolism
*Clostridium/metabolism
Interleukin-10/metabolism
T-Lymphocytes, Regulatory/immunology
*Microbiota
Fatty Acids, Volatile/metabolism
Mice, Inbred C57BL
*Gastrointestinal Microbiome

@article {pmid42711823,
year = {2026},
author = {Saragiotto, GK and de Oliveira, LFV and Geciana Tomaz Dos Santos, B and Nunes Sanches, R and Merizzi de Oliveira, M and Campos Freire, F and Dias de Oliveira Carvalho, R and Sivieri, K and Sartoratto, A and Cabral, L and Azevedo, V and Belli, T and Costa Antunes, AE},
title = {Exploratory case comparison of gut microbiome functional potential in ultramarathoners differing in adiposity and finish time.},
journal = {Journal of the International Society of Sports Nutrition},
volume = {23},
number = {1},
pages = {2725874},
doi = {10.1080/15502783.2026.2725874},
pmid = {42711823},
issn = {1550-2783},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Feces/chemistry/microbiology ; *Adiposity/physiology ; *Obesity/microbiology/physiopathology ; *Marathon Running/physiology ; Fatty Acids, Volatile/analysis/metabolism ; Male ; Body Mass Index ; *Physical Endurance/physiology ; *Running/physiology ; },
abstract = {Understanding variations in gut microbial functional potential among endurance athletes may inform future personalized nutritional strategies. This exploratory case-comparison study aimed to investigate predicted microbial functional potential using shotgun metagenomic sequencing and fecal metabolites, in two post hoc-selected runners who represented extreme and contrasting outcomes from the same single-stage 217 km mountain ultramarathon: a normal-BMI fast-finisher and an obese slow-finisher. The main descriptive findings suggest that the normal-BMI fast finisher exhibited smaller observed differences among the analyzed enzyme-coding functions and pathways in the sample collected after race completion, with a predominance of enzyme-coding functions associated with nucleic acid-related processes and protein biosynthesis. In contrast, the obese slow-finisher showed larger observed differences in predicted functional potential between the pre- and post-race samples. Distinct fecal metabolite patterns were also observed, with selective short-chain fatty acid (SCFA) changes in the normal-BMI fast-finisher and reductions across all analyzed SCFAs in the obese slow finisher. Given the limitations of this study, including the confounding effects of adiposity, unmeasured dietary intake, and post hoc selection bias, these descriptive observations provide hypothesis-generating data rather than establishing causal relationships with performance. Taken together, these findings encourage further investigation in larger cohorts.},
}

Humans
*Gastrointestinal Microbiome/physiology
Feces/chemistry/microbiology
*Adiposity/physiology
*Obesity/microbiology/physiopathology
*Marathon Running/physiology
Fatty Acids, Volatile/analysis/metabolism
Male
Body Mass Index
*Physical Endurance/physiology
*Running/physiology

@article {pmid42711968,
year = {2026},
author = {Liang, G and Wang, C and Liu, R and Ji, Q and Zhang, X and Zhao, L and Liu, X and Zhang, H and Zhuang, G and Zheng, J},
title = {Assembly Dynamics and Functional Divergence of Anaerobic Communities Driven by Iron Oxides.},
journal = {Environmental microbiology},
volume = {28},
number = {9},
pages = {e70412},
doi = {10.1111/1462-2920.70412},
pmid = {42711968},
issn = {1462-2920},
support = {GYY-NYHJ-2023-WT-002//the Weiqiao-UCAS Innovation Research Projects on Carbon Neutrality Technology/ ; },
mesh = {*Ferric Compounds/metabolism/chemistry ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Sewage/microbiology ; Anaerobiosis ; Minerals/metabolism ; Ferrosoferric Oxide/metabolism ; Methane/metabolism ; Iron Compounds ; },
abstract = {Iron oxides play an important role in regulating global biogeochemical cycles, yet how their physicochemical properties influence community structure, function, and assembly remains poorly understood. Here, we investigated the effects of four representative iron oxides-ferrihydrite (Fh), goethite (Gt), haematite (Ht), and magnetite (Mt)-serving as terminal electron acceptors on microbial communities enriched from activated sludge. Metagenomic profiling revealed mineral-dependent divergence in community composition and functional potential. The communities developed on amorphous Fh demonstrated low microbial diversity and were heavily dominated by Pseudomonas_A. In contrast, the communities associated with crystalline oxides (Gt and Ht) maintained intermediate diversity. Notably, the Mt. communities exhibited a more polycentric structure, possessing the highest richness and evenness, alongside a significant enrichment of Geobacter. Methane was detected in crystalline-oxide systems but remained below detection in Fh systems. Mineralogical analyses revealed substantial Fe(III) reduction and secondary mineral formation across treatments. Null-model analysis of pairwise turnover supports mineral-associated community turnover while highlighting that the relative contributions of selection versus undominated processes vary among minerals. Overall, these findings demonstrate that iron oxide identity is associated with differences in anaerobic community structure and biogeochemical outcomes.},
}

*Ferric Compounds/metabolism/chemistry
*Microbiota
*Bacteria/classification/genetics/metabolism/isolation & purification
*Sewage/microbiology
Anaerobiosis
Minerals/metabolism
Ferrosoferric Oxide/metabolism
Methane/metabolism
Iron Compounds

@article {pmid42711992,
year = {2026},
author = {Farese, M and Moraitou, M and Jin, C and Forsythe, A and Micarelli, I and van der Valk, T and Manzi, G and Parducci, L and Tafuri, MA and Guschanski, K},
title = {Lifestyle Impacts the Oral Microbiome of Classical and Post-Classical Societies in Italy.},
journal = {American journal of biological anthropology},
volume = {191},
number = {1},
pages = {e70357},
doi = {10.1002/ajpa.70357},
pmid = {42711992},
issn = {2692-7691},
support = {//Bertil Lundman Foundation for Anthropological Studies (Swedish Phytogeographical Society)/ ; DOT1326JZS//Italian Ministry of University and Research (MUR)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Italy ; History, Ancient ; *Life Style/history ; Dental Calculus/microbiology ; DNA, Ancient/analysis ; *Mouth/microbiology ; Roman World/history ; },
abstract = {OBJECTIVES: The fall of the Roman Empire (476 CE) profoundly affected the lives of its peoples due to the political, administrative, and territorial changes that occurred. The majority of written records of the time focus on the social élite, leaving larger parts of the population understudied. Here, we employ a bioarchaeological approach to understand how differences in lifestyle may be reflected in the oral microbiome of people from different social classes living before and after the fall.

MATERIAL AND METHODS: We analyzed shotgun sequencing data from dental calculus, the preserved oral microbiome, of 67 individuals belonging to different social classes from two Classical cemeteries (I-III century CE, Lucus Feroniae and Isola Sacra) and one post-Classical cemetery (IV-VIII century CE, Selvicciola), all located in proximity to the city of Rome, Italy.

RESULTS: We detect significant differences in the taxonomic and functional composition of the oral microbiome between the three sites, with the rural town of Lucus Feroniae standing out compared to its two counterparts. Reliable identification of dietary items was not possible.

DISCUSSION: The distinct oral microbiome of Lucus Feroniae could reflect differences in general health and subsistence practices, in line with previously published isotopic and morphological data. Its rural position may have mitigated the cyclical food crises that affected the contemporary Isola Sacra and the later community of Selvicciola, buffering it against the nutritional stress observed in these two locations. This finding supports the temporal stability of the dental calculus microbiome while highlighting the impact of lifestyle on the oral microbial communities.},
}

Humans
*Microbiota/genetics
Italy
History, Ancient
*Life Style/history
Dental Calculus/microbiology
DNA, Ancient/analysis
*Mouth/microbiology
Roman World/history

@article {pmid42712102,
year = {2026},
author = {Pellegrini, C and Ravaioli, F and De Fanti, S and Siliquini, A and Sala, C and Rochat, M and Pollarini, V and Polischi, B and Pasti, A and Grasso, M and Rambaldi, M and Cardoni, F and Grotteschi, N and Caraci, F and Cortelli, P and Provini, F and Lodi, R and Morandi, L and Parchi, P and Pirazzoli, GL and Sambati, L and Tonon, C and Bacalini, MG},
title = {Alterations of gut microbiota in Down syndrome and their association with Alzheimer's disease.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {9},
pages = {e71815},
doi = {10.1002/alz.71815},
pmid = {42712102},
issn = {1552-5279},
support = {PNC0000002//Italian Complementary National Plan PNC-1.1 "Research initiatives for innovative technologies and pathways in the health and welfare sector" D.D. 931 of 06/06/2022, "DARE-DigitAl lifelong pRvEntion" initiative/ ; B53C22006330001//Italian Complementary National Plan PNC-1.1 "Research initiatives for innovative technologies and pathways in the health and welfare sector" D.D. 931 of 06/06/2022, "DARE-DigitAl lifelong pRvEntion" initiative/ ; GR-2019-12369983-Theory-enhancing//Italian Ministry of Health/ ; //Italian Ministry of Health - "Ricerca Corrente" funding/ ; },
mesh = {Humans ; *Down Syndrome/microbiology/blood/complications ; *Alzheimer Disease/blood/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Aged ; Adult ; Biomarkers/blood ; Aged, 80 and over ; tau Proteins/blood ; Feces/microbiology ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Neurofilament Proteins/blood ; Glial Fibrillary Acidic Protein/blood ; },
abstract = {INTRODUCTION: Adults with Down syndrome (DS) have a higher risk of Alzheimer's disease (AD). As gut microbiota (GM) alterations have been reported in AD, we investigated their association with cognitive decline and plasma AD biomarkers in DS.

METHODS: Fecal and plasma samples were collected from 58 adults with DS (21-75 years) and 30 euploid controls (CTRL; 25-83 years). GM was profiled using 16S rRNA sequencing, filtering low prevalent taxa. Major neurocognitive disorder (NcD) was diagnosed with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) criteria. Plasma levels of phosphorylated tau 181 (p-tau181), neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP) were measured using Simoa.

RESULTS: DS showed no changes in overall microbial diversity compared to CTRL, but genera including UBA1819 and Intestinibacter were altered. Specific genera showed changes in DS with NcD, like Alistipes (increased) and Roseburia (decreased), with the latter negatively associated with plasma AD biomarkers.

DISCUSSION: Adults with DS display AD-associated changes in GM partially resembling those reported previously in euploid AD patients.},
}

Humans
*Down Syndrome/microbiology/blood/complications
*Alzheimer Disease/blood/microbiology
Female
Male
*Gastrointestinal Microbiome/physiology
Middle Aged
Aged
Adult
Biomarkers/blood
Aged, 80 and over
tau Proteins/blood
Feces/microbiology
Young Adult
RNA, Ribosomal, 16S/genetics
Neurofilament Proteins/blood
Glial Fibrillary Acidic Protein/blood

@article {pmid42712939,
year = {2026},
author = {Tiwari, SK and Telatin, A and Singh, D},
title = {Identifying fundamental gaps in functional metagenomics: a step towards unlocking microbiome research potential.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag110},
pmid = {42712939},
issn = {2631-9268},
mesh = {Humans ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Molecular Sequence Annotation ; },
abstract = {Incomplete functional annotation limits biological interpretation in microbiome studies and their translational potential. Poor annotation arises from multiple causes, with incomplete gene-protein-reaction mapping being one tractable yet under-examined contributor. We address this gap by developing a comprehensive hierarchical framework that systematically integrates gene families in UniRef, proteins in UniProt, and metabolic reactions in MetaCyc and BioCyc through UniProtKB accession, EC number, and Pfam-domain matching. Applied to a human gut metagenome dataset via HUMAnN3, our MetaCyc-based mapping recovers up to 2.3-fold more unique reaction identifiers than the default pipeline and increases reaction prevalence across samples from ≈32% to 52% core reactions, addressing the data sparsity that limits statistical and machine-learning applications in microbiome research. Biological plausibility for the tested functions was supported by positive and negative controls: gut-microbial hormone-metabolism reactions previously linked to this dataset were recovered, while vertebrate-specific hormone-metabolism reactions remained correctly undetected. These gains derive from systematic database integration alone, without predictive algorithms, indicating that a tractable, mapping-related component of functional dark matter and data sparsity in microbiome studies is directly addressable. Because Pfam- and BioCyc-derived mappings trade specificity for coverage, confidence in any individual reaction assignment depends on the supporting evidence tier and source database.},
}

Humans
*Metagenomics/methods
*Metagenome
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics
Molecular Sequence Annotation

@article {pmid42713785,
year = {2026},
author = {Thakur, R and Dhar, H and Kiran, S and Gulati, A},
title = {Metagenomic Insights Into Microbial Diversity of Tea Rhizosphere of the Kangra Valley.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70416},
doi = {10.1002/mbo3.70416},
pmid = {42713785},
issn = {2045-8827},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Fungi/classification/genetics/isolation & purification ; *Tea/microbiology ; Metagenomics ; Sequence Analysis, DNA ; Biodiversity ; Phylogeny ; DNA, Bacterial/genetics/chemistry ; China ; DNA, Fungal/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; DNA, Ribosomal Spacer/genetics/chemistry ; },
abstract = {This study provides the first metagenomic assessment of microbial diversity from the tea rhizosphere of the Kangra valley. Tea rhizosphere soil samples were collected from 4 locations (Dharamshala, Baijnath, Palampur, and Joginder Nagar) of the Kangra valley. DNA extracts of rhizosphere samples were analysed for bacterial and Archaeal diversity using amplicon sequencing (V3-V4) region of the 16S rRNA gene and Fungal diversity using ITS1 and ITS2 regions. Baijnath and Palampur samples showed the highest bacterial richness, while Dharamshala and Palampur had the highest fungal richness. Proteobacteria was a dominant phylum in all the rhizosphere samples, followed by Firmicutes, Actinobacteria, Acidobacteria, and Bacteroidetes. A total of 11 fungal phyla were identified among all the locations, with abundance of Ascomycota and Basidiomycota. For the Archaea domain, uncultured archaeon and Aeropyrum camini were the most common found among all the locations. A small fraction (< 0.5%) of Bacillus and Pseudomonas species were observed among all the locations. Alpha and beta diversity indices displayed notable differences within and between microbial diversities. Soil factors were variably associated with microbial diversity, with nitrogen positively aligned with fungal diversity, while EC and K were associated with Archaeal diversity. Soil pH and OM% showed moderate associations with bacterial diversity. These findings provided valuable and comprehensive insights into tea rhizosphere microbial ecology and could be used to better understand microbial functions and their role in plant health.},
}

*Rhizosphere
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Archaea/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Fungi/classification/genetics/isolation & purification
*Tea/microbiology
Metagenomics
Sequence Analysis, DNA
Biodiversity
Phylogeny
DNA, Bacterial/genetics/chemistry
China
DNA, Fungal/genetics/chemistry
DNA, Ribosomal/genetics/chemistry
DNA, Ribosomal Spacer/genetics/chemistry

@article {pmid42715940,
year = {2026},
author = {Jin, CH and Liu, SR and Song, WT and Yuan, SK and Zhang, YZ and Wang, P and Sun, XT and Liu, XQ and Fang, GY},
title = {Metagenomic Insights into Microbial Assembly and Key Metabolic Genes Driving Flavor Formation in Spontaneously Fermented Zhejiang Rosy Vinegar.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {35},
pages = {27821-27839},
doi = {10.1021/acs.jafc.6c10005},
pmid = {42715940},
issn = {1520-5118},
support = {32401323//National Natural Science Foundation of China/ ; 2024LFR050//Zhejiang A and F University/ ; 2026R412A027//Xinmiao Talent Program/ ; NA//Zhejiang Provincial College Students' Science & Technology Activity Plan/ ; },
mesh = {*Acetic Acid/metabolism/chemistry ; Fermentation ; Acetobacter/genetics/metabolism ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Flavoring Agents/metabolism/chemistry ; *Fungi/genetics/metabolism/classification/isolation & purification ; Saccharomyces cerevisiae/metabolism/genetics ; Metagenomics ; Microbiota ; Bacterial Proteins/genetics/metabolism ; },
abstract = {The spontaneous fermentation of Zhejiang rosy vinegar (ZRV) is driven by environmental microbiota, but the processes underlying its flavor formation remain poorly understood. Using metagenomic sequencing, we investigated microbial community assembly, environmental drivers, and metabolic networks during industrial-scale ZRV fermentation. Acetic acid dominated the final organic acids. Community assembly shifted toward deterministic selection with rising acidity, with a slight rebound of stochastic processes in the late stage (R2 values of 0.442 and 0.346 for bacteria and fungi, respectively). Mantel tests confirmed that environmental factors significantly regulated microbial assembly. Co-occurrence networks grew more complex, with positive interactions accounting for 85.24% (bacteria) and 90.10% (fungi) in the late stage. Key genes (ldh, gapA, pgk) from Acetobacter pasteurianus and Lactobacillus acetotolerans dominated late-stage fermentation, while genes (adhP, SDH) from Aspergillus oryzae and Saccharomyces cerevisiae supported early- and mid-stage fermentation. These findings elucidate microbiota-driven metabolic pathways in ZRV, supporting the fermentation window optimization and industrial vinegar quality standardization.},
}

*Acetic Acid/metabolism/chemistry
Fermentation
Acetobacter/genetics/metabolism
*Bacteria/genetics/metabolism/classification/isolation & purification
*Flavoring Agents/metabolism/chemistry
*Fungi/genetics/metabolism/classification/isolation & purification
Saccharomyces cerevisiae/metabolism/genetics
Metagenomics
Microbiota
Bacterial Proteins/genetics/metabolism

@article {pmid42200417,
year = {2026},
author = {Lin, L and Gao, G and Sun, S and Wu, X and Fan, S and Wang, H and Zhou, F and Zhang, X},
title = {Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.},
journal = {Insect molecular biology},
volume = {35},
number = {5},
pages = {489-503},
doi = {10.1111/imb.70046},
pmid = {42200417},
issn = {1365-2583},
support = {2024KJI002//Young Innovation Team Project of Higher Education in Shandong Province/ ; 2024ZDZX10//QLU Major Innovation Projects of Education-Industry Integration Pilot/ ; SDAIT-31-04//Shandong Province Key Agricultural Project for Application Technology Innovation/ ; 32272530//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Diptera/microbiology/growth & development ; Metagenomics ; Larva/microbiology/growth & development ; *Vitamin B 6/metabolism ; Symbiosis ; *Gastrointestinal Microbiome ; },
abstract = {Insect guts host a diverse and abundant array of microorganisms. These microbes improve host fitness by extensively involving in a range of crucial physiological processes, which have mainly been revealed by high-throughput sequencing, particularly metagenomics. However, it is almost impossible to make an accurate and complete distinction between the genetic functions of microbial symbionts and insect hosts without host genome data. By comparing metagenomic data from gut germ-free and nonaxenic larvae, we accurately identified the data belonging to the gut microbiome of the onion maggot Delia antiqua (Diptera: Anthomyiidae). Besides, a correlation between bacteria of the genus Wohlfahrtiimonas (Gammaproteobacteria: Pseudomonadaceae) and vitamin B6 metabolism was detected through collinearity analysis. Furthermore, in vitro tests confirmed that the gut bacterium Wohlfahrtiimonas larvae contributed to the growth of D. antiqua larvae via the independent synthesis of vitamin B6. This study provides a comprehensive view of the gut bacterial diversity in D. antiqua and reveals a functional profile that is strictly specific to the gut microbiota of this species. It has preliminarily revealed the functional differentiation between insect hosts and their symbiotic microorganisms. This study also offers a technical reference for the study of microbial symbiotic functions in other insect-microbe symbioses without host genomic data.},
}

Animals
*Diptera/microbiology/growth & development
Metagenomics
Larva/microbiology/growth & development
*Vitamin B 6/metabolism
Symbiosis
*Gastrointestinal Microbiome

@article {pmid42442593,
year = {2027},
author = {Qi, T and Liu, Q and Li, M and Li, H and Liang, G and Tu, W},
title = {Integrating lung microbiome, amino acid metabolism, and host immune response in elderly patients for severe lower respiratory Infections diagnosis: a multi-omics study.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {592},
number = {},
pages = {121232},
doi = {10.1016/j.cca.2026.121232},
pmid = {42442593},
issn = {1873-3492},
mesh = {Humans ; *Microbiota/immunology ; *Amino Acids/metabolism ; Male ; Multiomics ; Female ; *Respiratory Tract Infections/diagnosis/immunology/metabolism/microbiology ; Aged ; *Lung/microbiology/metabolism/immunology ; Prospective Studies ; Cytokines/metabolism ; Aged, 80 and over ; Metabolomics ; },
abstract = {BACKGROUND: Lower respiratory infections (LRIs) cause significant morbidity and mortality in elderly individuals, but the mechanisms driving severe deterioration remain unclear.

METHODS: This prospective study enrolled 105 patients aged ≥60 with suspected LRIs between October 2024 and April 2025. Bronchoalveolar lavage fluid (BALF) was analyzed using 16S rRNA sequencing, metagenomics, untargeted metabolomics, and cytokine profiling. Multi-omics data were integrated into a tripartite network, and severity-associated signatures were identified via PLS-DA, logistic regression, and ROC analysis.

RESULTS: The cohort included 40 severe (sLRIs) and 65 mild (mLRIs) cases. sLRIs exhibited reduced microbial diversity, shifting from commensal genera to opportunistic pathogens (Klebsiella, Corynebacterium, Elizabethkingia), with Klebsiella pneumoniae as a major bacterial hub. Metabolomics revealed 180 differential metabolites. Phenylalanine and beta-Alanine metabolism emerged as key severity-associated pathways. sLRIs showed accumulation of pro-inflammatory metabolites L-phenylalanine and phenylpyruvic acid. L-3-phenyllactic acid (PLA) served as the central metabolic hub. Cytokine profiling revealed local hyperinflammation (elevated IL-1β, IL-6, IL-8, TNF-α, IFN-γ), with IL-6 as central hubs. Multivariate analysis identified PLA and IL-8 as independently associated with severe status. Combined metabolic-immune signatures achieved high diagnostic accuracy (AUC: 0.858-0.882).

CONCLUSIONS: sLRIs in elderly patients are characterized by microbial dysbiosis, opportunistic pathogen enrichment, and remodeled Phenylalanine and beta-Alanine metabolism that correlates with hyperinflammation. BALF PLA and IL-8 represent promising metabolic-immune biomarkers for severity stratification.},
}

Humans
*Microbiota/immunology
*Amino Acids/metabolism
Male
Multiomics
Female
*Respiratory Tract Infections/diagnosis/immunology/metabolism/microbiology
Aged
*Lung/microbiology/metabolism/immunology
Prospective Studies
Cytokines/metabolism
Aged, 80 and over
Metabolomics

@article {pmid42706263,
year = {2026},
author = {He, W and Bobanga, T and Piantadosi, A and Popkin-Hall, ZR and Vulu, F and Collins, MH and Kashamuka, MM and Tshefu, AK and Juliano, JJ and Parr, JB},
title = {Evidence of dengue transmission and a diverse Aedes mosquito virome on the Congo's Angola border.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42706263},
issn = {2041-1723},
support = {INV-050353//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; K24AI134990//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; Yang Biomedical Scholar award//UNC | University of North Carolina at Chapel Hill (UNC-Chapel Hill)/ ; },
mesh = {Animals ; *Aedes/virology ; *Dengue Virus/genetics/isolation & purification ; Humans ; Angola/epidemiology ; *Dengue/transmission/epidemiology/virology ; *Virome/genetics ; *Mosquito Vectors/virology ; Democratic Republic of the Congo/epidemiology ; Female ; Congo ; },
abstract = {Aedes mosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collect Aedes mosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools, comprising 155 mosquitoes from three collection sites, confirm high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.},
}

Animals
*Aedes/virology
*Dengue Virus/genetics/isolation & purification
Humans
Angola/epidemiology
*Dengue/transmission/epidemiology/virology
*Virome/genetics
*Mosquito Vectors/virology
Democratic Republic of the Congo/epidemiology
Female
Congo

@article {pmid42706609,
year = {2026},
author = {Sun, YZ and Su, JW and Elsheikha, HM and Lou, WB and Song, YH and Li, JM and Liu, F and Cai, R and Leng, X and Gong, QL and Zhang, XX},
title = {Farming reshapes the gut resistome, virulome, and mobilome of Cervidae.},
journal = {Virulence},
volume = {17},
number = {1},
pages = {2728506},
doi = {10.1080/21505594.2026.2728506},
pmid = {42706609},
issn = {2150-5608},
mesh = {Animals ; Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Deer/microbiology/virology ; Metagenome ; Interspersed Repetitive Sequences ; Virulence Factors/genetics ; Plasmids/genetics ; Bacteriophages/genetics ; Virome ; Bacteria/genetics/drug effects/classification ; Agriculture ; },
abstract = {The rapid expansion of cervid farming raises concerns about antimicrobial resistance (AMR) dissemination, yet its impact on the Cervidae gut microbiome remains poorly characterized. We integrated 89 newly sequenced fecal metagenomes with 599 publicly available datasets, comprising 285 metagenomes from farmed cervids and 370 from wild cervids, to construct a catalog of 15,494 non-redundant metagenome-assembled genomes (MAGs) representing 2,401 species. Our analysis demonstrates that farming profoundly reshapes the gut microbiome's functional composition. Specifically, farmed cervids exhibited significantly higher relative abundance, diversity, and heterogeneity of antimicrobial resistance genes (ARGs) compared to wild counterparts. We observed a robust synergistic relationship between ARGs, virulence factor genes, and mobile genetic element (MGE)-associated genes, identifying 70 ARG-MGE combinations as evidence of potential horizontal gene transfer. Plasmid profiling further suggested that a subset of ARGs may be associated with conjugative plasmids, with plasmid-associated ARGs being significantly more abundant in farmed than in wild cervids. Virome analyses indicated that bacteriophages, particularly Siphoviridae, may serve as mobile reservoirs for ARGs. Notably, Cervidae shared 268 ARG types with humans, including 23 high-risk genes associated with resistance to clinically important antibiotics (e.g. tetX1, vanRD, and bla-CTX-M-178), with Escherichia coli as a key cross-host carrier. These findings highlight that human-impacted cervid gut microbiomes are significant environmental reservoirs of clinically relevant AMR, underscoring the necessity for enhanced antibiotic stewardship and resistance surveillance in managed wildlife within a One Health framework.},
}

Animals
Gene Transfer, Horizontal
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Deer/microbiology/virology
Metagenome
Interspersed Repetitive Sequences
Virulence Factors/genetics
Plasmids/genetics
Bacteriophages/genetics
Virome
Bacteria/genetics/drug effects/classification
Agriculture

@article {pmid42706715,
year = {2026},
author = {Sahil, R and Jain, M},
title = {Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70197},
doi = {10.1111/1755-0998.70197},
pmid = {42706715},
issn = {1755-0998},
support = {BT/PR40261/BTIS/137/55/2023//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Microbiota ; *Metagenomics/methods/standards ; *Plants/microbiology ; Benchmarking ; *Computational Biology/methods ; Metagenome ; },
abstract = {Strain-level identification of each microbe is crucial for understanding its role in the host. Most of the existing tools have primarily been evaluated on human metagenomic datasets, whereas the plant microbiome exhibits greater diversity and complexity and thus poses a challenge in the strain-level resolution of individual microbes. In this study, we conducted a comprehensive benchmarking of available reference-based tools for strain-level resolution of the plant microbiome. We evaluated seven tools on various performance parameters, like computational requirements, F1-score and relative abundances using synthetic datasets comprising microbes known to have strong associations with plants as well as real plant microbiome datasets. Our results demonstrated a better performance of StrainScan on the synthetic data, achieving higher F1-score and more accurate relative abundance estimates as compared to other tools, but its performance declined gradually with increasing strain diversity. However, StrainGE and StrainScan exhibited competitive performance on real plant metagenome data. Overall, though StrainGE exhibited better performance, it was more computationally expensive. However, StrainScan performed better in detecting low-abundance strains. Our findings suggest the comparative suitability of the available tools for the strain-level analysis of plant metagenome data and highlight the need for the development of more efficient and accurate taxonomic classifiers capable of handling the complex plant metagenome data while maintaining computational efficiency.},
}

*Microbiota
*Metagenomics/methods/standards
*Plants/microbiology
Benchmarking
*Computational Biology/methods
Metagenome

@article {pmid42707963,
year = {2026},
author = {Babu, P and Prakash, V and Subhash, S and Vanuopadath, M and Haripriyan, J and Rajan, K and Geetha, AA and P, S and Kumar, GB and Nair, BG and Madhavan, A},
title = {Gut-microbiota-mediated host immune modulation: mechanisms, pathological dysbiosis, and therapeutic frontiers.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1905445},
pmid = {42707963},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/immunology/therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/immunology ; Host-Pathogen Interactions/immunology ; *Immunomodulation ; },
abstract = {The mammalian immune system has evolved in constant dialogue with its diverse microbiota, forming an ecological and molecular partnership that is fundamental to health. This review examines how microbial communities shape immunity across developmental and functional axes, the immunological consequences of dysbiosis during infection and inflammatory disease, and emerging microbiota-targeted interventions. The host-microbiota-pathogen triad offers a framework to understand how commensals and pathogens compete for ecological niches and immune recognition, and how disturbances in this balance can cascade into chronic inflammation or infection. Microbial metabolites such as short-chain fatty acids, secondary bile acids, and tryptophan derivatives act as key bioactive intermediaries translating microbial activity into host immune architecture, influencing epigenetic programming, cellular differentiation, and mucosal barrier function. These interactions orchestrate tolerance toward commensals while maintaining effector readiness against pathogens, particularly through regulatory T cell (Treg)-Th17 balance, B cell education, and Immunoglobulin A (IgA) responses. When perturbed, as in infections caused by Clostridioides difficile, Klebsiella pneumoniae, Salmonella enterica, or Listeria monocytogenes, the ensuing dysbiosis reinforces immune dysfunction in a self-perpetuating cycle. Therapeutic frontiers now extend beyond conventional antimicrobial strategies to include live biotherapeutics, bacteriophage therapy, fecal microbiota transplantation, and metabolite-based (postbiotic) interventions. Future efforts must reconcile inter-individual microbiome variability with precision medicine, integrating metagenomic and metabolomic profiling to design safe, effective, and personalized microbiota-centered therapeutics.},
}

Humans
*Dysbiosis/immunology/therapy/microbiology
Animals
*Gastrointestinal Microbiome/immunology
Host-Pathogen Interactions/immunology
*Immunomodulation

@article {pmid42707980,
year = {2026},
author = {Li, ZL and Qu, RN and Liu, SX and Wang, W},
title = {Research progress and clinical translation prospects of the urinary tract microbiome in prostate cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1911969},
pmid = {42707980},
issn = {1664-3224},
mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/immunology ; *Microbiota ; *Urinary Tract/microbiology ; Translational Research, Biomedical ; Tumor Microenvironment ; Animals ; },
abstract = {Prostate cancer (PCa) is one of the most common malignancies in men worldwide, and its development is influenced by multiple factors, including genetic susceptibility, hormonal dysregulation, chronic inflammation, immune dysregulation, and remodeling of the tumor microenvironment. In recent years, the urinary tract microbiome has emerged as an important component of the tumor ecosystem and has attracted increasing attention in PCa research. Accumulating evidence indicates that patients with PCa exhibit characteristic microbial alterations in urine, expressed prostatic secretions, semen, and prostate tissue, and that certain taxa are associated with tumor grade, stage, and recurrence risk. These microbes may participate in tumor initiation and progression through a variety of mechanisms, such as inducing chronic inflammation, activating signaling pathways including TLR/NF-κB and STAT3, modulating the Treg/Th17 balance, influencing macrophage polarization, and interfering with androgen metabolism. Meanwhile, advances in 16S rRNA sequencing, metagenomics, metatranscriptomics, and multi-omics integration have provided powerful tools for characterizing host-microbe interactions and their functional relevance. In addition, microbiome-based biomarkers derived from non-invasive samples such as urine, together with artificial intelligence and causal inference approaches applied to multi-cohort data, may offer promising opportunities for early screening, risk stratification, treatment monitoring, and personalized intervention in PCa. However, current evidence remains largely associative, and the causal relationship between microbial changes and PCa has not yet been fully established. Major challenges, including contamination in low-biomass samples and inter-cohort heterogeneity, continue to hinder clinical translation. Future research should focus on longitudinal cohort studies, multicenter validation, standardized sampling workflows, and mechanistic experiments to clarify key microbial signatures and their biological functions, thereby accelerating the clinical application of the urinary tract microbiome in precision diagnosis and treatment of PCa.},
}

Humans
Male
*Prostatic Neoplasms/microbiology/immunology
*Microbiota
*Urinary Tract/microbiology
Translational Research, Biomedical
Tumor Microenvironment
Animals

@article {pmid42708949,
year = {2026},
author = {Jiang, Y and Chen, L and Dong, H and Li, Q and Zhao, W and Zhu, F and Jiang, J and Zhang, Y and Huang, S and Xue, S},
title = {Ecological Restoration of the Soil-Like Function in the Bauxite Residue: Natural Microbiomes Mediated Molecular Transformation of Dissolved Organic Matter.},
journal = {Environmental science & technology},
volume = {60},
number = {35},
pages = {24764-24775},
doi = {10.1021/acs.est.5c18355},
pmid = {42708949},
issn = {1520-5851},
support = {42030711//National Natural Science Foundation of China (NSFC)/ ; 42477437//National Natural Science Foundation of China (NSFC)/ ; 42671661//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil/chemistry ; *Microbiota ; *Dissolved Organic Matter ; Soil Microbiology ; Aluminum Oxide ; Carbon ; },
abstract = {Soilization of bauxite residues offers a scalable route for long-term carbon management and ecological restoration. However, the microbial processes that transform exogenous organic inputs into stable soil-like carbon pools remain poorly resolved. Here, we combined cross-ecosystem meta-analysis, machine-learning prediction, native synthetic community (SynCom) construction, 13C-labeled straw microcosms, field validation, Fourier transform ion cyclotron resonance mass spectrometry, and genome-resolved metagenomics to unravel microbiome-mediated carbon transformation at the dissolved organic matter (DOM) molecular scale. Our meta-analysis revealed that alkaline industrial wastes retained soil-like DOM signatures but were enriched in microbial humic- and protein-like components, indicating active yet incomplete carbon processing. Guided by these patterns, native SynCom inoculation increased 13C incorporation into total organic carbon (TOC) and dissolved organic carbon (DOC), enlarged biodegradable and adsorbable DOC fractions, and shifted DOM from recalcitrant aromatic pools toward oxygenated carbohydrate-, tannin-, and phenolic-like molecular classes. Genome-resolved analyses linked this transformation to complementary polymer degradation and nutrient-cycling functions across fungal and bacterial guilds, including enriched carbohydrate-active enzymes in straw-carbon-utilizing metagenome-assembled genomes. Null model and thermodynamic analyses further showed that microbial communities were constrained by homogeneous selection, whereas DOM molecules were diversified through variable selection and redox-dependent transformation. Field-scale validation confirmed that SynCom promoted TOC and DOC accumulation and humic-like, high-density DOM fractions under alkaline conditions. Together, these findings establish a mechanistic framework in which functional microbiomes couple plant carbon depolymerization, DOM molecular diversification, and mineral-interactive carbon stabilization, providing a microbiome-guided strategy for carbon sequestration and soilization in the bauxite residue.},
}

*Soil/chemistry
*Microbiota
*Dissolved Organic Matter
Soil Microbiology
Aluminum Oxide
Carbon

@article {pmid42708953,
year = {2026},
author = {Francescato, L and Ghiotto, G and Valerin, MC and De Bernardini, N and Fraulini, S and Sandon, A and Treu, L and Lavagnolo, MC and Campanaro, S},
title = {Adaptive Evolution Reveals Metabolic Plasticity and Functional Redundancy in an Anaerobic Microbiome under Extreme Ammonia Stress.},
journal = {Environmental science & technology},
volume = {60},
number = {35},
pages = {24776-24791},
doi = {10.1021/acs.est.6c05759},
pmid = {42708953},
issn = {1520-5851},
mesh = {*Ammonia ; *Microbiota ; Anaerobiosis ; Methane/metabolism ; },
abstract = {Ammonia toxicity represents a primary biochemical bottleneck governing microbial community structure and performance during the anaerobic digestion of the organic fraction of municipal solid waste. However, the mechanistic basis of microbial adaptation to chronic ammonia levels remains poorly characterized. In this study, a long-term sequential enrichment strategy under progressively increasing ammonia concentrations (350-1500 mgN L-1), integrated with genome-centric metagenomics and metatranscriptomics, was employed to resolve the response of an organic waste-degrading microbiome over a 240 day period. Increasing ammonia pressure induced a progressive decline in methanogenesis and accumulation of volatile fatty acids, particularly acetate. Despite these inhibitory pressures, methane production was only halved relative to the initial baseline reflecting a resilient methanogenic community. This stability was driven by a restructuring of the microbiome, where functional redundancy across divergent taxa preserved core metabolic functions. Key adaptive responses included the reconfiguration of carbon fixation pathways, specifically via a variant of the Wood-Ljungdahl pathway coupled with the glycine cleavage system acting as an alternative acetate oxidation route, as well as sustained osmoprotectant biosynthesis. Cellular homeostasis was preserved through H+ replenishment via multiple energy-converting complexes and K+ influx to maintain cation-proton balance. Collectively, these findings demonstrate that metabolic plasticity and the preservation of core metabolic functions are the primary determinants of ammonia resilience, sustaining methane production under inhibitory conditions.},
}

*Ammonia
*Microbiota
Anaerobiosis
Methane/metabolism

@article {pmid42236734,
year = {2026},
author = {Wei, Y and Xiao, J and He, J and Zhang, K and Xu, C and Zhang, N and Cheng, L},
title = {An integrated global resource of wetland microbiomes linking environmental metadata, community profiles, and genome-resolved metabolic traits.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42236734},
issn = {2052-4463},
support = {32501490//National Natural Science Foundation of China/ ; 32501489//National Natural Science Foundation of China/ ; 32571850//National Natural Science Foundation of China/ ; 32430070, 32025024 and 92251305//National Natural Science Foundation of China/ ; LQ24C030001//Zhejiang Provincial NSFC/ ; LQ21C030009//Zhejiang Provincial NSFC/ ; LZ24C030001//Zhejiang Provincial NSFC/ ; JYB2025XDXM909//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
mesh = {*Wetlands ; *Microbiota ; *Metadata ; *Metagenome ; Metagenomics ; },
abstract = {Wetlands are biogeochemical hotspots pivotal to global carbon and nutrient cycling, yet genome-resolved studies across diverse wetland types remain limited. To address this, we constructed a global wetland metagenomic dataset, integrating environmental metadata, community profiles, and genome-resolved metabolic traits. This dataset comprises 1,962 samples-including 129 newly sequenced field-collected samples-from lakes, rivers, paddies, marshes, and coastal wetlands, spanning water, soil, and sediment habitats. We generated comprehensive taxonomic profiles for all 1,962 samples, and used 251 samples to reconstruct 5,704 sample-specific metagenome-assembled genomes (MAGs). These MAGs were subsequently dereplicated to establish a normalized, non-redundant catalog of 4,164 representative genomes. We further mapped gene repertoires to 549 KEGG modules to decode the metabolic potential of all 5,704 MAGs. This dataset depicts an overview of microbial genomic diversity across global wetlands and provides a comprehensive resource for understanding the metabolic capabilities, ecology, and evolution of wetland microbiomes.},
}

*Wetlands
*Microbiota
*Metadata
*Metagenome
Metagenomics

@article {pmid42315898,
year = {2026},
author = {Mishra, S and Mutnuri, S},
title = {Exploring biohydrogen producing potential of Arctic ice and water through metagenomics and dark fermentation kinetics.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42315898},
issn = {2045-2322},
mesh = {*Fermentation ; *Metagenomics/methods ; Arctic Regions ; *Hydrogen/metabolism ; Kinetics ; Microbiota ; *Biofuels ; *Ice ; },
abstract = {Cryospheric ecosystems in the high Arctic harbor largely unexplored microbiomes with significant biotechnological potential. The present study evaluates the biohydrogen production capabilities of the indigenous microbiome of Ny-Ålesund, Svalbard, using glacial ice and surface water samples. Dark fermentation batch assays were performed at 4 °C and 20 °C with 2-bromoethanesulfonate (BES), a methanogenic inhibitor, to track the succession of metabolic and taxonomic diversity. Metagenomic and functional analyses revealed that under 20 °C and BES conditions, psychrotolerant microbial communities maximize biohydrogen production to 85% of the total biogas produced, with an acetate-dominant fermentation pathway, as inferred from volatile fatty acid (VFA) analysis. This evolves into a highly coordinated system utilizing a coupled Rnf-nitrogenase route alongside Formate Hydrogenlyase and [FeFe]-hydrogenase pathways. Kinetic modelling using the Modified Gompertz equation, along with Q10 temperature-sensitivity indices, demonstrated a very high latent catalytic potential in these cold-adapted microbiomes. This study indicates that Arctic microbiomes are highly elastic thermodynamically and could serve as highly efficient, manipulatable biocatalysts for the environmental recovery of bioenergy through engineered low-temperature systems.},
}

*Fermentation
*Metagenomics/methods
Arctic Regions
*Hydrogen/metabolism
Kinetics
Microbiota
*Biofuels
*Ice

@article {pmid42332773,
year = {2026},
author = {Liang, X and Zhu, L and Li, J and Li, Y and Ivey, KL and Lee, KH and Eliassen, AH and Chan, AT and Huttenhower, C and Zhang, C and Hu, FB and Qi, Q and Hu, Y and Rimm, EB and Sun, Q},
title = {Circulating imidazole propionate and coronary heart disease risk: interplay between histidine intake, fiber, and gut microbiome.},
journal = {BMC medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42332773},
issn = {1741-7015},
support = {UM1 CA186107/NH/NIH HHS/United States ; HL060712/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; HL035464/HL/NHLBI NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; DK119268/DK/NIDDK NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; U01CA152904/CA/NCI NIH HHS/United States ; DK120870//National Heart, Lung, and Blood Institute (NHLBI)/ ; UM1 CA186107/NH/NIH HHS/United States ; HL060712/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; HL035464/HL/NHLBI NIH HHS/United States ; DK126698/HL/NHLBI NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; DK119268/DK/NIDDK NIH HHS/United States ; DK129670/DK/NIDDK NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; ES036206/ES/NIEHS NIH HHS/United States ; U01CA152904/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Imidazoles/blood ; *Dietary Fiber/administration & dosage ; *Coronary Disease/blood/epidemiology/microbiology ; *Histidine/administration & dosage/metabolism ; Middle Aged ; Prospective Studies ; *Propionates/blood ; Adult ; },
abstract = {BACKGROUND: Imidazole propionate (ImP), a microbial metabolite of histidine, may impair glucose metabolism, but its relevance to coronary heart disease (CHD) risk and potential diet-microbiota regulations remain unclear. We aimed to examine prospective associations of plasma ImP levels and histidine intake with CHD risk, to identify ImP-predicting gut microbes, and to investigate diet-microbiome interactions influencing ImP levels.

METHODS: Associations of ImP and histidine with CHD risk were evaluated using Cox models in 7,432 participants from Nurses' Health Study (NHS), NHSII, and Health Professionals Follow-up Study. Microbiome-diet interactions influencing ImP levels were assessed using fecal metagenome and 7-day diet record data in 296 men from the Men's Lifestyle Validation Study, with replication in the Mind-Body Study.

RESULTS: Higher plasma ImP was associated with increased CHD risk (HR comparing extreme quintiles = 1.82; 95%CI = 1.17-2.81; p-trend = 0.002), while histidine intake showed a non-significant inverse association. Although histidine intake was not associated with ImP levels, the intake of fiber, especially pectin, emerged as a key negative predictor. We identified 17 distinct ImP-predicting species, including Clostridium and Blautia species. A parametric ImP-microbial score was constructed based on these species to represent the microbial capacity of producing ImP. Further functional characterization uncovered that the microbial urocanate reductase gene urdA was also associated with cardiovascular risk markers. No significant interaction was observed between histidine intake and the microbial score on ImP levels, but ImP levels increased with higher histidine intake and higher microbial score only under low pectin intake (p for 3-way interaction = 0.01). Similar interactions were seen for total fiber (p = 0.09), soluble fiber (p = 0.09), and insoluble fiber (p = 0.11), without statistical significance.

CONCLUSIONS: ImP, but not its dietary precursor histidine, was associated with a higher CHD risk. The gut microbial metabolism of ImP appeared context-dependent, with ImP production from histidine associated with a higher ImP-producing microbial capacity and lower fiber intake. These findings highlight the potential role of dietary fiber and gut microbiome in modulating diet-health associations related to ImP metabolism.},
}

Humans
*Gastrointestinal Microbiome
Male
*Imidazoles/blood
*Dietary Fiber/administration & dosage
*Coronary Disease/blood/epidemiology/microbiology
*Histidine/administration & dosage/metabolism
Middle Aged
Prospective Studies
*Propionates/blood
Adult

@article {pmid42508343,
year = {2026},
author = {Singh, CK and Sodhi, KK and Seth, R and Seth, RK},
title = {Gamma radiation-induced changes in the male adult gut bacterial community composition of a serious pest, Spodoptera litura (Noctuidae: Lepidoptera) and its F1 progeny.},
journal = {Applied radiation and isotopes : including data, instrumentation and methods for use in agriculture, industry and medicine},
volume = {237},
number = {},
pages = {112830},
doi = {10.1016/j.apradiso.2026.112830},
pmid = {42508343},
issn = {1872-9800},
mesh = {Animals ; Male ; *Gamma Rays ; *Spodoptera/microbiology/radiation effects ; *Gastrointestinal Microbiome/radiation effects ; Bacteria/radiation effects/genetics ; },
abstract = {Spodoptera litura (Fabr), a noctuid Lepidopteran pest, can be effectively controlled using Inherited Sterility Technique (IS), a modified version of the Sterile Insect Technique (SIT). To ensure its operational success, the role of the gut microbiome in irradiation-induced fitness effects needs to be characterized. The role of gut bacteriome of the irradiated (130Gy) male adult moth and their F1 progeny was systematically examined. The current study aims to assess the effect of irradiation on bacterial diversity and relate with the reproductive performance of radio-sterilized moths. A culture-independent, high-throughput amplicon sequencing approach targeting bacterial 16S rRNA gene regions was employed to profile microbiome composition and diversity. Three experimental regimens were established: (i) unirradiated control males (N), (ii) partially sterilized males exposed to 130Gy (130Gy P1), and (iii) male F1 progeny derived from irradiated male parent (130Gy F1). Bacterial diversity and richness were reduced in gut of both the irradiated male parent and its F1 progeny compared with control (N). The Proteobacteria abundance was increased in the gut of 130 Gy P as compared to the control, whereas in the 130Gy F1 gut, its abundance was decreased significantly. The Firmicutes dominated the gut microbiome of the 130Gy F1 male moths. Further, the principal component analysis plot showed that the normal male moths were more closely related to 130 Gy P male moths in terms of gut bacterial diversity than to 130Gy F1 male moths. The functional pathways involved in the chitin and chloramphenicol were enriched in the guts of irradiated parent moths, whereas lignin degradation was enriched in 130Gy F1 progeny with respect to the control. This study might indicate the relevance of microbiome in reproductive fitness of irradiated moths and help in the optimization of this radio-genetic technique by validating the proposed gamma dose of 130Gy, towards pest control operations.},
}

Animals
Male
*Gamma Rays
*Spodoptera/microbiology/radiation effects
*Gastrointestinal Microbiome/radiation effects
Bacteria/radiation effects/genetics

@article {pmid42518032,
year = {2026},
author = {Li, F and Zhao, H and Lei, Y and Luo, J and Chen, B and Li, C and Zhao, X and Jiang, H},
title = {Fufangteng Yixin Formula alleviates myocardial ischemia-reperfusion injury by modulating gut microbiota and resultant metabolites in rats.},
journal = {Journal of natural medicines},
volume = {80},
number = {5},
pages = {1521-1537},
pmid = {42518032},
issn = {1861-0293},
support = {2024GXNSFBA010207//Guangxi Natural Science Foundation Joint Special Project/ ; },
mesh = {Animals ; Rats ; *Myocardial Reperfusion Injury/drug therapy/metabolism ; *Gastrointestinal Microbiome/drug effects ; Male ; Rats, Wistar ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; },
abstract = {This study aimed to explore whether Fufangteng Yixin Formula (FFTYXF) can ameliorate myocardial ischemia-reperfusion injury (MIRI) by regulating the gut microbiota and resultant metabolites. Wistar rats were given FFTYXF by gavage for 7 days, and MIRI rat model was established. Serum level of inflammatory markers was determined by ELISA, and heart function was evaluated by echocardiography. Myocardial histological changes and infarct size were examined by hematoxylin-eosin and triphenyltetrazolium chloride staining, respectively. 16S rRNA gene and metagenomics analyses were employed to explore gut microbiota, while untargeted metabolomics analysis was used to explore serum metabolites. FFTYXF pretreatment could significantly improve cardiac function, reduce infarct size, decrease level of inflammatory factors (TNF-α and IL-6) and inflammatory cells infiltration. At genus level, g__Oscillibacter and g__Rikenellaceae_RC9_gut_group were identified as key microbial bacteria in MIRI rat response to FFTYXF pretreatment. After FFTYXF pretreatment, the functional categories of gut microbiota were participated in fatty acid (FA) biosynthesis/metabolism, glycolysis _ gluconeogenesis and sphingolipid metabolism. Genes response to FFTYXF pretreatment in MIRI rats included K00023 (phbB), K00281 (GLDC, gcvP), K03879 (ND2), K07827 (KRAS) and K15192 (BTAF1), and they were mainly participated in carbon, butanoate, glyoxylate and dicarboxylate metabolism. Differential metabolites were also mainly participated in FA biosynthesis/metabolism, such as alpha-Linolenic acid, omega-3/omega-6 FA, and flavan-3-ol metabolic pathway. Abundance of g__Rikenellaceae_RC9_gut_group positively correlated with differential metabolites FAHFA 34:0, FAHFA 16:1/18:3, and FA 24:5. FFTYXF could alleviate MIRI by modulating gut microbial bacteria alteration and resultant metabolites, particularly short-chain FAs.},
}

Animals
Rats
*Myocardial Reperfusion Injury/drug therapy/metabolism
*Gastrointestinal Microbiome/drug effects
Male
Rats, Wistar
*Drugs, Chinese Herbal/pharmacology/therapeutic use

@article {pmid42631636,
year = {2026},
author = {Azouz, S and Benabid, M and Zarrouk, S and Elati, J and Aoun, K and Bouratbine, A},
title = {Contribution of a combined approach using refined enterotyping and non-negative matrix factorization (NMF) to the characterization of the gut microbiota in Tunisia, North Africa.},
journal = {FEMS microbiology letters},
volume = {373},
number = {},
pages = {},
doi = {10.1093/femsle/fnag095},
pmid = {42631636},
issn = {1574-6968},
support = {//Ministry of Higher Education and Science/ ; },
mesh = {Humans ; Tunisia ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; Pilot Projects ; Adult ; Metagenomics/methods ; Metagenome ; Shotgun Sequencing ; Male ; Female ; },
abstract = {This pilot study aimed to assess the enhanced capabilities of a combined approach using refined enterotyping and non-negative matrix factorization (NMF) for identifying specific microbiota patterns in healthy adults in Tunisia. Shotgun metagenomic sequencing was performed on 21 stool samples. Taxonomic classification was carried out using Kraken2, followed by Bracken analysis. Enterotype (ET) assignment was performed using a publicly available, reference-based classification tool involving Fuzzy-k-means (FKM) clustering. Next, NMF was applied to identify 'enterosignatures' (ESs). The FKM approach revealed a co-dominance of Prevotella-ET (P-ET, 57%) and Firmicutes-ET (F-ET, 38%) with 41% of P-ET samples exhibiting a significant deviation from the reference enterotype center. These latter had a lower proportion of Prevotella-ES and a higher proportion of Bacteroides/Phocaeicola-, Firmicutes- and/or Bifidobacterium-enriched ESs. The F-ET samples were differentially enriched by Blautia (P = 0.007) and Vescimonas (P = 0.007). NMF revealed within this group, a candidate Firmicutes-associated ES driven by Blautia and encompassing Vescimonas, Akkermansia, and Methanobrevibacter. These findings demonstrate the combined power of refined enterotyping and NMF in characterizing gut microbiota, providing a key methodology for future large-scale research. However, our relatively small sample size limits statistical power and biological interpretation, making this study exploratory in nature. Candidate ES requires validation in larger independent datasets.},
}

Humans
Tunisia
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/genetics/isolation & purification
Feces/microbiology
Pilot Projects
Adult
Metagenomics/methods
Metagenome
Shotgun Sequencing
Male
Female

@article {pmid42641809,
year = {2026},
author = {Wang, J and Zhang, D and Hu, S and Guo, H and Zou, L and Wang, N and Xie, J and Wang, Z and Hao, M and Da, Y and Wang, M and Song, L and Li, H and Sun, B},
title = {Limosilactobacillus reuteri and Lactobacillus johnsonii intervention ameliorates gestational diabetes mellitus-associated sex-specific placental nutrient transporter abnormalities: Links with tryptophan metabolism and aryl hydrocarbon receptor signaling.},
journal = {Diabetes research and clinical practice},
volume = {240},
number = {},
pages = {113510},
doi = {10.1016/j.diabres.2026.113510},
pmid = {42641809},
issn = {1872-8227},
mesh = {Female ; Pregnancy ; Animals ; *Limosilactobacillus reuteri/physiology ; *Diabetes, Gestational/metabolism/microbiology/therapy ; Humans ; *Placenta/metabolism ; Mice ; *Tryptophan/metabolism ; *Probiotics/therapeutic use ; *Receptors, Aryl Hydrocarbon/metabolism ; Signal Transduction ; *Lactobacillus johnsonii ; Male ; Adult ; Gastrointestinal Microbiome ; },
abstract = {AIMS: Gestational diabetes mellitus (GDM) is a common pregnancy complication associated with maternal metabolic abnormalities and adverse offspring outcomes. Although GDM is closely linked to gut microbiota dysbiosis, key probiotic strains and underlying mechanisms remain unclear. This study aimed to identify potential probiotics using microbial signals from clinical GDM cases and a mouse model.

METHODS: Metagenomic sequencing was performed on fecal samples from normal and GDM pregnant women; a GDM mouse model was then established for candidate probiotic screening. Combined intervention with Limosilactobacillus reuteri and Lactobacillus johnsonii was applied to assess glucose metabolism, inflammation, intestinal barrier, placental structure, nutrient transporter expression and tryptophan metabolism.

RESULTS: Metagenomic analysis showed reduced Lactobacillaceae in GDM women, and the two strains were identified as candidates. The intervention improved glycemic control, insulin resistance, inflammation and colon barrier function, and alleviated placental lesions. Placental nutrient transporters expression showed sex-specific abnormalities that were normalized by probiotics. Maternal plasma 5-hydroxyindoleacetic acid (5-HIAA) was reduced in GDM mice and restored after intervention, correlating with metabolic indices, placental status, fetal growth and aryl hydrocarbon receptor (AhR) signaling.

CONCLUSIONS: Combined L. reuteri and L. johnsonii intervention improved GDM-associated maternal metabolic and sex-specific placental abnormalities.},
}

Female
Pregnancy
Animals
*Limosilactobacillus reuteri/physiology
*Diabetes, Gestational/metabolism/microbiology/therapy
Humans
*Placenta/metabolism
Mice
*Tryptophan/metabolism
*Probiotics/therapeutic use
*Receptors, Aryl Hydrocarbon/metabolism
Signal Transduction
*Lactobacillus johnsonii
Male
Adult
Gastrointestinal Microbiome

@article {pmid42702602,
year = {2026},
author = {Li, Y and Chen, T and Li, P and Zhang, G and Tian, Y and Wang, J and Ni, J},
title = {Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42702602},
issn = {2041-1723},
support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Ice Cover/virology ; Tibet ; *Rivers/virology ; Altitude ; Ecosystem ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; *Virome/genetics ; Genome, Viral ; },
abstract = {The Qinghai-Tibet Plateau, a climate-vulnerable source of Asia's major rivers, harbors underexplored viral communities critical to ecosystem functions. By integrating 597 metagenomes from the Yangtze, Yellow, Lancang, and Yarlung Tsangpo rivers with 85 public available glacial metagenomes (Tibetan Glacier Genome and Gene catalog), we built the Glacier-to-River Virome Catalogue, encompassing 36,358 vOTUs and 897,250 viral protein clusters, to decode viral adaptation and ecological influence across elevation gradients. Our results reveal that high-altitude conditions favor viruses with elevated Guanine-Cytosine content, larger genomes and more cold-adaptation genes. A central finding is a systematic viral lifestyle shift from temperate in glaciated regions to lytic viruses downstream, accompanied with decline of pathogens carrying antibiotic resistance genes along the glacier-to-river gradients. Further, viral auxiliary metabolic genes transition from glacier nutrient scavenging (e.g., nitrogen and sulfur transporters) to downstream mineralization processes (e.g., denitrification) in plains highlights their role in biogeochemical cycling. These findings position viruses as pivotal regulators of microbial community structural and functional dynamics to glacier-to-river gradient change and biogeochemistry in the Qinghai-Tibet Plateau, providing critical insights into climate response in vulnerable Asian water towers.},
}

*Ice Cover/virology
Tibet
*Rivers/virology
Altitude
Ecosystem
*Viruses/genetics/classification/isolation & purification
Metagenome
*Virome/genetics
Genome, Viral

@article {pmid42702845,
year = {2026},
author = {Xue, Z and Xu, H and Zhu, L and Zhao, D},
title = {Prevotella melaninogenica Alleviate Mycoplasma pneumoniae Infection Through the Butyrate Based on Multi-Omic Analysis and Experimental Validation.},
journal = {Chemical biology & drug design},
volume = {108},
number = {3},
pages = {e70397},
doi = {10.1111/cbdd.70397},
pmid = {42702845},
issn = {1747-0285},
mesh = {Animals ; Humans ; Multiomics ; *Prevotella melaninogenica/metabolism/physiology ; *Pneumonia, Mycoplasma/microbiology/metabolism/drug therapy ; *Mycoplasma pneumoniae ; Mice ; *Butyrates/metabolism ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Child ; Child, Preschool ; Disease Models, Animal ; Microbiota ; },
abstract = {Mycoplasma pneumoniae (MP) is one of the main pathogens causing atypical pneumonia in children. The susceptible population is mainly children and adolescents over 5 years old, and the infection rate has increased in recent years. At present, there is limited research on the pulmonary microbiota of patients with Mycoplasma pneumoniae pneumonia, and the characteristics of their microbiota are not yet clear. We included MPP children in stages and established two independent cohorts. Cohort I (n = 175) performed 16S rRNA sequencing on bronchoalveolar lavage fluid (BALF) to explore microbial genus level characteristics, while Cohort II (n = 41) performed metagenomic and transcriptome sequencing to explore microbial species level characteristics and predict inter group differential metabolic pathways. Finally, a murine model infected with MP was established to validate the effects of Prevotella melaninogenica and its metabolite butyrate. Based on Multi-Omic Analysis, we discovered that P. melaninogenica was the most discriminative species enriched in the critically ill group. Functional profiling demonstrated that butanoate metabolism pathways were significantly enriched in the severe group and positively correlated with P. melaninogenica abundance. Transcriptomic analysis revealed that P. melaninogenica-associated host genes were significantly enriched in immune regulation pathways. Animal experiments confirmed that both P. melaninogenica and butyrate pretreatment significantly attenuated MP-induced pulmonary inflammation, pathogen load, and immune cell infiltration. Respiratory microbiota dysbiosis may be associated with MPP severity. Prevotella melaninogenica, a potential protective commensal enriched in severe group MPP patients, may alleviate airway inflammation through its metabolite butyrate.},
}

Animals
Humans
Multiomics
*Prevotella melaninogenica/metabolism/physiology
*Pneumonia, Mycoplasma/microbiology/metabolism/drug therapy
*Mycoplasma pneumoniae
Mice
*Butyrates/metabolism
Male
Female
RNA, Ribosomal, 16S/genetics
Bronchoalveolar Lavage Fluid/microbiology
Child
Child, Preschool
Disease Models, Animal
Microbiota

@article {pmid42703994,
year = {2026},
author = {Kar, P and Halder, J and Rout, SR and Dash, P and Das, C and Ghosh, G and Rath, G and Kar, B},
title = {Marine-derived Bioactive Compounds: A Promising Frontier against Multidrug-resistant Microbial Infections.},
journal = {Mini reviews in medicinal chemistry},
volume = {26},
number = {12},
pages = {841-858},
pmid = {42703994},
issn = {1875-5607},
mesh = {Humans ; *Biological Products/chemistry/pharmacology/isolation & purification ; *Anti-Bacterial Agents/pharmacology/chemistry/isolation & purification ; Animals ; *Aquatic Organisms/chemistry/metabolism ; *Drug Resistance, Multiple, Bacterial/drug effects ; Bacteria/drug effects ; *Bacterial Infections/drug therapy ; Microbial Sensitivity Tests ; },
abstract = {The global escalation of Multidrug-Resistant (MDR) bacterial infections poses a serious and growing threat to public health, contributing to increased morbidity, mortality, and substantial economic burden worldwide. The widespread and often indiscriminate use of antibiotics in clinical and agricultural settings has accelerated the emergence of resistance, significantly diminishing the efficacy of conventional antimicrobial therapies. This pressing challenge necessitates the exploration of alternative sources for novel antibiotics. Marine ecosystems-renowned for their immense biodiversity and ecological complexity-have gained attention as a rich and largely untapped reservoir of bioactive natural products with potent antimicrobial activity. Marine organisms, such as sponges, tunicates, algae, and bacteria and fungi derived from marine sources, produce structurally diverse and pharmacologically active metabolites, including peptides, polyketides, alkaloids, terpenoids, sterols, lactones, and halogenated compounds. Many of these marine-derived molecules possess unique chemical scaffolds and novel mechanisms of action, offering the potential to circumvent existing resistance pathways. Some compounds have shown promising activity against MDR pathogens, including Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumannii. However, challenges such as low natural abundance, difficulty in cultivation, and structural complexity have limited their clinical translation. Recent advancements in marine biotechnology, genomics, metagenomics, and synthetic biology have opened new avenues for the discovery, biosynthesis, and structural optimization of these compounds. These innovative approaches not only facilitate sustainable production but also enhance the pharmacological properties.},
}

Humans
*Biological Products/chemistry/pharmacology/isolation & purification
*Anti-Bacterial Agents/pharmacology/chemistry/isolation & purification
Animals
*Aquatic Organisms/chemistry/metabolism
*Drug Resistance, Multiple, Bacterial/drug effects
Bacteria/drug effects
*Bacterial Infections/drug therapy
Microbial Sensitivity Tests

@article {pmid42704537,
year = {2026},
author = {de Freitas Germano, J and Leite, G and Pimentel, M},
title = {Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42704537},
issn = {1534-312X},
mesh = {Humans ; Multiomics ; *Intestine, Small/microbiology ; Proteomics/methods ; *Blind Loop Syndrome/diagnosis/microbiology ; Breath Tests/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; Syndrome ; },
abstract = {PURPOSE OF REVIEW: This review investigates how advances in breath testing (BT), small bowel (SB) culture, metagenomics, metatranscriptomics, transcriptomics and proteomics are reshaping the definition and diagnosis of small intestinal bacterial overgrowth (SIBO). It also discusses whether SIBO should be redefined as part of a larger group of microbial overgrowth syndromes.

RECENT FINDINGS: Recent studies identify distinct hydrogen-, methane-, and hydrogen sulfide-associated overgrowth phenotypes, termed SIBO, intestinal methanogen overgrowth (IMO), and intestinal sulfide overproduction (ISO). SB sampling shows that these conditions involve different microbial patterns and functional activity, symptoms, and host responses. Quantitative shotgun metagenomics provides greater taxonomic and functional resolution than culture, while metatranscriptomics reveals active microbial pathways. On top of that, host transcriptomics and proteomics contribute to the better understanding of the predominant microbial effects in host cellular mechanisms in each of the distinct small bowel overgrowth types. SIBO has been increasingly identified as a disorder of microbial ecology and function rather than bacterial quantity alone. Integrating BT with SB sampling and multi-omics approaches may improve classification, clarify symptom mechanisms, and support a more individualized treatment, although standardized methods and further clinical validation remain necessary.},
}

Humans
Multiomics
*Intestine, Small/microbiology
Proteomics/methods
*Blind Loop Syndrome/diagnosis/microbiology
Breath Tests/methods
Gastrointestinal Microbiome
Metagenomics/methods
Syndrome

@article {pmid42704656,
year = {2026},
author = {Bates, KA and Rivera, VB and Glicklich, D and Diflo, T and Chaturvedi, V and Nog, R},
title = {Urinary microbiome in renal transplant patients with BK polyomavirus reactivation.},
journal = {Journal of medical microbiology},
volume = {75},
number = {9},
pages = {},
doi = {10.1099/jmm.0.002196},
pmid = {42704656},
issn = {1473-5644},
mesh = {Humans ; *BK Virus/physiology/genetics ; *Kidney Transplantation/adverse effects ; *Polyomavirus Infections/urine/microbiology/virology ; *Microbiota ; Male ; Female ; Middle Aged ; Adult ; *Virus Activation ; Bacteria/classification/genetics/isolation & purification ; *Tumor Virus Infections/urine/microbiology/virology ; Aged ; DNA, Viral/blood ; *Urine/microbiology ; },
abstract = {Introduction. BK polyomavirus (BKPyV) reactivation is a significant health risk among renal transplant recipients that can lead to nephropathy and allograft loss.Hypothesis/Gap statement. While the microbiota is increasingly recognized as an important determinant of viral infection and pathogenesis, as well as itself undergoing compositional changes in response to infection, the urinary microbiome has yet to be investigated in the context of BK polyomavirus reactivation.Aim. This study aimed to investigate associations between the urinary microbiome and BKPyV-DNAemia in renal transplant patients.Methodology. Shotgun metagenomics of the urinary microbiome was conducted for 22 renal transplant recipients, 11 of whom had BKPyV-DNAemia. Sequence data were analysed using two complementary approaches to identify common microbiome associations with BKPyV-DNAemia: (1) Kaiju - a DNA-to-Protein method that captures bacteria, archaea, fungi, microeukaryotes and DNA viruses and (2) MetaPhlAn4 - a DNA-to-Marker method using a reference database of specific marker genes of prokaryotes.Results. We found increased observed diversity of bacterial taxa in control patients compared to those with BKPyV-DNAemia for data analysed with MetaPhlAn4 (P=0.037) but not Kaiju (P>0.05), which followed a similar trend. Significant differences in microbial beta diversity between the control and BKPyV-DNAemia patient group were identified for the Kaiju dataset (P=0.027) but not for MetaPhlAn4 (P>0.05), with viral reads likely driving these differences in the Kaiju dataset. Both Kaiju and MetaPhlAn4 identified Proteobacteria, Firmicutes and Actinobacteria as bacterial phyla with greatest relative abundance across samples. Screening bacterial species data generated from Kaiju and MetaPhlAn4 against a database of 243 human pathogens identified 8 pathogenic species recovered from both datasets that were present in the urinary microbiome of renal transplant patients.Conclusion. The observed evidence for differences in microbiome diversity and composition associated with BKPyV-DNAemia may play an important role in its pathology and guide the development of diagnostic biomarkers. Our findings warrant further investigation across larger patient cohorts that are more evenly balanced for gender.},
}

Humans
*BK Virus/physiology/genetics
*Kidney Transplantation/adverse effects
*Polyomavirus Infections/urine/microbiology/virology
*Microbiota
Male
Female
Middle Aged
Adult
*Virus Activation
Bacteria/classification/genetics/isolation & purification
*Tumor Virus Infections/urine/microbiology/virology
Aged
DNA, Viral/blood
*Urine/microbiology

@article {pmid42705715,
year = {2026},
author = {Li, G and Shen, L and Nie, L and Tang, P and Shan, Q and Qin, L and Fan, S and Guo, X},
title = {Integrated electronic nose, GC-MS, and metagenomic analyses reveal volatile flavor and microbial community differences in heap-fermented grains of Jiangxiangxing Baijiu across different fermentation degrees.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120307},
doi = {10.1016/j.foodres.2026.120307},
pmid = {42705715},
issn = {1873-7145},
mesh = {*Fermentation ; *Volatile Organic Compounds/analysis ; *Gas Chromatography-Mass Spectrometry/methods ; *Electronic Nose ; *Metagenomics/methods ; *Microbiota ; *Food Microbiology/methods ; Taste ; Odorants/analysis ; *Edible Grain/microbiology/chemistry ; *Fermented Foods/microbiology/analysis ; Bacteria/classification/metabolism/genetics ; },
abstract = {The fermentation degree of heap-fermented grains in Jiangxiangxing Baijiu production is a critical factor influencing base Baijiu quality. However, conventional assessment methods largely rely on empirical experience and therefore suffer from limited objectivity and accuracy. In this study, integrated volatile profiling and metagenomic approaches were employed to investigate volatile characteristics and microbial functional potential differentiation in fermented grains with different fermentation degrees (under-fermented, normally fermented, and over-fermented). Significant differences in physicochemical properties were observed among fermentation degrees, particularly in acidity and reducing sugar content. Electronic nose analysis revealed distinct sensor response patterns among different fermentation degrees, indicating differences in overall volatile odor fingerprint patterns. A total of 81 volatile compounds were identified by HS-SPME-GC-MS, with aldehydes, ketones, and pyrazines showing pronounced variations among fermentation degrees, and acetaldehyde exhibiting strong discriminatory potential. LEfSe analysis identified 18 microbial taxa as potential biomarkers associated with different fermentation degrees, including Pichia kudriavzevii, Lentibacillus daiqui, and Acetobacter pasteurianus. Correlation analysis revealed significant positive associations between acetaldehyde levels and Acetobacter abundance. Furthermore, KEGG, CAZy, and eggNOG analyses revealed differentiated functional potentials among fermentation degrees, providing insights into the potential metabolic basis associated with flavor differentiation. Overall, these findings highlight that fermentation degree differentiation is closely associated with coordinated changes in physicochemical conditions, microbial communities, and functional potentials, providing ecological insights into flavor differentiation and theoretical support for objective fermentation degree evaluation and quality control of Jiangxiangxing Baijiu production.},
}

*Fermentation
*Volatile Organic Compounds/analysis
*Gas Chromatography-Mass Spectrometry/methods
*Electronic Nose
*Metagenomics/methods
*Microbiota
*Food Microbiology/methods
Taste
Odorants/analysis
*Edible Grain/microbiology/chemistry
*Fermented Foods/microbiology/analysis
Bacteria/classification/metabolism/genetics

@article {pmid42705723,
year = {2026},
author = {Tong, W and Wang, H and Yang, Y and Xu, J and Huang, Z and Huang, D and Luo, H and Zhao, L and Zhang, S},
title = {Enzyme-driven synthesis and metabolic mechanism of ferulic acid in strong-flavor Daqu: pathway elucidation and microbial drivers.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120354},
doi = {10.1016/j.foodres.2026.120354},
pmid = {42705723},
issn = {1873-7145},
mesh = {*Coumaric Acids/metabolism/analysis ; Fermentation ; Carboxylic Ester Hydrolases/metabolism ; *Alcoholic Beverages/microbiology/analysis ; *Flavoring Agents/metabolism ; Carboxy-Lyases/metabolism ; Bacteria/metabolism ; Metabolic Networks and Pathways ; Microbiota ; },
abstract = {Ferulic acid (FA) is a bioactive phenolic compound in strong-flavor Baijiu with important health functions. Its microbial synthesis and metabolic mechanisms in strong-flavor Daqu remain unclear, limiting the understanding of its production. This study explored FA synthesis and metabolic dynamics during Daqu fermentation from D0-D90 using physicochemical detection, feruloyl esterases (FAEs) activity assay, and metagenomic sequencing. Results indicated that FA content fluctuated dynamically throughout fermentation, reaching a final level of 4.39 ± 0.17 mg/kg, and FAEs activity was significantly positively correlated with FA content. Genera significantly associated with FA dynamics were identified. High-abundance genera including Lichtheimia, Saccharopolyspora, Aspergillus, Byssochlamys and Rasamsonia exhibited significantly positive correlations with FA accumulation at respective fermentation stages. This phenomenon may be attributed to their capacity to secrete FAEs, thereby promoting the release of FA. The dynamic change of free FA content was also associated with the expression of ferulic acid decarboxylase, a key enzyme potentially involved in free FA degradation. A comprehensive FA metabolic network in Daqu was constructed, including the cell wall release pathway and the shikimate biosynthesis pathway. A metabolic association model was established based on the phasic succession of fungal and bacterial communities and their coupling with FA metabolic enzyme systems, which suggested a potential division of labor. Fungi are likely to participate in free FA release through secretion of FAEs and auxiliary degrading enzymes, while bacteria may mainly participate in the metabolic turnover and consumption of free FA. This study expands the current understanding of phenolic acid metabolism in strong-flavor Daqu, and provides a theoretical basis for interpreting FA metabolic characteristics during Daqu fermentation.},
}

*Coumaric Acids/metabolism/analysis
Fermentation
Carboxylic Ester Hydrolases/metabolism
*Alcoholic Beverages/microbiology/analysis
*Flavoring Agents/metabolism
Carboxy-Lyases/metabolism
Bacteria/metabolism
Metabolic Networks and Pathways
Microbiota

@article {pmid42705725,
year = {2026},
author = {Xiao, L and Wan, Y and Jiang, M and Liu, Z and Chen, G and Ke, S and Jiang, J and Guo, S and Yu, P and Wu, H and Wang, A and Ning, M and Zhou, Z},
title = {Effects of extraction methodologies on structural characterization and gut microbiota fermentation properties of Apocynum venetum polysaccharides.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120357},
doi = {10.1016/j.foodres.2026.120357},
pmid = {42705725},
issn = {1873-7145},
mesh = {*Fermentation ; *Polysaccharides/chemistry/isolation & purification/metabolism/pharmacology ; *Gastrointestinal Microbiome/physiology ; *Apocynum/chemistry ; Prebiotics ; Bacillus/metabolism ; *Plant Extracts/chemistry ; Hydrogen-Ion Concentration ; },
abstract = {Apocynum venetum L. polysaccharides are classified into neutral-to-acidic heteropolysaccharides rich in glucuronic acid, exhibiting antioxidant, immunomodulatory, and potential prebiotic activities. Different extraction methods have a significant impact on the structural characterization and biological activity of polysaccharides. This study aims to compare the structural characteristics and in vitro prebiotic activity of the Apocynum venetum L. polysaccharides BAC and CEL-U obtained via Bacillus velezensis fermentation and the combined ultrasonic-cellulase method, respectively. The results showed that BAC and CEL-U were acidic heteropolysaccharides composed of rhamnose, arabinose, galactose, glucose and galacturonic acid, and they all showed linear branching structure. Compared with CEL-U, BAC had lower molecular weight (17.51 kDa), higher uronic acid content (27.27%) and typical triple helix structure. In vitro fermentation showed that BAC can produce more propionic acid and butyric acid, maintain a lower pH, promote the proliferation of beneficial bacteria (Segatella and Prevotella), and inhibit potentially harmful bacteria. Metagenome analysis further revealed that BAC played a prebiotic role by activating specific glycosidase-mediated degradation pathways and enriching functional pathways related to carbohydrate metabolism. These findings clarify the structure-activity relationship of Apocynum venetum polysaccharide and provide a theoretical basis for its targeted application in the field of intestinal health.},
}

*Fermentation
*Polysaccharides/chemistry/isolation & purification/metabolism/pharmacology
*Gastrointestinal Microbiome/physiology
*Apocynum/chemistry
Prebiotics
Bacillus/metabolism
*Plant Extracts/chemistry
Hydrogen-Ion Concentration

@article {pmid42705727,
year = {2026},
author = {Xu, S and Li, J and Wang, F and Bian, H and Yan, W and Wang, H and Jiang, C and Sun, J and Wang, Z and Li, X},
title = {Depth-dependent microbial succession and interspecies hydrogen transfer drive pit mud maturation in Chinese strong-flavor baijiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120362},
doi = {10.1016/j.foodres.2026.120362},
pmid = {42705727},
issn = {1873-7145},
mesh = {*Hydrogen/metabolism ; *Fermentation ; Bacteria/metabolism/classification/genetics ; Archaea/metabolism/genetics/classification ; *Wine/microbiology/analysis ; *Food Microbiology ; *Microbiota ; Metagenomics ; China ; *Alcoholic Beverages/microbiology ; },
abstract = {Microbial communities in fermentation pit mud play a key role in determining the quality of Chinese strong-flavor baijiu (CSFB). However, the ecological processes underlying pit mud maturation across spatial and temporal scales remain unclear. In this study, amplicon sequencing and metagenomic analyses were employed to investigate the taxonomic succession, community assembly, and metabolic functions of bacterial and archaeal communities during the transition from fresh pit mud (FPM) to new pit mud (NPM) and old pit mud (OPM). A pronounced depth-dependent succession pattern was observed, with 4 cm representing a critical ecological boundary separating distinct community structures and maturation trajectories. During surface-layer maturation, community assembly shifted from stochastic to deterministic processes, accompanied by homogeneous selection and increasing network complexity. In contrast, stochastic processes remained dominant throughout deep-layer maturation. Metagenomic analyses revealed a functional transition from lactate and acetate production, primarily associated with Lactobacillus in FPM and NPM, to butyrate and caproate production associated with Clostridium and Caproiciproducens in OPM. This functional transition was accompanied by enhanced amino acid metabolism, which was associated with the enrichment of Proteiniphilum and Aminobacterium. Notably, methanogen-mediated interspecies hydrogen transfer (IHT) emerged as a key ecological feature during pit mud maturation. In OPM, IHT networks primarily involving Methanobacterium and Methanosarcina linked methanogenesis with reverse β-oxidation through diverse hydrogen-transfer pathways, reinforcing metabolic interactions underlying caproate production. These findings provide new insights into the ecological mechanisms underlying pit mud maturation and offer a theoretical basis for the directed cultivation of high-quality pit mud in CSFB production.},
}

*Hydrogen/metabolism
*Fermentation
Bacteria/metabolism/classification/genetics
Archaea/metabolism/genetics/classification
*Wine/microbiology/analysis
*Food Microbiology
*Microbiota
Metagenomics
China
*Alcoholic Beverages/microbiology

@article {pmid42705729,
year = {2026},
author = {Li, Y and Li, J and Deng, J and Xia, P and Zhou, G and Zhu, Z and Ding, Y and Yang, J and Zhang, F},
title = {Phocaeicola vulgatus alleviates obesity through cross-species arginine production and hepatic retinoic acid signaling.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120365},
doi = {10.1016/j.foodres.2026.120365},
pmid = {42705729},
issn = {1873-7145},
mesh = {*Arginine/biosynthesis/metabolism ; Animals ; *Obesity/therapy/microbiology/metabolism ; *Liver/metabolism ; Signal Transduction ; *Tretinoin/metabolism ; Rats ; Humans ; Fecal Microbiota Transplantation ; Male ; Gastrointestinal Microbiome ; Diet, High-Fat ; },
abstract = {Fecal microbiota transplantation (FMT) shows inconsistent clinical efficacy in treating obesity, and the specific microbial determinants dictating its success remain poorly characterized. Our previous clinical FMT trial identified Phocaeicola vulgatus as a key microbe contributing to the therapeutic efficacy of obesity treatment. Here, to investigate its role in obesity, we established an independent clinical cohort comprising obese and lean individuals, revealing that the P. vulgatus-centered network and ornithine synthesis are impaired in the obese group. We then confirmed causality by utilizing a humanized rat model carrying microbiota from a P. vulgatus-deficient obese patient, demonstrating that P. vulgatus supplementation significantly mitigates HFD-induced obesity, including reductions in body weight and serum total cholesterol levels, as well as the alleviation of hepatic steatosis. To further explore the functional mechanisms of P. vulgatus, integrated metagenomic and metabolomic analyses revealed a potential functional association between P. vulgatus and Phascolarctobacterium faecium that is associated with enhanced intestinal arginine biosynthesis and systemic availability. Furthermore, hepatic transcriptomics linked these elevated circulating arginine levels to the upregulation of retinoic acid (RA) signaling. Taken together, our findings outline a potential microbial-host network wherein P. vulgatus mitigates obesity via the arginine-RA axis, providing a valuable scientific basis for exploring this strain as a probiotic candidate for metabolic health.},
}

*Arginine/biosynthesis/metabolism
Animals
*Obesity/therapy/microbiology/metabolism
*Liver/metabolism
Signal Transduction
*Tretinoin/metabolism
Rats
Humans
Fecal Microbiota Transplantation
Male
Gastrointestinal Microbiome
Diet, High-Fat