@article {pmid42805588,
year = {2026},
author = {Metris, A and Guan, R and Ampatzoglou, A and Murphy, B},
title = {Methods to Address Compositional Data Challenges in Clinical Studies for the Safety Assessment of Human Microbiome Perturbations.},
journal = {Journal of food protection},
volume = {89},
number = {11},
pages = {100933},
doi = {10.1016/j.jfp.2026.100933},
pmid = {42805588},
issn = {1944-9097},
mesh = {Humans ; *Microbiota ; },
abstract = {Advances in sequencing technologies have enabled increasingly detailed characterization of the human microbiome in clinical studies, but interpretation of microbiome modulation that has relevance to health and disease characterization or safety assessments remains methodologically challenging. Taxonomic profiles generated by amplicon or shotgun sequencing are inherently compositional, sparse, and limited by detection, which complicates differential abundance analysis and may lead to unstable or misleading conclusions, especially in low-biomass settings where contamination and under-detection are concerns. Here, we review strategies used to analyze and complement sequencing-derived taxonomic count data, with the aim of obtaining more quantitative information on microbial differential abundance and viability. These include transformations for relative abundance-based analyses and bias corrections between samples based on mathematical assumptions or additional experimental measurements such as spike-ins, broad-range qPCR, and flow cytometry. We find that there is no consensus on which method best addresses compositionality and that detection level and significance of low-level microbes in health and disease are overlooked. We discuss the limitations of sequence-based methods, such as the biases induced by the experimental and analytical process, as well as viability measurements for meaningful differential abundance assessment. We illustrate the need to integrate prevalence as well as abundance and the importance of covariates in models in the case of bacterial vaginosis. Overall, meaningful assessment of microbiome perturbations requires not only statistical correctness of differential abundance analysis but also careful study design, appropriate measurement choices, quantitative context, and explicit recognition of the biological and analytical limits of sequencing-derived data.},
}

Humans
*Microbiota

@article {pmid42965683,
year = {2026},
author = {Li, S and Cheng, R and He, M and Hu, Q and Xu, H and Wu, X and Liu, X and Cai, X and Miao, Z},
title = {Exploring the relationship among nutrition, gut microbiota and musculoskeletal health in children with Duchenne muscular dystrophy: a cross-sectional study.},
journal = {European journal of nutrition},
volume = {65},
number = {8},
pages = {},
pmid = {42965683},
issn = {1436-6215},
support = {S23053//Sichuan Medical Association Foundation/ ; 2024-YF05-00493-SN//Foundation of Chengdu Municipal Science and Technology/ ; 82404268//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Cross-Sectional Studies ; Male ; Child ; Female ; *Gastrointestinal Microbiome/physiology ; *Nutritional Status ; Bone Density ; *Muscular Dystrophy, Duchenne/physiopathology/microbiology/complications ; Body Composition ; China ; Energy Intake ; Child, Preschool ; Adolescent ; Diet ; },
abstract = {AIMS: This study was aimed to explore the nutritional risk standards and nutritional support strategies in Chinese children with DMD.

METHODS: This cross-sectional study included 217 children with DMD. Nutritional status was determined by measuring body composition and clinical testing indicators. Three-day 24-h diet recalls were used to assess nutrient intake. Metagenomic sequencing was performed to detect gut microbiota.

RESULTS: Children with obesity or high body fat percentage (BF%) had higher levels of caloric intake and lower levels of bone mineral density (BMD) and osteocalcin. Age increased the risk of low muscle mass (95% confidence interval [CI] 1.053‒2.152). Overweight (95% CI 0.078‒0.658), obesity (95% CI 0.003‒0.139), low BF% (95% CI 0.015‒0.524) and high levels of calories from protein (95% CI 0.001‒0.001) were protective factors for low muscle mass. The GC exposure (95% CI 1.03‒1.53) increased the risk of low BMD, whereas low body fat percentage (95% CI 0.11‒0.71) decreased the risk of low BMD. Gut microbiota was closely associated with the BMD Z-score, body fat percentage (P < 0.01), age, GC exposure, and P1NP (P < 0.05). DMD children with low BMD had a higher abundance of Bacteroides vulgatus and a lower abundance of Prevotella copri (P < 0.05).

CONCLUSION: BF% rather than obesity was the risk factor for low muscle mass in DMD. SMI may be a more accurate index for muscle mass assessment than SMM. High level of calories from protein may be benefit to SMI. Treatments targeting gut microbiota may alleviate glucocorticoid-induced low BMD in DMD.},
}

Humans
Cross-Sectional Studies
Male
Child
Female
*Gastrointestinal Microbiome/physiology
*Nutritional Status
Bone Density
*Muscular Dystrophy, Duchenne/physiopathology/microbiology/complications
Body Composition
China
Energy Intake
Child, Preschool
Adolescent
Diet

@article {pmid42965706,
year = {2026},
author = {Haferkamp, S and Schilling, B and Baumgart, L and Gesierich, A and Glutsch, V and Drexler, K and Wein, L and Morak, M and Erdmann, M and Berking, C and Piccinno, G and Derosa, L and Zitvogel, L and Wang, Y and Heinzerling, L},
title = {Microbiome-derived TOPOSCORE is associated with response to immune checkpoint inhibitor re-induction after chemotherapy in primary resistant metastatic melanoma.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {75},
number = {11},
pages = {},
pmid = {42965706},
issn = {1432-0851},
support = {70113416//German Cancer Aid / Stiftung Deutsche Krebshilfe/ ; },
mesh = {Humans ; *Melanoma/drug therapy/microbiology/pathology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Male ; *Drug Resistance, Neoplasm ; Female ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; Prospective Studies ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Aged ; },
abstract = {BACKGROUND: Primary resistance to immune checkpoint inhibitors (ICIs) remains a major challenge in metastatic melanoma. The prospective multicenter PROMIT trial showed that intermittent chemotherapy could restore sensitivity to ICI re-induction in a subset of patients. We investigated whether gut microbiome ecosystem states characterized by TOPOSCORE were associated with tumor response in this setting.

METHODS: In the phase II PROMIT trial (NCT04225390), 24 patients with longitudinal stool samples were included in this exploratory microbiome analysis. ICI-resistant patients received two cycles of dacarbazine followed by ICI re-induction. Stool samples underwent shotgun metagenomic sequencing. Microbiome ecosystem states were classified into SIG1- or SIG2-associated ecosystem states using the TOPOSCORE framework, which is based on species-interacting groups (SIGs) defined by ecological co-abundance patterns.

RESULTS: Baseline TOPOSCORE distributions and s-scores were not associated with clinical outcome. In the nine patients with complete BL-CTX-ICI sampling, six retained the same TOPOSCORE category throughout treatment and three changed category. Of the two patients with PR, one remained SIG2 throughout, whereas the other changed from SIG2+ to SIG1+ after chemotherapy and returned to SIG2+ during ICI re-induction. Analyses using all available samples at each phase likewise did not show significant differences in s-score among PR, SD, and PD groups.

CONCLUSIONS: Baseline TOPOSCORE classification was insufficient to predict treatment outcome in this cohort. Longitudinal TOPOSCORE patterns were heterogeneous, and the small number of complete longitudinal profiles precludes conclusions that chemotherapy induced a favorable microbiome transition. These exploratory findings support further evaluation of microbiome ecosystem dynamics in larger prospective cohorts.},
}

Humans
*Melanoma/drug therapy/microbiology/pathology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Male
*Drug Resistance, Neoplasm
Female
*Gastrointestinal Microbiome/drug effects
Middle Aged
Prospective Studies
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use
Aged

@article {pmid42967695,
year = {2026},
author = {Feng, T and Guan, XY and Shang, Q and Jiang, Y and Li, ZY and Qi, J and Yu, MM},
title = {Dynamics of biogenic amine formation in fermented mandarin fish: Insights from precursor utilization and microbial succession.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 4},
pages = {120858},
doi = {10.1016/j.foodres.2026.120858},
pmid = {42967695},
issn = {1873-7145},
mesh = {Animals ; *Biogenic Amines/analysis/metabolism ; *Fermentation ; Amino Acids/analysis/metabolism ; Bacteria/metabolism/classification/genetics ; *Fishes/metabolism ; *Food Microbiology ; Putrescine/analysis ; Microbiota ; *Fermented Foods/microbiology ; Histamine/analysis ; Metagenomics ; Cadaverine/analysis ; },
abstract = {The high protein content of mandarin fish (Siniperca chuatsi) provides abundant substrates for biogenic amines (BAs) formation during fermentation, but the temporal dynamics and microbial drivers of BAs accumulation remain unclear. This study systematically investigated the succession of free amino acids (FAAs), BAs, and bacterial communities during fermentation. Results showed that the total FAAs peaked on day 5, whereas total BAs reached a maximum on day 10 (767.58 mg/kg). The BAs surge initiated at day 7.5, approximately 2.5 days after the FAAs peak. Putrescine, cadaverine, histamine, and tyramine were the predominant BAs, accounting for >98% of total BAs. Correlation analysis revealed strong negative correlations between BAs and their precursor FAAs (|R| = 0.588-0.842), suggesting the decarboxylation-driven conversion. Microbial succession identified candidate genera positively associated with BAs accumulation, including Vibrio and Morganella, while the late-stage decline of Vibrio and the increase of Vagococcus coincided with BAs reduction. Metagenomic analysis revealed that amino acid decarboxylase gene abundance peaked at day 10, while BA-degrading gene abundance peaked at day 15, consistent with the BAs dynamics. Days 5 to 10 are identified as a period that may warrant enhanced monitoring in industrial practice. A sequential temporal pattern linking substrate availability, microbial shifts, and BAs dynamics is described. These findings provide insights into the sequential dynamics of BAs formation in fermented mandarin fish and provide a scientific foundation for quality management in traditional fermented fish products.},
}

Animals
*Biogenic Amines/analysis/metabolism
*Fermentation
Amino Acids/analysis/metabolism
Bacteria/metabolism/classification/genetics
*Fishes/metabolism
*Food Microbiology
Putrescine/analysis
Microbiota
*Fermented Foods/microbiology
Histamine/analysis
Metagenomics
Cadaverine/analysis

@article {pmid42758297,
year = {2026},
author = {Xu, H and Zhong, T and Li, J},
title = {The link of oral microbiome diversity to stroke risk: evidence from the national cohort study in the United States.},
journal = {The International journal of neuroscience},
volume = {136},
number = {11},
pages = {1507-1518},
doi = {10.1080/00207454.2026.2736054},
pmid = {42758297},
issn = {1563-5279},
mesh = {Humans ; Female ; *Microbiota ; Male ; *Stroke/epidemiology/microbiology ; United States/epidemiology ; Cross-Sectional Studies ; Middle Aged ; Cohort Studies ; *Mouth/microbiology ; Adult ; Aged ; Risk Factors ; Nutrition Surveys ; },
abstract = {OBJECTIVE: To assess whether oral microbiome diversity and periodontal health are independently associated with stroke prevalence in a U.S. adult cohort, with implications for risk stratification in physical medicine and rehabilitation.

METHODS: We analyzed cross-sectional NHANES 2009-2012 data from 4,438 adults. Survey-weighted logistic regression estimated associations of stroke with oral microbiome β-diversity (unweighted UniFrac), α-diversity (Shannon and Simpson), and periodontal measures (probing depth, attachment loss, tooth count), adjusting for demographic, socioeconomic, behavioral, and cardiometabolic covariates.

RESULTS: In crude models, each 1-mm increase in probing depth (odds ratio [OR] 1.89, 95% CI 1.39-2.56) and attachment loss (OR 1.50, 95% CI 1.32-1.71) raised stroke odds; each additional tooth lowered them (OR 0.91, 95% CI 0.88-0.94). After stepwise adjustment, attachment loss (OR 1.23, 95% CI 1.04-1.46; P=0.017) and tooth count (OR 0.96, 95% CI 0.92-0.99; P=0.024) remained significant, whereas probing depth did not (OR 1.30, 95% CI 0.90-1.88; P=0.156), with a threshold near 1.46 mm. β-Diversity clusters did not differ after adjustment (global P=0.61), and neither α-diversity index was significant (Shannon fully adjusted OR 1.29, 95% CI 0.97-1.72; P=0.081). Periodontal associations were consistent across sex and age strata; null findings in younger participants reflected limited power.

CONCLUSION: Attachment loss and tooth count were associated with stroke prevalence independently of traditional risk factors, whereas microbiome diversity indices were not. These measures may help refine risk assessment. The cross-sectional design precludes causal inference, and prospective cohorts with adjudicated outcomes and metagenomic profiling are needed.},
}

Humans
Female
*Microbiota
Male
*Stroke/epidemiology/microbiology
United States/epidemiology
Cross-Sectional Studies
Middle Aged
Cohort Studies
*Mouth/microbiology
Adult
Aged
Risk Factors
Nutrition Surveys

@article {pmid42833075,
year = {2026},
author = {Wang, X and Wang, J and Rehman, A and Ming, H},
title = {Response mechanisms of marine microbial communities during sulfamethoxazole co-metabolic degradation.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108421},
doi = {10.1016/j.marenvres.2026.108421},
pmid = {42833075},
issn = {1879-0291},
mesh = {*Sulfamethoxazole/metabolism ; *Microbiota/drug effects ; *Water Pollutants, Chemical/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; *Anti-Bacterial Agents/metabolism ; Seawater/microbiology ; },
abstract = {Antibiotics, as typical emerging contaminants posing significant ecological risks, are frequently detected in global coastal environments. Their biotransformation in marine environments depends on the stress responses of functional microbial communities, while the underlying response mechanisms remain unclear. Through integrated metagenomic and metabolomic approaches, this study systematically investigated the structural and functional responses of marine microbial communities during the co-metabolic degradation of sulfamethoxazole (SMX), a representative antibiotic. A marine microbial consortium was employed for SMX co-metabolism with alginate, prototypical marine natural organic matter, as the co-substrate. Results revealed that under SMX stress, the microbial community underwent a marked shift in OTU composition, alongside significant increases in richness and diversity. The dominant functional taxon Vibrionaceae exhibited a significant decrease in relative abundance from 97.0% to 82.7%, while Paracoccaceae with SMX degradation potential and other low-abundance (<0.01%) functional taxa were significantly enriched, collectively sustaining stable alginate metabolism and facilitating SMX co-metabolism. Co-occurrence network analysis revealed enhanced interspecies associations. Moreover, the functional profile of the microbial community was profoundly reshaped. Specifically, the microbial community activated adaptive responses, enhancing TCS activation, EPS and endospore production, flagellar motility and chemotaxis, antioxidant capacity and DNA repair, and antibiotic resistance, to mitigate the toxicity of SMX and its intermediates. Concurrently, metabolic strategies were altered via regulation of key pathways (e.g., carbohydrate metabolism and amino acid metabolism), which increased by 7.8% and 17.5% in relative abundance compared to the control, boosting energy supply and SMX-degrading enzyme synthesis to enable SMX co-metabolism. This study provides new insights into the response mechanisms of marine microbial communities to SMX stress and the ecological risk assessment of antibiotics in coastal waters.},
}

*Sulfamethoxazole/metabolism
*Microbiota/drug effects
*Water Pollutants, Chemical/metabolism
Bacteria/metabolism
Biodegradation, Environmental
*Anti-Bacterial Agents/metabolism
Seawater/microbiology

@article {pmid42961364,
year = {2026},
author = {Alghafri, M and Edwards, L and Moyes, D and Nibali, L},
title = {Antimicrobial Resistance in Periodontal Disease: Rethinking Adjunctive Therapy in the Metagenomics Era, the Pressing Need for Precision Treatment and Periodontal Resistome Mapping.},
journal = {Journal of cellular and molecular medicine},
volume = {30},
number = {21},
pages = {},
pmid = {42961364},
issn = {1582-4934},
mesh = {Humans ; *Metagenomics/methods ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Microbiota/drug effects ; *Periodontal Diseases/microbiology/drug therapy ; *Precision Medicine ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial ; },
abstract = {Systemic antibiotics are effective when used as adjunctive therapy in the treatment of periodontitis; however, their use must be balanced against antimicrobial resistance, which is a major threat to global public health. This review provides an expert synthesis of the literature and a field-level overview of antimicrobial resistance in periodontal therapy, highlighting current knowledge and emerging directions, while examining how adjunctive antibiotic protocols may contribute to resistance within the periodontal microbiome through emerging metagenomic insights. To provide this synthesis, the PubMed database was searched for English-language publications using combinations of the terms periodontitis, systemic antibiotics, antimicrobials, resistance, resistome, therapeutic adjuncts, resistance genes, susceptibility, antibacterial and drug resistance, and the findings are presented as a narrative review. The evidence indicates that a substantial proportion of patients with periodontitis harbour subgingival microbiota that are non-susceptible to at least one antibiotic used in periodontal therapy. Across the included studies, antimicrobial resistance was most frequently reported in Prevotella and Porphyromonas species, while some studies also identified virulence-associated factors in Staphylococcus aureus, a non-classical periodontal organism detected within the subgingival microbiota. Overall, current evidence indicates a high prevalence of antibiotic resistance genes in the subgingival microbiota of patients with periodontitis and highlights the ecological consequences of adjunctive antibiotic use. These findings reinforce the need to optimize antibiotic prescribing protocols within an antibiotic stewardship framework and support further metagenomic investigations to refine understanding of resistance patterns, gene-transfer mechanisms and microbiome disruption, with the aim of advancing precision-based periodontal care.},
}

Humans
*Metagenomics/methods
*Anti-Bacterial Agents/therapeutic use/pharmacology
Microbiota/drug effects
*Periodontal Diseases/microbiology/drug therapy
*Precision Medicine
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial

@article {pmid42961615,
year = {2026},
author = {Dolker, S and Ghosh, A and Singh, VK and Joshi, BD and Sharma, LK and Thakur, M},
title = {Exploring sex- and captivity-associated gut microbial diversity in Bengal Tigers (Panthera tigris tigris).},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42961615},
issn = {1573-4978},
mesh = {Animals ; *Tigers/microbiology/genetics ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Feces/microbiology ; Bacteria/genetics/classification ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; Endangered Species ; },
abstract = {BACKGRO UND: The gut microbiome plays a critical role in host nutrition, immune regulation, metabolic stability, and overall physiological health in wildlife. However, gut microbiome data from large carnivores remain limited, particularly for endangered tiger populations. This study conducted a comparative analysis of fecal microbiomes from captive and wild Bengal tigers, integrated with publicly avai lable datasets from Amur, Malayan, and South China tigers, to understand how captivity and host factors influence microbial assembly. ME THOD S AND RESULTS: Across all tiger subspecies, Firmicutes and Proteobacteria dominated as core bacterial phyla, with Actinobacteriota, Bacteroidota, and Fusob acteriota forming a conserved microbial backbone. Wild Bengal tigers exhibited higher microbial richness and diversity than captive tigers . Beta diversity analyses demonstrated clear clustering by habitat (captive versus wild), but substantial overlap between male and female captive Bengal tigers, indicating that captivity-associated conditions exert influences on gut microbiome structure than sex. Comparative analyses among tiger subspecies revealed broad overlap in microbial community composition, suggesting limited phylogenetic influence. South China and Amur tigers displayed the lowest richness compared to Bengal and Malayan tigers. Furthermore, analysis identified an enrichment of protein fermentation-associated taxa in captive tigers, whereas wild tigers showed a greater abundance of environmentally associated taxa. CONCLUSIONS: The study provides evidences that captivity promotes reduction in gut microbial diversity in Bengal tigers, and highlights the potential utility of microbiome-informed captive management. Integrating gut microbiome monitoring into conservation breeding, zoo exchange and reintroduction programmes may improve adaptive fitness in endangered tiger populations.},
}

Animals
*Tigers/microbiology/genetics
Female
Male
*Gastrointestinal Microbiome/genetics
Phylogeny
Feces/microbiology
Bacteria/genetics/classification
Biodiversity
RNA, Ribosomal, 16S/genetics
Sex Factors
Endangered Species

@article {pmid42963371,
year = {2026},
author = {Li, S and Huang, J and Lin, D and Luo, D and Fu, W and Liu, J},
title = {Electroacupuncture alleviates chronic pain and comorbid depression through Gut-Metabolite-Brain axis remodeling to restore mPFC Glu/GABA balance.},
journal = {Translational psychiatry},
volume = {16},
number = {1},
pages = {},
pmid = {42963371},
issn = {2158-3188},
mesh = {Animals ; *Electroacupuncture ; *gamma-Aminobutyric Acid/metabolism ; Rats ; *Chronic Pain/therapy/metabolism ; Male ; *Glutamic Acid/metabolism ; *Gastrointestinal Microbiome/physiology ; *Depression/therapy/metabolism ; *Prefrontal Cortex/metabolism ; Rats, Sprague-Dawley ; Disease Models, Animal ; Comorbidity ; },
abstract = {The comorbidity of chronic pain and depression is increasingly recognized as a systemic disorder involving dysregulated microbiota-gut-brain communication. Although electroacupuncture (EA) has demonstrated therapeutic efficacy for both pain and depression, the mechanisms linking peripheral microbial-metabolic remodeling to central neurotransmitter regulation remain incompletely understood. Here, we employed an integrated multi-omics approach in a spared nerve injury (SNI) rat model to investigate the gut-metabolite-brain mechanisms underlying EA's efficacy. EA significantly alleviated mechanical hypersensitivity and depressive-like behaviors while restoring mPFC Glu/GABA balance, accompanied by normalization of the glutamate transporter EAAT2 and the GABA-synthesizing enzyme GAD67. Metagenomic analysis showed that EA remodeled the gut microbial ecosystem by increasing microbial diversity, suppressing opportunistic pathobionts, including Bacillus cereus, Alistipes onderdonkii, while enriching SCFA-associated genera, including Butyricimonas and Romboutsia. These alterations were accompanied by coordinated remodeling of amino acid and butanoate metabolism. Correlation network analysis identified Pipecolic acid as a central metabolic node linking gut microbial alterations with mPFC GABAergic neurotransmission and behavioral recovery. Although individual bacterial genera did not significantly mediate its restoration, causal mediation analysis demonstrated that the Pipecolic acid-GABA axis significantly mediated improvements in both mechanical allodynia and anhedonia, supporting Pipecolic acid as a functional metabolic hub linking peripheral metabolic remodeling to central GABAergic regulation. Collectively, these findings identify peripheral metabolic remodeling as a key mechanistic interface through which EA coordinates gut microbial ecology and central neurochemical homeostasis, providing a systems-level framework for understanding the therapeutic mechanisms of acupuncture in pain-depression comorbidity.},
}

Animals
*Electroacupuncture
*gamma-Aminobutyric Acid/metabolism
Rats
*Chronic Pain/therapy/metabolism
Male
*Glutamic Acid/metabolism
*Gastrointestinal Microbiome/physiology
*Depression/therapy/metabolism
*Prefrontal Cortex/metabolism
Rats, Sprague-Dawley
Disease Models, Animal
Comorbidity

@article {pmid42264215,
year = {2026},
author = {Hou, P and Che, Y and Han, J and Deming, C and Amirkhani, A and Kim, CS and Taylor, ME and Velez, D and Cho, E and Holmes, CJ and Suh, G and Castelo-Soccio, L and , and McDermott, DH and Murphy, PM and Segre, JA and Kong, HH},
title = {Permissive skin microbiomes in WHIM syndrome: HPV and pathogen expansion.},
journal = {The Journal of investigative dermatology},
volume = {146},
number = {11},
pages = {3142-3154.e6},
pmid = {42264215},
issn = {1523-1747},
support = {Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA AR041218/ImNIH/Intramural NIH HHS/United States ; ZIA AR041219/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Humans ; *Skin Microbiome/immunology ; *Warts/microbiology/immunology/virology/drug therapy ; *Immunologic Deficiency Syndromes/immunology/microbiology/virology/drug therapy ; Female ; Male ; *Skin/microbiology/immunology/virology ; Receptors, CXCR4/antagonists & inhibitors/genetics ; *Human Papillomavirus Viruses/isolation & purification/immunology ; Adult ; *Papillomavirus Infections/immunology/virology/microbiology ; Primary Immunodeficiency Diseases/immunology ; Adolescent ; Young Adult ; Child ; Metagenomics ; *Genetic Diseases, X-Linked/immunology/microbiology ; Microbiota/immunology ; Papillomaviridae/isolation & purification ; },
abstract = {Warts, hypogammaglobulinemia, infections, and myelokathexis syndrome is a rare inborn error of immunity caused by hyperfunctional pathogenic variants in CXCR4, predisposing individuals to recurrent bacterial skin and airway infections and warts. The targeted CXCR4 antagonist plerixafor has shown efficacy in wart regression and a potential reduction in bacterial infection frequency. Here, we investigated the skin microbiomes of 14 patients with warts, hypogammaglobulinemia, infections, and myelokathexis syndrome using shotgun metagenomics, compared with those of healthy controls. Warts, hypogammaglobulinemia, infections, and myelokathexis skin microbial communities displayed greater inter-individual variability, with highly diverse human papillomavirus profiles and an expansion of airway-associated pathogens on the skin. Among patients receiving plerixafor therapy, we observed shifts in the viral composition and a downward trend in viral abundances. Together, these findings demonstrate the distinctive and permissive skin microbiome in warts, hypogammaglobulinemia, infections, and myelokathexis syndrome and highlight the potential microbiome-modulating effects of targeted CXCR4 antagonism.},
}

Humans
*Skin Microbiome/immunology
*Warts/microbiology/immunology/virology/drug therapy
*Immunologic Deficiency Syndromes/immunology/microbiology/virology/drug therapy
Female
Male
*Skin/microbiology/immunology/virology
Receptors, CXCR4/antagonists & inhibitors/genetics
*Human Papillomavirus Viruses/isolation & purification/immunology
Adult
*Papillomavirus Infections/immunology/virology/microbiology
Primary Immunodeficiency Diseases/immunology
Adolescent
Young Adult
Child
Metagenomics
*Genetic Diseases, X-Linked/immunology/microbiology
Microbiota/immunology
Papillomaviridae/isolation & purification

@article {pmid42271211,
year = {2026},
author = {Ying, K and Song, X and Chen, J and Wang, Y and Wu, H and Zhang, Q and Yang, X and Peng, W and Wu, H and Zhang, W and Zhang, Q},
title = {Metagenomic characterization and genetic profiling of hepatic viromes in Marmota himalayana from the Three-River-Source region of Qinghai Province.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42271211},
issn = {1471-2180},
support = {2024-SF-124//the Key research and development and transformation plan of Qinghai Province/ ; 2023YFD1801300//the National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Marmota/virology ; Phylogeny ; *Metagenomics/methods ; *Virome/genetics ; *Liver/virology ; Genome, Viral ; China ; *Viruses/genetics/classification/isolation & purification ; Rivers ; Tibet ; Sequence Analysis, DNA ; Metagenome ; },
abstract = {The Himalayan marmot (Marmota himalayana) is a keystone species in the Tibetan Plateau ecosystem and serves as a potential reservoir host for multiple zoonotic pathogens. To characterize its hepatic virome, this study conducted a systematic analysis of 70 marmot liver samples collected from the Three-River-Source Region in Qinghai Province using viral metagenomics. We identified more than 60 viral species belonging to 13 families. The species accumulation curve indicated that the sequencing effort captured the majority of the viral diversity present. Community analysis revealed that the family Retroviridae was the dominant viral group across all samples, though significant heterogeneity was observed among geographically distinct populations. Specifically, the relative abundance of Anelloviridae was markedly higher in the Chengduo group, whereas Parvoviridae exhibited exceptionally high library-specific enrichment in specific libraries. Furthermore, the study successfully assembled complete or near-complete genomic sequences of multiple strains belonging to the families Polyomaviridae, Anelloviridae, and Parvoviridae. Phylogenetic analysis demonstrated that these newly identified viral strains were most closely related to known marmot-origin viruses, clustering within distinct, host-specific evolutionary clades. This clustering pattern indicating host-associated of the viruses with their marmot hosts. Previous virome studies in marmots have primarily focused on the gut, peripheral blood, and other extrahepatic tissues, with no systematic viral metagenomic profiling of the liver in this species to date. The findings offer crucial scientific insights for the early warning and control of wildlife-origin diseases on the Tibetan Plateau.},
}

Animals
*Marmota/virology
Phylogeny
*Metagenomics/methods
*Virome/genetics
*Liver/virology
Genome, Viral
China
*Viruses/genetics/classification/isolation & purification
Rivers
Tibet
Sequence Analysis, DNA
Metagenome

@article {pmid42953986,
year = {2026},
author = {Shum-Tim, C and Islam, P and Boyajian, JL and Abosalha, A and Kassab, A and Santos, M and Khan, KA and Stern, K and Emad, A and Prakash, S},
title = {Artificial Intelligence-Driven Graph Methods for Microbiome Research: A Systematic Review.},
journal = {WIREs mechanisms of disease},
volume = {18},
number = {6},
pages = {},
pmid = {42953986},
issn = {2692-9368},
support = {252743//Canadian Institute of Health Research/ ; 335999//Fonds de Recherche du Québec-Santé/ ; 351337//Fonds de Recherche du Québec-Santé/ ; 2020-245622//Islamic Development Bank Scholarship/ ; //Ministry of Higher Education of the Arab Republic of Egypt/ ; 504933//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; },
mesh = {*Microbiota/genetics ; *Artificial Intelligence ; Humans ; Animals ; },
abstract = {The complexity of high-throughput sequencing data in microbiome research necessitates advanced analytical methods to decipher microbial community structures and interactions. Graph-based methods, which model taxa as nodes and their relationships as edges, have emerged as a powerful framework for this purpose. However, the rapid evolution of these techniques, from classical network analysis to modern graph representation learning, has created a fragmented and complex methodological landscape. This systematic review provides a comprehensive synthesis and structured overview of the field. We systematically review the literature and propose a three-part classification to categorize the primary contribution of each study: (1) novel methods for microbial network representation, (2) applications of classical graph analysis, and (3) the emerging use of graph representation learning for predictive modeling. We summarize the most frequent applications within each class, including keystone species identification, community clustering, and graph-based disease classification. Furthermore, we identify critical cross-cutting challenges, such as the lack of standardized tools and the need for improved model interpretability. By structuring the current landscape of graph-based methods, this review serves as a crucial guide for researchers to select appropriate models and highlights key gaps to direct future research.},
}

*Microbiota/genetics
*Artificial Intelligence
Humans
Animals

@article {pmid42955203,
year = {2026},
author = {Sagawa, T and Hirakawa, M and Nagashima, H and Fujikawa, K},
title = {Gut Microbiome Signatures and Immune Checkpoint Inhibitor Response in Gastrointestinal Cancers: Reproducibility and Translational Readiness.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42955203},
issn = {1534-6269},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Neoplasms/drug therapy/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects/immunology ; Reproducibility of Results ; Translational Research, Biomedical ; },
abstract = {PURPOSE OF REVIEW: Gut microbial features have been associated with immune checkpoint inhibitor (ICI) outcomes, but whether these signatures are robust across gastrointestinal (GI) tumor types, treatment regimens, and populations remains uncertain. This critical narrative review assesses human evidence, experimental mechanisms, longitudinal sampling, and the criteria needed for clinical implementation.

RECENT FINDINGS: A gastric cancer cohort showed different response-associated microbial features for immunotherapy alone, chemotherapy alone, and combined treatment. Cross-cancer strain-resolved analyses found that signature transportability was strongly conditional on matching ICI regimens. A large primary liver cancer cohort analyzed 315 patients and 777 serial samples and explored a baseline score derived from on-treatment species selection; later samples were available only in a selected subgroup, complicating interpretation. Experimental studies link selected microbes and metabolites with antitumor immunity, but these mechanistic findings do not establish therapeutic efficacy in humans. Fecal microbiota transplantation (FMT) studies in melanoma demonstrate feasibility yet do not establish benefit in GI malignancies. Stool profiles may not represent mucosal or tumor-adjacent communities in upper GI cancer. No stool microbiome signature is currently validated to select ICI therapy in GI oncology. Meaningful translation requires standardized assays, non-ICI comparators to establish treatment-effect prediction, strict separation of discovery and external validation, prospectively handled missingness, and randomized clinical-utility studies.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use
*Gastrointestinal Neoplasms/drug therapy/microbiology/immunology
*Gastrointestinal Microbiome/drug effects/immunology
Reproducibility of Results
Translational Research, Biomedical

@article {pmid42957705,
year = {2026},
author = {Anani, H and Destras, G and Semanas, Q and Martin, FP and Petrier, M and Oddoux, E and Burfin, G and Bulteau, S and Poulain, C and Sinha, D and Motos, A and Gourain, V and Cremet, L and Montassier, E and Bressollette-Bodin, C and Roquilly, A and Josset, L},
title = {Identification of functional bacterial-viral pneumotypes associated with airway inflammation and all-cause mortality in critically ill patients.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42957705},
issn = {2041-1723},
mesh = {Humans ; *Critical Illness/mortality ; Female ; Male ; Klebsiella pneumoniae/genetics/virology ; *Lung/microbiology/virology ; Middle Aged ; Bacteriophages/genetics/isolation & purification/pathogenicity ; Aged ; Microbiota/genetics ; Cross Infection/microbiology/mortality/virology ; Metagenomics ; Dysbiosis/microbiology ; Streptococcus/genetics ; },
abstract = {Alterations in lung virome and bacteriome compositions have been associated with hospital-acquired pneumonia in critically ill patients, but data on lung microbiome functions underlying progression to severe complications remain unclear. Here, we analyse 184 endotracheal aspirates (ETAs) collected in 94 intubated critically ill patients enrolled in a clinical trial (NCT04793568). Combining viral-metagenomics with metatranscriptomics analyses, we identify a high-risk functional pneumotype observed before the onset of hospital-acquired pneumonia and associated with lung inflammation and mortality. This unfavourable pneumotype is characterised by enrichment in virulent Streptococcus-bacteriophages and temperate Klebsiella-bacteriophages, decreased transcriptional activity of commensal taxa such as Streptococcus and Alloprevotella, and increased transcriptional activity of Klebsiella pneumoniae. Machine-learning models define two-viral- and four-bacterial-factor signatures predicting unfavourable pneumotype (AUC 0.8 and 0.7, respectively). Validation in an independent cohort (NCT02003196) of 117 ICU patients (239 ETAs) demonstrates the robustness of the association of these signatures with the risk of mortality. Causal inference identifies virulent bacteriophages associated with Streptococcus and host genes including IL18R1, ADM and PTX3, as key regulators of severe lung dysbiosis linked to mortality in critically ill patients.},
}

Humans
*Critical Illness/mortality
Female
Male
Klebsiella pneumoniae/genetics/virology
*Lung/microbiology/virology
Middle Aged
Bacteriophages/genetics/isolation & purification/pathogenicity
Aged
Microbiota/genetics
Cross Infection/microbiology/mortality/virology
Metagenomics
Dysbiosis/microbiology
Streptococcus/genetics

@article {pmid42957707,
year = {2026},
author = {Pulliam, C and Xu, M and Holandez-Lopez, K and Xue, D and Shang, Z and Gupta, G and Dioli, OE and Xiao, H and Gou, L and Wu, C and Brodbelt, JS and Wu, E and Peng, X and Chen, H and Li, J},
title = {Genome mining of the tumor microbiome reveals biosynthetic diversity and potential pathology-modulating metabolites.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42957707},
issn = {2041-1723},
support = {1R35GM150565//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM139658//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; F-1155//Welch Foundation/ ; },
mesh = {Humans ; *Neoplasms/microbiology/metabolism/pathology ; *Microbiota/genetics ; Multigene Family ; Fusobacterium/genetics/metabolism ; Metagenome ; Biosynthetic Pathways/genetics ; Genome, Bacterial ; },
abstract = {Human tumor-associated microbes - the tumor microbiome - have demonstrated an increasingly important role in human health due to their relevance to cancer progression and treatment response. While the metabolism at the host-microbiota interface, such as in the human gut, has been extensively investigated in recent years, the specialized metabolites from the tumor microbiome remain uncharted territory. To address this knowledge gap, we report a survey of the biosynthetic potential of the human tumor microbiome. Utilizing high-quality microbial metagenome-assembled genomes from 3,526 human tumor tissue samples, we identify 528 biosynthetic gene clusters with the potential to encode specialized metabolites relevant to tumor pathology. We reveal that the tumor microbiome encodes known and unknown metabolites spanning multiple biosynthetic classes. From this diverse biosynthetic landscape, we express a conserved family of biosynthetic genes from the genus Fusobacterium, which has a well-established role in cancer, and discover distinct families of long-chain fatty acyl amides. We subsequently find that one of these fatty acyl amides, oleoyl γ-aminobutyric acid, has immunomodulatory and G-protein-coupled receptor partial agonist activities, potentially supporting the influence of Fusobacterium in tumor pathology. The findings of our investigation lay a foundation for further research into the roles of tumor microbe-derived metabolites in cancer.},
}

Humans
*Neoplasms/microbiology/metabolism/pathology
*Microbiota/genetics
Multigene Family
Fusobacterium/genetics/metabolism
Metagenome
Biosynthetic Pathways/genetics
Genome, Bacterial

@article {pmid42957759,
year = {2026},
author = {Nasr, EMT and Pechlivanis, N and Strepis, N and Amato, P and Bernt, M and Bhardwaj, A and Blankenberg, D and Brites, D and Cumbo, F and Do, KT and Ferrari, E and Griffin, TJ and Grüning, BA and Hiltemann, S and Hyde, CJ and Jagtap, PD and Kumar, A and Malla, MA and Mehta, S and Métris, KL and Momin, S and Nelson, T and Oba, AJ and Pavloudi, C and Péguilhan, R and Price, GR and Psomopoulos, F and Rosic, N and Schatz, MC and Schiml, VC and Siguret, C and Soranzo, N and Stubbs, AP and van Heusden, P and Vohra, M and Zierep, PF and Batut, B},
title = {Microbiology Galaxy Lab: a community-driven gateway for reproducible and FAIR analysis of microbiological data.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42957759},
issn = {2399-3642},
support = {ANR-11-INBS-0013//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-MPGA-0013//Agence Nationale de la Recherche (French National Research Agency)/ ; U41HG006620//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U24AI183870//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 75N92023P00302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U41HG006620//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; INV-046492//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; INV-079648//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; 228162/Z/23/Z//Wellcome Trust (Wellcome)/ ; LIBIS/de.NBI Freiburg,//Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg (Ministry of Science, Research and Art Baden-Württemberg)/ ; HORIZON-INFRA-2021-EOSC-01-04//European Commission (EC)/ ; REA.B.3, BGE 101059492//European Commission (EC)/ ; REA.B.3, BGE 101059492//European Commission (EC)/ ; },
mesh = {Reproducibility of Results ; *Microbiology ; *Computational Biology/methods ; Microbiota ; Proteomics ; *Software ; },
abstract = {The explosion of microbial omics data has outpaced the ability of many researchers to analyse it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab (MGL): a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports the creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbiological data analysis. The MGL enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community (microbiology.usegalaxy.org , .eu , .org.au , . fr).},
}

Reproducibility of Results
*Microbiology
*Computational Biology/methods
Microbiota
Proteomics
*Software

@article {pmid42958435,
year = {2026},
author = {Rao, B and Liu, S and Cui, G and Jiang, J and Li, N and Hu, J and Sun, R and Li, A and Zhang, R and Lu, H and Wen, P and Xue, J and Aji, T and Wang, H and Chen, X and Zheng, S and Yu, Z and Ren, Z},
title = {Multikingdom and functional gut microbiota markers for cholangiocarcinoma.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42958435},
issn = {1756-994X},
support = {82570691//National Natural Science Foundation of China/ ; 81672422//National Natural Science Foundation of China/ ; 82470654//National Natural Science Foundation of China/ ; 2022D01C219//Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; JNL-2025007B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2025ZD01906305//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; 24HASTIT063//University Science and Technology Innovation Talent Support Plan of Henan Province/ ; HNCMS202423//Henan Province "Three 100" Program, Special Project for Clinical Medical Scientist Cultivation/ ; },
mesh = {Humans ; *Cholangiocarcinoma/microbiology/diagnosis ; *Gastrointestinal Microbiome ; *Bile Duct Neoplasms/microbiology/diagnosis ; Female ; Metagenomics/methods ; Male ; Middle Aged ; Feces/microbiology ; Liver Neoplasms/microbiology/diagnosis ; Biomarkers, Tumor ; Metagenome ; Carcinoma, Hepatocellular/microbiology ; Aged ; },
abstract = {BACKGROUND: While the association between gut microbiota and cholangiocarcinoma (CCA) has been explored, existing research has been limited to bacterial components. The alterations in non-bacterial members (fungi, archaea, and viruses) and their functional characteristics in CCA remain unclear. This study aimed to comprehensively characterize the multi-kingdom gut microbiota and functional profiles in CCA patients and develop a non-invasive diagnostic model.

METHODS: We performed metagenomic sequencing on 700 fecal samples collected from three distinct regions in China, comprising 289 CCA patients, 312 healthy controls, and 99 hepatocellular carcinoma (HCC) patients. Multi-kingdom microbial composition and functional profiles were analyzed. We integrated multiple machine learning algorithms to generate 117 distinct modeling schemes for constructing and screening the optimal CCA diagnostic model. The model was validated across three independent cohorts and tested for specificity against HCC. We also benchmarked the model against established diagnostic approaches by reviewing 15 CCA clinical practice guidelines/consensus statements and their cited evidence and by evaluating model detection in CA19-9-positive and CA19-9-negative patients.

RESULTS: Extensive alterations were identified in CCA patients across multi-kingdom and functional layers, including 198 archaeal, 154 bacterial, 78 fungal, and 120 viral species, as well as 278 genes, 99 pathways, and 151 carbohydrate-active enzymes (CAZymes). A panel of 21 multi-kingdom and functional markers demonstrated superior diagnostic accuracy with an average AUC of 91% across three validation cohorts, outperforming any single-kingdom model. The model exhibited high specificity in distinguishing CCA from HCC, achieving an AUC of 99.74% with a false positive rate of 11.11%. Benchmarking supported a complementary role as a noninvasive screening aid, the model showed pooled sensitivity and specificity of 96.2%, and 78.5%, respectively, and detected 97.6% of CA19-9-negative CCA cases.

CONCLUSIONS: This study represents the first comprehensive characterization of multi-kingdom gut microbiome and functional markers in cholangiocarcinoma. Gut multi-kingdom and functional microbial signatures represent a promising noninvasive tool that may aid the screening and early identification of cholangiocarcinoma in high-risk populations, complementing existing diagnostic approaches.},
}

Humans
*Cholangiocarcinoma/microbiology/diagnosis
*Gastrointestinal Microbiome
*Bile Duct Neoplasms/microbiology/diagnosis
Female
Metagenomics/methods
Male
Middle Aged
Feces/microbiology
Liver Neoplasms/microbiology/diagnosis
Biomarkers, Tumor
Metagenome
Carcinoma, Hepatocellular/microbiology
Aged

@article {pmid42959031,
year = {2026},
author = {Songel-Sanchis, B and Cosín-Roger, J},
title = {Gut mycobiome dysbiosis in inflammatory bowel disease: a systematic review and meta-analysis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1960101},
pmid = {42959031},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/microbiology/immunology ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Mycobiome/immunology ; *Fungi/classification/genetics ; },
abstract = {BACKGROUND: The intestinal mycobiome is increasingly recognized as an important component of host-microbiota interactions in inflammatory bowel disease (IBD), yet its contribution to intestinal immune dysregulation remains incompletely characterized. We aimed to characterize alterations in the intestinal mycobiome in patients with inflammatory bowel disease, including Crohn's disease and ulcerative colitis, compared with individuals without IBD, focusing on fungal diversity, taxonomic composition, and relative abundance, as well as their potential associations with disease phenotype and inflammatory activity.

METHODS: A systematic review and meta-analysis was conducted according to PRISMA 2020 guidelines. PubMed/MEDLINE, Embase, and Cochrane Central Register of Controlled Trials were systematically searched from inception to March 2026, with no language or publication-date restrictions. The review was not prospectively registered. Human studies assessing gut fungal communities by internal transcribed spacer (ITS)-based sequencing or shotgun metagenomics were eligible. Alpha and beta diversity, taxonomic composition, and clinically relevant fungal alterations were extracted. Study quality was assessed independently by two reviewers using the Newcastle-Ottawa Scale (NOS), and quantitative analyses were performed using standardized effect estimates and pooled prevalence.

RESULTS: Twenty-eight studies were included in the qualitative and quantitative synthesis. CD was consistently associated with reduced fungal alpha diversity compared with healthy controls, with a pooled weighted mean difference in Shannon diversity of -0.84 (p<0.001), whereas the reduction in UC was more modest (-0.31, p=0.04). Fungal beta diversity consistently differed between IBD and healthy controls. Expansion of Candida spp. was the most reproducible taxonomic alteration, occurring in 82.1% of analyzed cohorts, while depletion of Saccharomyces cerevisiae was reported in 71.4%. Malassezia enrichment was also associated with mucosal inflammation and CARD9-related immune responses. Cross-kingdom interactions involving Candida, Escherichia coli, and Serratia marcescens further highlighted potential fungal-bacterial mechanisms underlying persistent inflammation. Persistent fungal dysbiosis despite clinical remission supported the concept of a "mycobiotic scar."

CONCLUSION: IBD is characterized by substantial disruption of the intestinal mycobiome, particularly in CD, with reduced fungal diversity, expansion of potentially pathogenic Candida spp., and depletion of protective fungal taxa. These alterations may contribute to immune dysregulation and therapeutic refractoriness and support the mycobiome as a potential source of biomarkers and therapeutic targets in IBD.},
}

Humans
*Dysbiosis/microbiology/immunology
*Inflammatory Bowel Diseases/microbiology/immunology
*Gastrointestinal Microbiome/immunology
*Mycobiome/immunology
*Fungi/classification/genetics

@article {pmid42585927,
year = {2026},
author = {Ma, J and Qin, K and Qiao, Z and Ren, Z and Yang, X and Liu, Y},
title = {Integrative multi-omics reveals comprehensive gut-liver-adipose metabolic changes in peak laying hens with high or low egg production.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107493},
pmid = {42585927},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/metabolism/genetics/microbiology ; Female ; *Liver/metabolism ; Multiomics ; *Adipose Tissue/metabolism ; *Gastrointestinal Microbiome ; *Metabolome ; *Reproduction ; },
abstract = {Eggs serve as an indispensable global nutritional resource, sustaining the economic foundation of the commercial poultry industry. To meet this continuous demand, egg formation involves an exceptionally energy-intensive biological process requiring continuous yolk precursor synthesis, which imposes a massive metabolic burden on laying hens. However, the comprehensive metabolic differences across the gut-liver-adipose axis between peak laying hens with high or low egg production remain incompletely characterized. A total of 180 healthy Hy-Line Brown laying hens (45-week-old) were continuously fed and monitored for production performance over a 6-week period. Following the exclusion of individuals with extremely low egg production (≤10 eggs during the 6-week monitoring period; n = 5) and candidate hens that repeatedly produced unqualified eggs over multiple weeks (n = 20), the remaining hens were ranked by 6-week average laying rate and allocated into FH (high-production hens at 50 weeks of age, n = 15) and FL (low-production hens at 50 weeks of age, n = 14) groups. Initial body weight did not differ significantly between groups (FH: 1936 ± 29.0 g; FL: 1894 ± 48.2 g; P-value = 0.446). We integrated transcriptomic, untargeted metabolomic, targeted bile acid metabolomics, and microbiome (16S rRNA and metagenomic) profiles to characterize comprehensive metabolic changes across the gut-liver-adipose axis associated with divergent egg-production phenotypes. The results showed that: (1) FH hens exhibited higher serum APOB and lower conjugated bile acids (TCDCA, TCA, and THDCA), with hepatic upregulation of FASN, PPARA, CPT1A, and VTG1 along with downregulation of CYP7A1, CYP7B1, CYP8B1, and CYP27A1; (2) intersecting module hub genes (MHGs) with differentially expressed genes (DEGs) identified 354 upregulated and 299 downregulated core genes, with EEF2 identified as the primary hepatic downregulated hub gene; (3) in abdominal fat, GSEA revealed significant enrichment in fatty acid transport (NES = 1.54), long-chain fatty acid metabolic process (NES = 1.39), and steroid hormone biosynthesis (NES = 1.85), accompanied by significant downregulation of ANGPTL4 and upregulation of HSD3B1, VTG1, VTG2, and VTG3; (4) ileal mucosal transcriptomics identified 619 DEGs (502 upregulated), with GSEA highlighting enrichment in cell junction organization (NES = 1.52) and tube morphogenesis (NES = 1.39), which were further categorized into functional modules including enteric synaptic signaling, epithelial adhesion, mucosal vascularization, and tissue renewal; (5) the functional profile of the ileal microbiota in FH hens showed enrichment of functions related to complex carbohydrate degradation and carbohydrate-binding modules, with keystone taxa including Blautia and Bifidobacterium associated with production and lipid markers. Collectively, these findings suggest that high egg production during the peak laying period is associated with coordinated metabolic differences across the liver, abdominal fat tissue, and intestine. The observed profiles included reduced hepatic translation-related and primary bile acid synthesis-related signatures, adipose endocrine-related changes and microbial functional potential related to carbohydrate utilization and antioxidant-related functional potential. These findings provide candidate multi-omics features for precision nutritional strategies and genetic improvement in commercial poultry.},
}

Animals
*Chickens/physiology/metabolism/genetics/microbiology
Female
*Liver/metabolism
Multiomics
*Adipose Tissue/metabolism
*Gastrointestinal Microbiome
*Metabolome
*Reproduction

@article {pmid42603397,
year = {2026},
author = {Geng, D and Ding, Y and Jiang, Y and Wang, Z and Chen, G and Chang, G and Bai, H},
title = {Multi-omics analysis of cecal microbiota-hypothalamus axis interactions in small-sized meat ducks with divergent residual feed intake.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107310},
pmid = {42603397},
issn = {1525-3171},
mesh = {Animals ; *Ducks/physiology/microbiology/genetics ; *Hypothalamus/physiology/metabolism ; Multiomics ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; *Eating ; Male ; Diet/veterinary ; },
abstract = {Residual feed intake (RFI) is an indicator of feed efficiency that reflects variation in nutrient utilization independent of growth. This study characterized physiological traits and multi-omics profiles associated with divergent RFI in small-sized meat ducks. From an initial population of 500 1-day-old ducks, a total of 420 healthy ducks were individually housed from 21 to 42 d to record feed intake, and ducks with low RFI (LRFI) and high RFI (HRFI) were identified for further analyses. During the experiment, 30 ducks per group for growth performance, 15 ducks per group for plasma biochemical and 5 per group for multi-omics. Compared with HRFI ducks, LRFI ducks showed lower feed intake, lower feed conversion ratio (FCR), and lower plasma triglyceride concentrations, whereas body weight gain did not differ between groups. Shotgun metagenomic analysis showed that LRFI ducks were enriched in Bacteroides-related lineages and had higher predicted capacities for complex carbohydrate degradation, lipid and energy metabolism, and cofactor synthesis, whereas HRFI ducks were enriched in taxa including Subdoligranulum variabile and Clostridioides difficile. Untargeted cecal metabolomics revealed distinct lipid- and bile acid-related metabolic profiles between the 2 groups, including differences in long-chain lipid species and bile acid-associated metabolites. Hypothalamic transcriptomic analysis identified differentially expressed genes related to neuropeptide signaling, serotonin biosynthesis, intracellular signaling, and inflammatory regulation, including NMUR2, TPH1, and PTK2B. Correlation analysis integrating microbial taxa, metabolites, and hypothalamic transcripts further revealed coordinated associations among these features in small-sized meat ducks with divergent RFI. Overall, variation in feed efficiency in ducks was associated with differences in cecal microbiota, metabolite profiles, and hypothalamic gene expression, and these results highlight candidate microbial taxa, metabolites, and genes for further validation.},
}

Animals
*Ducks/physiology/microbiology/genetics
*Hypothalamus/physiology/metabolism
Multiomics
*Cecum/microbiology
*Gastrointestinal Microbiome
*Eating
Male
Diet/veterinary

@article {pmid42617270,
year = {2026},
author = {Li, Y and Li, Q and Zhang, X and Wang, Y and Gao, G and Chen, D and Qin, S and Cui, Z and Liu, L and Liu, A and Wang, H and Wang, Q and Tang, B},
title = {Microbiota contributes to regulates the external genitalia development through gut-testis axis in male geese.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107476},
pmid = {42617270},
issn = {1525-3171},
mesh = {Animals ; Male ; *Geese/growth & development/microbiology ; *Testis/growth & development ; *Gastrointestinal Microbiome ; *Genitalia, Male/growth & development ; },
abstract = {Geese is one of the few poultry species with complete external genitalia, and the external genitalia abnormal development has become an important factor limiting the reproductive efficiency of the goose industry. Recent studies have shown that the gut microbiota plays an important role in regulating male reproductive processes, but its regulatory mechanisms in male geese's external genitalia development remain unclear. In this study, male geese with normal development (ND) and abnormal development (AD) external genitalia were selected as the research object, and multi-omics were used to investigate the regulatory of the microbe-mediated gut-testis axis on external genitalia development. At the transcriptomic level, we identified key DEGs (KNG1, P2RY4, SSTR5, and HRH3) in the testis and external genitalia between ND and AD groups, which were significantly enriched in the neuroactive ligand-receptor interaction pathway. Metabolomics analysis revealed that DMs in the ND and AD groups were significantly enriched in pathways related to aromatic amino acid metabolism and neural signal transduction. Furthermore, metagenomic results showed that the ND group was identified key bacterial genera g_Blautia and g_Faecousia affecting external genitalia development, which were associated with SCFAs synthesis and neuroendocrine signaling regulation. Integrated with multi-omics data, it was revealed that gut-derived neuroactive metabolic signals may participate in the molecular regulation of external genitalia development in male goose by modulating GPCRs signaling. Our findings not only provide new insights into the gut-testis axis regulates the development of external genitalia in male geese, but also contribute to improving the reproductive performance of male geese.},
}

Animals
Male
*Geese/growth & development/microbiology
*Testis/growth & development
*Gastrointestinal Microbiome
*Genitalia, Male/growth & development

@article {pmid42623770,
year = {2026},
author = {Li, X and Wang, Y and Wang, Z and Deng, M and Zheng, J and Geng, H and Zhao, G and Wang, Q},
title = {Gut Faecalibacterium regulates host immunity and metabolic profiles to confer resistance against Salmonella infection in chicks.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107550},
pmid = {42623770},
issn = {1525-3171},
mesh = {Animals ; *Chickens/immunology ; *Poultry Diseases/immunology/microbiology ; *Salmonella Infections, Animal/immunology/microbiology ; *Gastrointestinal Microbiome ; Salmonella enteritidis/physiology ; *Immunity, Innate ; *Metabolome ; *Disease Resistance ; Cecum/microbiology ; },
abstract = {To explore the pathogenic mechanism of Salmonella Enteritidis (SE) infection in chicks and the regulatory role of Faecalibacterium, we established a chick SE infection model, systematically analyzing intestinal damage, systemic inflammation, and cecal microbial community changes. Focusing on the differentially abundant Faecalibacterium, we elucidated its regulatory mechanism via metagenomics, transcriptomics, and serum metabolomics. Results showed that SE successfully colonized the chick cecum, causing significant reductions in the thickness of the intestinal mucosal and muscular layers, a decrease in gland depth, and a loss of goblet cells. Concurrently, serum levels of IgA and IL-6 were markedly elevated, indicating the induction of systemic inflammatory responses and severe intestinal damage. Microbiome analysis revealed SE significantly altered cecal microbiota β-diversity, increased Actinobacteria abundance, and decreased the abundance of beneficial bacterial families (Lachnospiraceae and Oscillospiraceae) and the key beneficial genus Faecalibacterium. Functional prediction indicated microbial function remodeling towards enhanced pathogen colonization and pro-inflammation. β-diversity analysis of Faecalibacterium gene set showed clear separation between the Ctrl and SE groups in two-dimensional space: the control group was enriched in immune-related pathways such as Th17 cell differentiation and IL-17 signaling pathway, while the infected group was enriched in pathways related to Salmonella infection and pathogenic Escherichia coli infection. Validation in uninfected chicks showed High_ Faecalibacterium abundance was associated with lower serum IL-6, IL-8, IFN-γ and distinct gene expression profiles. Differentially expressed genes (DEGs) were enriched in immune regulation pathways such as cytokine-cytokine receptor interaction, NOD-like receptor signaling pathway, and intestinal immune network for IgA. LASSO regression screening identified 16 key associated genes including TM4SF4 and FABP4. Serum metabolomics showed distinct metabolic profiles between High_ and Low_ Faecalibacterium abundance groups, with 26 differential metabolites; N-(2,4-dinitrophenyl) ethylenediamine and Val-Gly-Phe (AUC > 0.8) were potential biomarkers. In conclusion, SE induces pathogenesis by damaging intestinal barrier, triggering inflammation, and disrupting cecal microbiota. Faecalibacterium enhances chick resistance to SE via regulating immune and metabolic homeostasis, providing a basis for avian salmonellosis microecological control.},
}

Animals
*Chickens/immunology
*Poultry Diseases/immunology/microbiology
*Salmonella Infections, Animal/immunology/microbiology
*Gastrointestinal Microbiome
Salmonella enteritidis/physiology
*Immunity, Innate
*Metabolome
*Disease Resistance
Cecum/microbiology

@article {pmid42680886,
year = {2026},
author = {Liu, CC and Dong, SS and Guo, J and Xu, Z and Wang, C and Li, YX and Meng, LL and Yang, XC and Li, M and Fu, K and Guo, Y and Yang, TL},
title = {MetaCAT enables reconstruction of high-quality microbial genomes and their association with host traits from metagenomic data.},
journal = {Nature microbiology},
volume = {11},
number = {10},
pages = {2853-2866},
pmid = {42680886},
issn = {2058-5276},
support = {2023M732810//China Postdoctoral Science Foundation/ ; 2024M762573//China Postdoctoral Science Foundation/ ; 82372458//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401762//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370653//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Metagenomics/methods ; Polymorphism, Single Nucleotide ; Colorectal Neoplasms/microbiology/genetics ; *Genome, Microbial/genetics ; Humans ; *Metagenome ; *Host Microbial Interactions/genetics ; Cluster Analysis ; Clustering Algorithms ; Microbiota/genetics ; *Computational Biology/methods ; },
abstract = {Recovering high-quality microbial genomes from metagenomic sequencing data is essential for accurate profiling and understanding microbial variation. However, existing clustering methods often suffer from limited accuracy and scalability. Here we present MetaCAT (Metagenome Clustering and Association Tool), a framework that combines recovery of microbial genomes from metagenomic data and analysis of their associations with host traits. MetaCAT incorporates a Sparse Weighted Dirichlet Process Gaussian Mixture Model (SWDPGMM) to accurately and efficiently decompose complex datasets and combines k-mer frequency with read coverage to improve genome reconstruction. It also provides a dedicated workflow for microbial single-nucleotide polymorphism identification and metagenome-wide association studies with the host. MetaCAT outperforms existing methods in both clustering accuracy and computational efficiency across diverse datasets. Using metagenomic data from colorectal cancer cohorts, it revealed previously unrecognized marker species and microbial single-nucleotide polymorphisms associated with colorectal cancer. MetaCAT provides a scalable framework for microbial community profiling and advances our understanding of host-microbe interactions.},
}

*Metagenomics/methods
Polymorphism, Single Nucleotide
Colorectal Neoplasms/microbiology/genetics
*Genome, Microbial/genetics
Humans
*Metagenome
*Host Microbial Interactions/genetics
Cluster Analysis
Clustering Algorithms
Microbiota/genetics
*Computational Biology/methods

@article {pmid42705201,
year = {2026},
author = {Zhao, X and Meng, T and Zhang, Z and Hu, L and Xiang, X},
title = {Vegetable trimming pellets in laying hen diets drive cecal remodeling and dose-dependent plasma-egg metabolomic dissociation.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107637},
pmid = {42705201},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/blood/microbiology ; Female ; Diet/veterinary ; *Cecum/physiology/microbiology ; Animal Feed/analysis ; *Ovum/physiology/metabolism/chemistry ; *Metabolome ; Animal Nutritional Physiological Phenomena ; *Vegetables/chemistry ; *Gastrointestinal Microbiome/drug effects ; Dose-Response Relationship, Drug ; },
abstract = {Vegetable trimming pellets (TVP) provide a potential route for recovering plant biomass as poultry feed, but their dose-dependent effects across production and biological compartments remain unclear. We evaluated diets containing 0% (A), 3% (B), 6% (C), or 9% (D) TVP (80% lettuce and 20% cabbage trimmings) in 240 17-wk-old Hy-Line Grey hens (6 pens of 10 hens per diet) for 12 wk. Diets had similar calculated crude protein, while calculated metabolizable energy decreased from 2.854 to 2.659 Mcal/kg. We assessed production, egg quality, serum, intestine, cecal microbiota and metagenome, and plasma and egg metabolomes. Full-period feed conversion ratio increased from 2.74 in A to 2.88 in D (P = 0.026), and average daily feed intake differed (P = 0.001), while egg production, egg weight, and egg mass remained similar (P > 0.05). At wk 12, shell breaking strength was lower in D than in A to C (3.55 vs. 3.92 to 4.02 kgf/cm[2]; P = 0.030), and yolk color differed among diets (P = 0.007). Serum hormones, several biochemical indices, catalase, and malondialdehyde differed at wk 12 (P < 0.05; marker-specific n = 3 to 6). Cecal community composition differed (permutational multivariate analysis of variance: R[2] = 0.571, P = 0.0006; dispersion P = 0.229), while Shannon diversity remained similar (P = 0.582). Five A-vs.-D metagenomic pathways met a false discovery rate (FDR) < 0.05. In D vs. A, exploratory screening identified 254 annotated plasma and 338 annotated egg candidates, of which 62 and 80, respectively, also met FDR < 0.05; exact annotation matching identified one shared candidate. Graded TVP inclusion maintained major egg-output traits while producing dose-related shifts in feed use, cecal microbial features, and compartment-specific molecular profiles. At the higher inclusion levels, less favorable feed conversion and the lower late-period shell strength at 9% were the principal practical responses.},
}

Animals
*Chickens/physiology/blood/microbiology
Female
Diet/veterinary
*Cecum/physiology/microbiology
Animal Feed/analysis
*Ovum/physiology/metabolism/chemistry
*Metabolome
Animal Nutritional Physiological Phenomena
*Vegetables/chemistry
*Gastrointestinal Microbiome/drug effects
Dose-Response Relationship, Drug

@article {pmid42722277,
year = {2026},
author = {Xue, X and Ge, Y and Meng, T and Chen, Y and Zhou, L and Xu, D},
title = {Anthropogenic disturbance enhances bacteria-mediated resistome transmission across the sediment-benthos-demersal fish trophic continuum.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129137},
doi = {10.1016/j.envpol.2026.129137},
pmid = {42722277},
issn = {1873-6424},
mesh = {Animals ; *Food Chain ; *Fishes/microbiology ; *Bacteria/genetics ; *Geologic Sediments/microbiology ; *Anthropogenic Effects ; China ; Lakes/microbiology ; Ecosystem ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Microbiota ; },
abstract = {Aquatic ecosystems are important environmental reservoirs of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), yet how anthropogenic disturbance influences their distribution and cross-niche transmission through benthic food webs remains poorly understood. Here, we systematically characterized resistome and virulome profiles across trophic niches, including sediments, benthic invertebrates and demersal fishes, along a gradient of anthropogenic disturbance in Gehu Lake, China. Metagenomic analysis identified 1645 ARG and 1939 VFG subtypes, with both gene pools exhibiting pronounced niche differentiation. Sediments harbored the highest abundance and diversity of both gene pools, whereas animal-associated niches exhibited substantial but host-dependent attenuation. Notably, anthropogenic disturbance significantly altered ARG and VFG profiles across all ecological niches, with stronger effects in sediments and benthic organisms than in fish guts, and was generally associated with higher ARG and VFG abundance and diversity. Integrative source-tracking and bacteria-gene association network analyses further demonstrated that bacterial transmission was the primary vector mediating the cross-trophic dissemination of both gene pools. Anthropogenic disturbance reshaped bacterial community structure across niches and enhanced bacterial migration along the food chain, as reflected by the increased contribution of bacteria derived from upstream trophic compartments. KEGG functional profiling suggested that these transmitted bacterial assemblages processed enhanced metabolic and adaptive capacities functions such as xenobiotic degradation. Among the enriched bacterial lineages, Pseudomonadota, Actinomycetota and Bacillota were dominant and showed a higher propensity to harbor ARGs and VFGs, thereby facilitating their persistence, amplification and trophic transfer. Collectively, our findings reveal a disturbance-driven, microbiome-mediated mechanism underlying the co-dissemination of ARGs and VFGs across aquatic food webs, highlighting the critical role of host-associated microbial selection in amplifying environmental health risk.},
}

Animals
*Food Chain
*Fishes/microbiology
*Bacteria/genetics
*Geologic Sediments/microbiology
*Anthropogenic Effects
China
Lakes/microbiology
Ecosystem
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Genes, Bacterial
Microbiota

@article {pmid42727575,
year = {2026},
author = {Deng, ZL and Safaei, N and McHardy, AC},
title = {Metax enables accurate cross-domain taxonomic profiling of metagenomes.},
journal = {Cell},
volume = {189},
number = {22},
pages = {7196-7211.e7},
doi = {10.1016/j.cell.2026.08.024},
pmid = {42727575},
issn = {1097-4172},
mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; Humans ; Bacteria/genetics/classification ; },
abstract = {Taxonomic profiling is fundamental to microbiome research, yet achieving high species-level accuracy remains challenging for complex communities that span bacteria, viruses, eukaryotes, and archaea, and these limitations are exacerbated in low-biomass, host-dominated samples. We introduce Metax, a cross-domain taxonomic profiler that integrates coverage-based probabilistic modeling with an expectation-maximization framework to distinguish true microbial signals from artifacts. Across >600 samples from host-associated, environmental, wastewater, and low-biomass clinical settings, including benchmarks with limited reference representation, Metax improved profiling accuracy, achieving on average 55% higher F1 scores and 45% lower Bray-Curtis dissimilarity than other methods. Moreover, this broad evaluation demonstrated that Metax resolved bacterial and viral signatures of peri-implantitis in oral microbiomes and revealed signals suggestive of reagent-borne contaminants and reference misassemblies in plasma-cell-free DNA. By leveraging genome-wide coverage evidence, Metax enables robust cross-domain profiling across diverse sample types and sequencing depths, including settings where reference databases are highly incomplete.},
}

*Metagenome/genetics
*Microbiota/genetics
*Metagenomics/methods
Humans
Bacteria/genetics/classification

@article {pmid42731219,
year = {2026},
author = {Xie, B and Hua, X and Geng, L and Li, K and Liu, G and Fang, Y and Zhao, T and Lu, C and Zhang, C and Han, Z and Yu, B and Li, X},
title = {Cecal microbiota regulates meat quality of Yanshan red jade broilers: insights from metagenomics and targeted metabolomics.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107619},
pmid = {42731219},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology/physiology/growth & development ; Female ; *Meat/analysis ; *Cecum/microbiology ; Metagenomics ; *Gastrointestinal Microbiome ; Metabolomics ; *Metabolome ; Fatty Acids ; },
abstract = {This study aimed to elucidate the molecular mechanism of cecal microbiota regulating muscle flavor in Yanshan red jade broilers with natural body weight variation. Eighteen-week-old hens were selected for this study. Targeted metabolomics was applied to determine the fatty acid and amino acid composition of muscle. Metagenomic sequencing was used to analyze the structure and function of cecal microbial communities. A regulatory network between gut microbiota and meat flavor was constructed via correlation analysis. The results showed that the high-weight female (HF) group had significantly better slaughter performance and leg muscle intramuscular fat (IMF) than the low-weight female (LF) group. Metabolomic analysis identified a total of 38 fatty acids and 25 amino acids. The HF group was enriched in umami amino acids such as arginine and serine, while the LF group had higher content of long-chain polyunsaturated fatty acids (PUFAs) and 1-methyl-l-histidine. Metagenomic analysis showed that Eubacterium and Anaerostipes were the characteristic bacteria in the HF group, while Odoribacter was dominant in the LF group. Functional annotation identified a total of 12 differential metabolic pathways, including core pathways such as lipid metabolism and amino acid synthesis. The association network showed that Eubacterium sp. An11 enhanced growth performance and umami quality by promoting muscle protein deposition, Odoribacter_splanchnicus affected muscle nutritional characteristics by regulating fatty acid metabolism, and Pseudoflavonifractor_capillosus was involved in both growth and flavor regulation. This study provides theoretical support and functional strain targets for flavor improvement of high-quality broilers and precise nutritional regulation of gut microbiota.},
}

Animals
*Chickens/microbiology/physiology/growth & development
Female
*Meat/analysis
*Cecum/microbiology
Metagenomics
*Gastrointestinal Microbiome
Metabolomics
*Metabolome
Fatty Acids

@article {pmid42731224,
year = {2026},
author = {Kerek, Á and Hetyésy, M and Tornyos, GÁ and Kaszab, E and Fehér, E and Jerzsele, Á and Tóth, T and Zsédely, E and Fébel, H},
title = {Timing of an antioxidant-acidifier feed additive modulates growth performance and cecal microbiota in broiler chickens during enrofloxacin exposure.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107639},
pmid = {42731224},
issn = {1525-3171},
mesh = {Animals ; *Enrofloxacin/administration & dosage ; *Chickens/growth & development/microbiology/physiology ; Male ; Animal Feed/analysis ; Diet/veterinary ; Cecum/microbiology ; *Anti-Bacterial Agents/administration & dosage/pharmacology ; Dietary Supplements/analysis ; *Antioxidants/administration & dosage/metabolism ; *Gastrointestinal Microbiome/drug effects ; Random Allocation ; Fluoroquinolones ; },
abstract = {Nutritional interventions targeting oxidative stress and gut ecology may help sustain broiler performance during antimicrobial perturbation. This study evaluated the timing-dependent effects of an antioxidant-acidifier feed additive, alone or combined with enrofloxacin, on growth performance and cecal microbiota in broilers. A total of 1,200 Ross 308 male broilers were assigned to six treatments (4 pens/treatment; 50 birds/pen) and reared to 42 d: control, enrofloxacin (d15-19), additive for 4 weeks (A4; d15-42), A4+enrofloxacin, additive for 6 weeks (A6; d1-42), and A6+enrofloxacin. The additive was included at 4% of the diet, providing fumaric acid, heat-stable vitamin C, and all-rac-α-tocopheryl acetate. Performance traits were recorded by phase and overall. Cecal contents were collected from 2 birds/pen on d14, d20, and d42 and analyzed by shotgun metagenomic sequencing; microbiota analyses were conducted on pen-level aggregated profiles. Growth performance showed modest, timing-dependent numerical differences: A4 had numerically higher finisher and overall average daily gain, whereas A4+enrofloxacin was associated with lower overall gain than enrofloxacin alone. Cecal community structure was driven primarily by sampling time point. No detectable enrofloxacin-associated separation was observed at d20, whereas a trend toward separation was evident at d42. By d42, only limited genus-level differences were detected, with the strongest signal observed for Phocaeicola in the targeted differential abundance analysis. Overall, additive timing influenced growth responses and cecal microbiota trajectories during enrofloxacin exposure, supporting the importance of supplementation timing when nutritional strategies are used to improve robustness under antibiotic perturbation.},
}

Animals
*Enrofloxacin/administration & dosage
*Chickens/growth & development/microbiology/physiology
Male
Animal Feed/analysis
Diet/veterinary
Cecum/microbiology
*Anti-Bacterial Agents/administration & dosage/pharmacology
Dietary Supplements/analysis
*Antioxidants/administration & dosage/metabolism
*Gastrointestinal Microbiome/drug effects
Random Allocation
Fluoroquinolones

@article {pmid42731658,
year = {2026},
author = {Cui, J and Yan, S and Wang, S and Xia, H and Chen, L and Liu, H and Ma, J and Fu, Y},
title = {Cerium dioxide nanoparticle exposure attenuates mobility-linked antibiotic resistome signatures across the soil-lettuce continuum.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129133},
doi = {10.1016/j.envpol.2026.129133},
pmid = {42731658},
issn = {1873-6424},
mesh = {*Cerium/toxicity ; *Soil Microbiology ; *Nanoparticles ; *Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; Anti-Bacterial Agents/pharmacology ; Soil/chemistry ; *Soil Pollutants ; },
abstract = {Antibiotic resistance genes (ARGs) are contaminants of emerging concern in agricultural microbiomes. Their association with mobile genetic elements (MGEs) can enhance dissemination across soil-plant interfaces, creating potential environmental and food-chain exposure risks. However, how engineered nanoparticles modulate relative ARG abundance and mobility-linked resistome features in plant-associated microbiomes remains poorly understood. Here, we examined the effects of graded, experimentally elevated cerium dioxide nanoparticle (CeO2 NP) loadings in a soil-lettuce system by integrating compartment-resolved metagenomics, ARG-MGE co-occurrence analysis, putative host-reservoir profiling, transcriptomics, and functional assays. Metagenomic profiling identified 16 ARG types and 125 subtypes and revealed niche-dependent microbiome restructuring under CeO2 NP exposure. Rhizosphere relative ARG abundance showed a negative dose-associated trend, although overall inter-group differences were not significant, whereas leaf endophytes showed a weaker response. Relative MGE abundance decreased significantly in both compartments, and lower assembly-level ARG-MGE co-occurrence reflected fewer ARGs detected in MGE-associated genomic contexts, whereas fewer multi-ARG contigs suggested reduced ARG clustering and potential co-selection. Putative host-reservoir analysis associated key efflux determinants with bacterial families whose relative representation declined following CeO2 NP exposure. Transcriptomic profiling of representative putative ARG hosts revealed host-specific responses, including downregulation of genes involved in central metabolism and Sec-dependent trafficking. Complementary host assays showed reduced apparent envelope permeability and lower recovery of tetracycline-resistant recipient-identity colonies in the plasmid-associated host system. Together, under the tested elevated-loading conditions, CeO2 NP exposure was associated with lower relative ARG signals and weaker mobility-linked resistome features across the soil-lettuce continuum, providing mechanistic insight into nanoparticle-resistome interactions in soil-plant systems.},
}

*Cerium/toxicity
*Soil Microbiology
*Nanoparticles
*Drug Resistance, Microbial/genetics
Microbiota/drug effects
Anti-Bacterial Agents/pharmacology
Soil/chemistry
*Soil Pollutants

@article {pmid42759909,
year = {2026},
author = {Hou, J and Li, Q and Li, Y and Liu, M and Xue, M and An, Y and Yao, Y and Xu, H},
title = {Intraspecific rice intercropping reduces the rhizosphere resistome in association with organic acid and low-ARG-burden microbiota enrichment.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129180},
doi = {10.1016/j.envpol.2026.129180},
pmid = {42759909},
issn = {1873-6424},
mesh = {*Rhizosphere ; *Oryza/growth & development ; *Soil Microbiology ; *Agriculture/methods ; *Microbiota ; *Drug Resistance, Microbial/genetics ; Soil/chemistry ; Genes, Bacterial ; },
abstract = {Antibiotic resistance genes (ARGs) in agricultural soils are an emerging environmental concern. However, sustainable strategies for reducing ARG in crop rhizospheres remain limited. Here, we investigated associations among rhizosphere metabolites, microbial communities, and ARG profiles in an intraspecific rice intercropping system. Compared with monoculture, intraspecific intercropping reduced the relative abundances of total ARGs and ARGs assigned to the Ranks I and II. Intercropping also altered rhizosphere metabolite profiles, with increased organic acid abundance, and was associated with convergent changes in microbial community composition. Nitrospirales, particularly Candidatus Sulfobium, was enriched under intercropping. Metagenome-assembled genomes (MAGs) assigned to this lineage contained relatively few annotated ARGs, which were predominantly classified as ARGs assigned to the Rank IV. Exogenous supplementation reproduced this field-associated pattern: citric acid treatment reduced total ARG and ARGs assigned to the Ranks I and II abundance and concurrently increased the relative abundance of Candidatus Sulfobium. These results support an association among rhizosphere organic acids, low-ARG-burden taxa, and reduced ARG abundance. Collectively, these findings highlight intraspecific rice intercropping as a low-input, source-control approach for cleaner rice production and ARG-risk mitigation.},
}

*Rhizosphere
*Oryza/growth & development
*Soil Microbiology
*Agriculture/methods
*Microbiota
*Drug Resistance, Microbial/genetics
Soil/chemistry
Genes, Bacterial

@article {pmid42778012,
year = {2026},
author = {Fu, X and He, H and Li, C and Huang, Q and Bu, Y and Zhang, D and Hashim, JH and Hashim, Z and Wispriyono, B and Sary, L and Pratama, S and Wieslander, G and Norback, D and Sun, Y},
title = {Classroom dust microbiome-metabolome signatures and ocular health in students: Cross-sectional associations with putative pollutant-transformation and microbial functional profiles.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129217},
doi = {10.1016/j.envpol.2026.129217},
pmid = {42778012},
issn = {1873-6424},
mesh = {*Microbiota ; *Dust/analysis ; Humans ; *Metabolome ; Schools ; Cross-Sectional Studies ; *Air Pollution, Indoor/analysis ; },
abstract = {Ocular irritation and tear-film instability are common among school-aged children, yet the microbial and chemical features of classroom dust associated with these outcomes remain poorly characterized. We conducted a cross-sectional multi-omics study in 32 classrooms from eight Indonesian junior high schools, integrating shotgun metagenomics and untargeted LC-MS metabolomics of settled dust with ocular symptoms and tear film break-up time (TFBUT) from 380 students. Classrooms with a low prevalence of ocular irritation were enriched in Actinobacteriota such as Allosaccharopolyspora coralli, Saccharopolyspora dendranthemae, and Brevibacterium epidermidis (LDA > 2, P < 0.05, LEfSe), and in microbial pathways annotated for the degradation of aromatic pollutants and xenobiotics, including xylene, benzoate, toluene and polycyclic aromatic hydrocarbons (LDA > 2, P < 0.05). Consistent with this, classrooms with more stable tear film showed higher signals of metabolites consistent with aromatic-compound and xenobiotic transformation, including 4-hydroxyphenylpyruvic acid, the phthalate-degradation intermediate 4-hydroxyphthalate, 3-hydroxybenzoic acid and 4-hydroxycinnamic acid (q < 0.05), indicating potential microbial degradation of aromatic pollutants in these classrooms. Statistical interactions linked specific genera to these features (e.g. Brevibacterium with trans-cinnamate and p-hydroxyphenylacetic acid, and Sphingomonas with 3-hydroxyphenylacetic acid) in relation to TFBUT, and taxa such as Janibacter and Nocardioides co-occurred with multiple degradation intermediates. These signatures point to microbial pollutant-transformation potential as a candidate modifier of the indoor exposome, warranting longitudinal and mechanistic follow-up.},
}

*Microbiota
*Dust/analysis
Humans
*Metabolome
Schools
Cross-Sectional Studies
*Air Pollution, Indoor/analysis

@article {pmid42805174,
year = {2026},
author = {Perl, M and Guetter, S and Shah, D and Holzinger, S and Becker, L and Tariq, M and Menauer, P and Delahais, S and Lutzny-Geier, G and Scherer, JN and Göttert, S and Herfeld, K and Heinrich, P and Kreitmeier, KG and Gebhard, C and Herr, W and Trefny, MP and Doerr, J and Sameri, S and Harrer, DC and Ziegler-Martin, K and Staudt, S and Hansmann, L and Edinger, M and Wolff, D and Weber, D and Meedt, E and Denk, A and Gessner, A and Holler, E and Wertheimer, T and Neuhaus, K and Zheng, T and Cordas Dos Santos, DM and Theurich, S and Schirmer, M and Kleigrewe, K and Schluter, J and van den Brink, M and Schmitt, M and Feuerer, M and Heuser-Loy, C and Baldwin, J and Gattinoni, L and Rehli, M and Hudecek, M and Bigenwald, C and Zitvogel, L and Subklewe, M and Blumenberg, V and Schubert, ML and Stein-Thoeringer, C and Luu, M and Kobold, S and Fante, MA and Thiele Orberg, E and Poeck, H},
title = {Opposing functions of gut immunomodulatory metabolites on CAR-T therapy.},
journal = {Cell},
volume = {189},
number = {22},
pages = {6968-6987.e14},
doi = {10.1016/j.cell.2026.09.004},
pmid = {42805174},
issn = {1097-4172},
support = {DP2 AI164318/AI/NIAID NIH HHS/United States ; R01 CA269617/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/immunology ; Mice ; *Immunotherapy, Adoptive/methods ; Pentanoic Acids/metabolism ; Indoles/metabolism ; *Receptors, Chimeric Antigen/metabolism/immunology ; Fatty Acids, Volatile/metabolism ; Female ; },
abstract = {Chimeric antigen receptor (CAR)-T cell therapy has transformed hematological cancer treatment, yet nearly half of patients still relapse or progress. Increasing evidence implicates the gut microbiome and antibiotic exposure as key modulators of clinical outcomes. In a cohort of 129 patients across three German centers, shotgun metagenomics and targeted mass spectrometry revealed that reduced short-chain fatty acids, particularly valeric acid, prior to CAR-T cell therapy correlated with increased risk of disease progression. Conversely, high levels of indole metabolites, including indole-3-carboxaldehyde and indole-3-acetic acid as well as the branched-chain fatty acid isovaleric acid, were linked to adverse outcomes. Functional validation in human and murine CAR-T cell models demonstrated that valeric acid supplementation enhanced, while indole-3-carboxaldehyde and isovaleric acid impaired, CAR-T cell efficacy. These findings reveal the opposing roles of immunomodulatory metabolites on CAR-T cell therapy, carrying significant implications for the design of metabolite-guided, microbiome-based therapeutics.},
}

Humans
Animals
*Gastrointestinal Microbiome/immunology
Mice
*Immunotherapy, Adoptive/methods
Pentanoic Acids/metabolism
Indoles/metabolism
*Receptors, Chimeric Antigen/metabolism/immunology
Fatty Acids, Volatile/metabolism
Female

@article {pmid42838722,
year = {2026},
author = {Ware, K and Ollberding, N and Duan, Q and Haslam, D and Phipatanakul, W and Glazman, M and Bernstein, JA},
title = {Ultraviolet irradiation and the home microbiome in childhood asthma: An exploratory environmental analysis.},
journal = {Allergy and asthma proceedings},
volume = {47},
number = {6},
pages = {394-398},
doi = {10.2500/aap.2026.47.260079},
pmid = {42838722},
issn = {1539-6304},
support = {K24 AI106822/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Asthma/etiology/microbiology/epidemiology/diagnosis ; *Microbiota/radiation effects ; *Ultraviolet Rays ; Female ; Male ; Child ; Dust/analysis ; *Air Pollution, Indoor/adverse effects ; Housing ; Environmental Exposure ; Child, Preschool ; },
abstract = {Background: Ultraviolet (UV) filtration units installed into central heating, ventilation, and air conditioning systems have been shown to modify indoor environmental microbiomes (EM), but it remains unclear whether central UV air filtration systems as a targeted intervention alters the EM sufficiently to modify asthma outcomes. Objective: The objective was to investigate changes in the microbiome from dust samples collected before and after installation of a central UV filtration system in homes of children with mild-moderate persistent asthma. Methods: Enrolled pediatric subjects with asthma were randomized to receive UV filtration or sham devices in their heating, ventilation, and air conditioning units. Dust samples were collected from the furnace filters and each child's bedroom inflow air ducts from the first 20 homes randomized at the two largest recruiting sites at the time of device placement and at study completion (12 months), along with periodic measurements of asthma outcomes markers by using the Composite Asthma Severity Index. Microbial DNA from each paired dust sample underwent shotgun metagenomic sequencing, and taxonomic profiles were generated with MetaPhlAn 4. Associations between changes in bacterial species abundance and changes in asthma severity were assessed with Microbiome Multivariable Associations with Linear Models in R. Results: A total of 14 paired dust samples (7 from the UV homes and 7 from the sham homes) from inflow air ducts with sufficient quantity of dust were included for EM analysis. Within the UV filtration homes, false discovery rate adjusted q-values < 0.05 identified associations between worsening asthma severity and reduced relative abundance of common gastrointestinal commensals, such as Bacteroides and Bifidobacterium, previously linked to a reduced risk of allergic disease and asthma; no associations at this threshold were observed in the sham homes. Conclusion: An exploratory study of UV air filtration units installed in homes of children with asthma identified hypothesis-generating associations between bacterial species changes and asthma severity; because the study was underpowered for between-arm comparisons, these findings do not establish that UV air filtration caused the microbiome changes and should not be interpreted as confirmatory of a UV-specific effect.Clinical trial NCT02715375, www.clinicaltrials.gov.},
}

Humans
*Asthma/etiology/microbiology/epidemiology/diagnosis
*Microbiota/radiation effects
*Ultraviolet Rays
Female
Male
Child
Dust/analysis
*Air Pollution, Indoor/adverse effects
Housing
Environmental Exposure
Child, Preschool

@article {pmid42849293,
year = {2026},
author = {Zhou, X and Cui, G and Dong, H and Wen, S and Li, Y and Han, M and Wang, G},
title = {Genotype-dependent phosphorus acquisition responses of two soybean genotypes under combined low phosphorus and salt stress: evidence from root traits, exudates and rhizosphere microbiome.},
journal = {Plant physiology and biochemistry : PPB},
volume = {239},
number = {},
pages = {111810},
doi = {10.1016/j.plaphy.2026.111810},
pmid = {42849293},
issn = {1873-2690},
mesh = {*Phosphorus/metabolism ; *Rhizosphere ; *Glycine max/genetics/metabolism/microbiology ; *Plant Roots/metabolism/microbiology/genetics ; Genotype ; *Microbiota ; *Salt Stress ; Plant Exudates/metabolism ; },
abstract = {Soil salinization and phosphorus (P) deficiency often co-occur in coastal saline-alkali soils, severely limiting crop productivity. Although root exudates are known to mediate rhizosphere microbiome assembly, the coordinated associations among root exudates, rhizosphere microbes, and P acquisition under combined salinity stress and phosphate deficiency remain unclear. In this study, we used two salt-tolerant soybean genotypes differing in P efficiency (A74, P-efficient; A6, P-inefficient) as materials. In a controlled pot experiment, four treatments were established: control (CK), low P (LP), salt (S), and combined stress (LPS). By integrating root phenotypes, P acquisition traits, root exudate metabolomics, and rhizosphere metagenomics, the genotype-dependent rhizosphere responses were investigated. Results showed that, compared to A6, A74 maintained a more extensive root-soil interface and superior P nutritional status under LP and LPS, exhibiting more robust P acquisition responses. Metabolomics and metagenomics identified 16 candidate metabolites and 12 candidate microbial taxa, respectively. Effect-size and correlation analyses prioritized naringenin and Sinorhizobium as candidate components associated with genotype-dependent P acquisition responses. KO annotation identified Sinorhizobium-associated genes with potential roles in phosphonate and phosphinate metabolism and benzoate degradation (e.g., phnJ, pcaC, and mhpD). In summary, these results support a genotype-dependent rhizosphere response pattern involving naringenin and Sinorhizobium, in which coordinated changes in root traits, exudate profiles, and microbial functional potential were associated with the stronger P acquisition response of A74 under combined stress. These findings identify candidate relationships for future functional validation under saline conditions.},
}

*Phosphorus/metabolism
*Rhizosphere
*Glycine max/genetics/metabolism/microbiology
*Plant Roots/metabolism/microbiology/genetics
Genotype
*Microbiota
*Salt Stress
Plant Exudates/metabolism

@article {pmid42949970,
year = {2026},
author = {Pigani, E and Simoens, K and Bernardi, D and Campese, L and Iudicone, D and Azaele, S and Suweis, S},
title = {Scaling laws link conserved gene-abundance distributions to adaptive expression in diatom communities worldwide.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {44},
pages = {e2615743123},
doi = {10.1073/pnas.2615743123},
pmid = {42949970},
issn = {1091-6490},
support = {862923//AtlantECO/ ; 101059915//Biocean5D/ ; C53D23003420001//NRRP/ ; C93C22002810006//NRRP/ ; 101082021//MARCO-BOLO/ ; },
mesh = {*Diatoms/genetics ; Ecosystem ; Oceans and Seas ; Transcriptome ; Metagenomics ; },
abstract = {Marine microbes sustain Earth's major biogeochemical cycles, yet how they maintain stable ecosystem functions across diverse environments remains unclear. We analyzed metagenomic and metatranscriptomic data from diatom communities sampled during the Tara Oceans global expedition. While gene abundance distributions remain statistically similar across sample, gene expression varies systematically across geographical locations, a global pattern we show reflects predictable scaling laws. Global distributions, scaling relationships, and variability among sampling stations are captured by a stochastic model linking gene abundance dynamics to gene expression. While colder waters are associated with higher transcriptional activity and warmer regions show more selective gene usage, we find that transcript abundance increases nonlinearly with transcript richness. This general scaling is captured by our model and suggests that diatom communities balance high expression of core genes with specific functional diversity. These scaling relationships hold consistently across ocean basins, with temperature, used as an effective large-scale environmental descriptor whose signature cannot be fully disentangled from spatial structure, sufficing to predict transcriptional patterns from genetic composition. Our findings reveal how the stability of gene-abundance structure in diatom ecosystems coexists with transcriptional variability, enabling flexible functional responses.},
}

*Diatoms/genetics
Ecosystem
Oceans and Seas
Transcriptome
Metagenomics

@article {pmid42950786,
year = {2026},
author = {Li, MM and Liu, MC and Lv, AP and Ortúzar, M and OuYang, YT and Chen, LB and Chen, Y and Bian, BR and Yuan, Y and Gao, L and Liu, L and Jiao, JY and Li, WJ},
title = {Metagenome-assembled genomes reveal Labilithrix thermalis sp. nov., an uncultured microorganism in hot springs.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126780},
doi = {10.1016/j.syapm.2026.126780},
pmid = {42950786},
issn = {1618-0984},
abstract = {Geothermal environments harbor diverse microbial communities, including numerous phylogenetically novel lineages that remain largely unexplored. This study characterized two high quality metagenome assembled genomes (MAGs) from hot spring sediments in Yunnan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences and genome sequences indicated that the two MAGs (JZ-3_bin_45[TS] and QQ_bin_234) should be assigned to the genus Labilithrix. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two MAGs and other genomes of the genus Labilithrix were below the recommended species thresholds (95% and 70%, respectively), indicating that the two MAGs represent a novel species within the genus Labilithrix. Genome annotation suggested an aerobic, chemoheterotrophic, and motile lifestyle, with the genetic potential for oxidative phosphorylation, tricarboxylic acid (TCA) cycle, starch degradation, assimilatory sulfate reduction, arsenic detoxification, geothermal adaptation, and diverse biosynthetic gene clusters (BGCs). Based on genomic and phylogenetic analysis, these MAGs should be classified as a novel species within this genus, for which the name Labilithrix thermalis sp. nov. is proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This study expands the known diversity of the genus Labilithrix and highlights the value of metagenomics for uncovering previously uncultivated microbial taxa and function.},
}

@article {pmid42945300,
year = {2026},
author = {Andrade, B and Ramírez, M and Reyes, G},
title = {Microbial community structure of Penaeus vannamei post-larvae naturally infected with multiple viruses in hatchery tanks.},
journal = {PloS one},
volume = {21},
number = {10},
pages = {e0361576},
pmid = {42945300},
issn = {1932-6203},
mesh = {Animals ; *Penaeidae/virology/microbiology ; Larva/virology/microbiology ; Aquaculture ; *Microbiota ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This study offers an observational evaluation of how viral and bacterial infections co-occur with alterations in the microbiome and survival of Penaeus vannamei post-larvae, one of the most economically important species in global aquaculture.

METHODS: Eleven commercial larval production tanks were classified into three distinct infection scenarios using histology and PCR: Baculovirus penaei (BP) monoinfection, mixed infections (BP, white spot syndrome virus [WSSV], and acute hepatopancreatic necrosis disease [AHPND]-causing bacteria), and non-infected controls. High-molecular-weight DNA was subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform, followed by evaluation of microbial diversity, community structure, and infection-associated microbial signatures.

RESULTS: Although BP was the most abundant viral genus across infected groups, severe mortality was observed only under mixed-infection conditions, which were closely associated with AHPND-causing bacteria presence and microbiome disruption rather than with BP alone. Deep metagenomic sequencing revealed reduced, distinct microbiome structures in shrimp infected with BP and in those with mixed infections, compared to non-infected individuals. Non-infected post-larvae maintained complex and well-balanced bacterial communities, predominantly composed of Donghicola and Muricauda. Nudiviridae and Oscillospiraceae showed comparable relative abundances in BP-only and mixed-infection groups. In contrast, mixed infections were characterized by a relative increase in Vibrio, together with the PCR-detection of PirAB toxin genes, whereas WSSV remained detectable in the metagenomic dataset despite its comparatively low relative abundance, while the infection remained thermally suppressed and asymptomatic in the larvae. Functionally, infected larval microbiomes were enriched for transposases, retrotransposons, and virulence-factor genes. The near-complete BP-GR25 genome (119,245 bp) was assembled and annotated from larval metagenomes.

CONCLUSION: These results highlight the value of high-throughput sequencing in the early detection of pathogens in aquaculture, where subtle microbial shifts during postlarval stages can be valuable indicators of health status for production.},
}

Animals
*Penaeidae/virology/microbiology
Larva/virology/microbiology
Aquaculture
*Microbiota
Metagenomics
Metagenome

@article {pmid42945345,
year = {2026},
author = {Zang, C and Tang, L and Deek, RA},
title = {Supervised and covariate-adjusted dimension reduction for prediction and visualization using microbiome data.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
pmid = {42945345},
issn = {1477-4054},
support = {R56LM014522/LM/NLM NIH HHS/United States ; S10OD028483/OD/NIH HHS/United States ; //University of Pittsburgh's CTSI Trans-disciplinary Collaboration Pilot Award/ ; RRID:SCR_022735//University of Pittsburgh Center for Research Computing and Data/ ; },
mesh = {Humans ; Principal Component Analysis ; Algorithms ; *Microbiota ; Dimensionality Reduction ; *Gastrointestinal Microbiome ; *Computational Biology/methods ; Prediction Algorithms ; },
abstract = {Given that the gut microbiome has been shown to play a critical role in human health, discerning the relationship between microbial taxa and disease outcomes or phenotypes is of interest. Often, this involves association testing, predictive modeling, and visualizing trends in the data. Principal coordinates analysis (PCoA) is a commonly used dimension reduction technique in microbiome studies. PCoA relies on pairwise distances between samples and serves as a nonlinear alternative to the classic principal component analysis when non-Euclidean distances are used. Its low-dimensional embeddings provide intuitive visualizations but do not incorporate outcome-related information. Therefore, the low-dimensional principal coordinates may have poor performance in visualizing outcome differences, as well as in downstream disease prediction tasks. Additionally, covariates, such as demographics, lifestyle factors, and technical artifacts, can obscure true biological signals, leading to masked or spurious associations and limited generalizability. To address these limitations, we propose a supervised and covariate adjusted PCoA algorithm. By utilizing outcome information, while simultaneously minimizing the influence of nuisance variables, our method produces low-dimensional embeddings that better separate disease outcomes in visualizations and result in improved accuracy in downstream regression and classification tasks. We demonstrate the effectiveness of the proposed method and highlight its ability to extract important associations between the microbiome and disease outcomes while mitigating nuisance variation through simulations and application to real microbiome profiling studies.},
}

Humans
Principal Component Analysis
Algorithms
*Microbiota
Dimensionality Reduction
*Gastrointestinal Microbiome
*Computational Biology/methods
Prediction Algorithms

@article {pmid42946708,
year = {2026},
author = {Wang, Y and Kim, H and Malmuthuge, N and Zhou, M and Chen, Y and Alexander, TW and Timsit, E and Yao, J and Liang, G and Guan, LL},
title = {Early-life bovine respiratory virome analysis reveals phage-driven adaptation and cross-host evolutionary signatures.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42946708},
issn = {2041-1723},
mesh = {Animals ; Cattle ; *Virome/genetics ; *Bacteriophages/genetics/physiology ; Phylogeny ; Humans ; Genome, Viral ; *Respiratory System/virology ; Metagenomics ; Respiratory Tract Infections/virology/veterinary ; Evolution, Molecular ; },
abstract = {Past outbreaks of zoonotic viral infections highlight the importance of understanding respiratory virome ecology. As major food-producing animals with frequent human contact, cattle represent a critical host at the human-animal interface; however, the early-life establishment of their respiratory virome and its evolutionary connections to viruses from other hosts remain underexplored. Here, we longitudinally profile the upper respiratory tract (URT) virome of beef calves from birth to weaning using an optimized viral enrichment procedure and metagenomic workflow. Viral communities exhibited increased richness and turnover, reflecting ecological structuring during early life. Temperate phages dominate the URT phage community and share virulence- and mobility-associated genes with bacterial hosts, likely contributing to host adaptation and colonization persistence. Vertebrate-associated viruses emerge after the first week of life. Targeted reassembly from bovine URT viromes recovers near-complete betacoronavirus-like (CoV-D180) and adenovirus-like (AdV-D56) genomes positioned phylogenetically between bovine and human viral lineages. Competitive mapping of bovine-derived CoV-D180 and AdV-D56 to human respiratory metatranscriptomic datasets reveals genome-specific, regionally structured coverage patterns distinct from reference viruses, supporting shared sequence features in conserved genomic regions across host-associated viral lineages. Collectively, these findings reveal early-life assembly dynamics of the bovine respiratory virome and highlight cross-host signatures in a One Health framework.},
}

Animals
Cattle
*Virome/genetics
*Bacteriophages/genetics/physiology
Phylogeny
Humans
Genome, Viral
*Respiratory System/virology
Metagenomics
Respiratory Tract Infections/virology/veterinary
Evolution, Molecular

@article {pmid42399252,
year = {2026},
author = {Dai, D and Wang, P and Zhang, H and Qi, G and Wang, J},
title = {Temporal landscapes of the gut microbiota-host axis reveal mechanisms of age-related eggshell quality decline in laying hens.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42399252},
issn = {2055-5008},
support = {32402797//National Natural Science Foundation of China/ ; 32322078//National Natural Science Foundation of China/ ; CARS-40//China Agriculture Research System/ ; ASTIP//Agricultural Science and Technology Innovation Program/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Egg Shell/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Aging ; Metagenomics ; *Host Microbial Interactions ; *Bacteria/classification/genetics/isolation & purification ; Oviposition ; },
abstract = {Age-related shifts in the gut microbiota of laying hens significantly affect eggshell quality. However, the temporal interactions of the gut microbiota during the eggshell mineralization cycle remain unclear. Existing research often overlooks the rhythmic synchronization required for mineralization, as well as the specific cellular landscape of the aging intestine that impairs effective host-microbe crosstalk. We integrated 16S rRNA sequencing, metagenomics, untargeted metabolomics, and single-cell RNA sequencing to compare young and aged hens during the initial (7 h post-oviposition) and rapid growth (17 h post-oviposition) phases of eggshell mineralization. Aged hens exhibited significantly lower eggshell strength, thickness, and Ca/P concentrations (P < 0.05), which were associated with mitochondrial cristae disruption and necrocytosis in ileal tissues. 16S and metagenomic analyses revealed that young hens maintain stochastic microbial assembly, whereas aged hens shift toward deterministic processes driven by environmental stress. Rhythmic shifts in Lactobacillus and Ligilactobacillus were observed in young hens, supporting energy metabolism and mineral absorption pathways. In contrast, the aged hen microbiome remained focused on basal survival and oxidative stress responses. scRNA-seq identified nine cell populations, highlighting T cell exhaustion and HIF-1-driven metabolic reprogramming in epithelial cells of aged hens. Mediation analysis identified Ligilactobacillus salivarius as a keystone species that enhances eggshell breaking strength and thickness by increasing rhamnose and tyrosol levels and modulating host CALB1 and BLB2 expression. These findings indicate that aging disrupts proactive host-microbe synergy required for eggshell formation and identify L. salivarius-derived metabolites as promising candidates for restoring mineralization function in aged hens.},
}

Animals
*Chickens/microbiology
*Egg Shell/chemistry/microbiology
Female
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Aging
Metagenomics
*Host Microbial Interactions
*Bacteria/classification/genetics/isolation & purification
Oviposition

@article {pmid42399687,
year = {2026},
author = {Wang, X and Wang, H and Wang, X and Liao, H and Yang, J and Jin, H and Hoffnagle, E and Jeon, MK and Cui, Y and Li, X and Liu, X and Chen, X and Liao, L and Dong, Y and Jiang, L and Xiu, Z and Yang, Y},
title = {Fermentative iron reduction by a psychrotolerant Clostridium-dominant consortium enriched from Antarctic penguin-impacted soils.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42399687},
issn = {2399-3642},
mesh = {*Spheniscidae ; Antarctic Regions ; Animals ; *Soil Microbiology ; Oxidation-Reduction ; *Clostridium/metabolism/genetics ; *Iron/metabolism ; Fermentation ; *Microbial Consortia ; },
abstract = {Microbial iron cycling regulates nutrient availability and redox balance in global ecosystems, yet its pathways remain underexplored in ice-free Antarctic terrestrial ecosystems. This study reports the enrichment of a psychrotolerant microbial consortium from penguin-impacted soils on Beaufort Island, Antarctica, capable of reducing Fe(III) to Fe(II) at 4 °C via an anaerobic (likely fermentative) iron-reducing pathway. The consortium was dominated by Clostridium sensu stricto 13 and completely reduced 230 mg L[-1] Fe(III) citrate within three months and drove the biogenic formation of magnetite (Fe3O4). Metagenomic binning yielded four high-quality Clostridium genomes harboring multiple hydrogenases and cold-shock proteins (csp), revealing genomic strategies for energy conservation and psychrotolerance. Hydrogen production was strongly suppressed in the presence of Fe(III) citrate, indicating an intimate coupling of fermentation-derived electron flow to Fe(III) reduction. Our findings reveal a previously unrecognized low-temperature iron reduction mechanism and highlight the ecological significance of anaerobic (likely fermentative) iron reducers in ornithogenic soils-microhabitats enriched in organic matter and metals by penguin guano. This work expands the known diversity of Fe(III)-reducing microorganisms, demonstrates their role in magnetite biomineralization under extreme conditions, and provides insights into microbial modulation of iron speciation in Antarctic ornithogenic soils.},
}

*Spheniscidae
Antarctic Regions
Animals
*Soil Microbiology
Oxidation-Reduction
*Clostridium/metabolism/genetics
*Iron/metabolism
Fermentation
*Microbial Consortia

@article {pmid42401622,
year = {2026},
author = {Real, MVF and Vitousek, MN and Sheehan, MJ and Moeller, AH},
title = {The mouse gut microbiota responds to predator odor and predicts host behavior.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42401622},
issn = {2055-5008},
support = {R01 DK139214/DK/NIDDK NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; R35 GM138284//National Institutes of Health (NIH)/ ; },
mesh = {Animals ; *Odorants/analysis ; Mice ; *Gastrointestinal Microbiome ; *Behavior, Animal ; Metagenomics/methods ; Feces/microbiology ; Male ; *Bacteria/classification/genetics/isolation & purification ; Foxes ; Gene Expression Profiling ; Mice, Inbred C57BL ; Stress, Physiological ; },
abstract = {Chronic stressors can alter the mammalian gut microbiota in ways that mediate host stress responses, but the impacts of acute stressors on these interactions are less well understood. Here, we show that brief exposure of wild-derived mice to predator odor altered gut-microbiota composition, which in turn predicted host behavior. We investigated the individual and combined effects of 15-minute exposures to synthetic fox fecal odor and 30 days of chronic social isolation, an established chronic stressor. Using ethological assays, visceral adipose tissue transcriptomics, and genome-resolved metagenomics, we found that predator-odor exposure significantly affected mouse behavior, gene expression, and gut microbiota. Predator odor-responsive bacteria were associated with the expression of genes involved in anti-microbial defense, and host behavioral responses were predicted by random forest models trained on gut-microbiota profiles. These findings indicate interactions between the gut microbiota and wild-mouse responses to the threat of predation, an ecologically relevant acute stressor.},
}

Animals
*Odorants/analysis
Mice
*Gastrointestinal Microbiome
*Behavior, Animal
Metagenomics/methods
Feces/microbiology
Male
*Bacteria/classification/genetics/isolation & purification
Foxes
Gene Expression Profiling
Mice, Inbred C57BL
Stress, Physiological

@article {pmid42570745,
year = {2026},
author = {Xia, H and Xie, J and Wang, XY and Wang, Y},
title = {Detection, occurrence, development, diagnosis and treatment of vaginal microbiome in gynecological cancers.},
journal = {Critical reviews in oncology/hematology},
volume = {227},
number = {},
pages = {105531},
doi = {10.1016/j.critrevonc.2026.105531},
pmid = {42570745},
issn = {1879-0461},
mesh = {Humans ; Female ; *Genital Neoplasms, Female/diagnosis/therapy/microbiology/etiology ; *Microbiota ; *Vagina/microbiology ; },
abstract = {Gynecological cancers, including cervical, endometrial, and ovarian cancers, represent a growing global health burden with increasing incidence and mortality. The vaginal microbiome has emerged as a promising target for early cancer diagnosis and therapeutic intervention. Therefore, this review summarizes the composition and dynamics of the vaginal microbiome, emphasizing its association with the pathogenesis of gynecological cancers through chronic inflammation, immune modulation, and hormonal interactions. Advances in technologies such as 16S rRNA sequencing, metagenomics, and multi-omics have enabled the identification of potential microbial biomarkers. Probiotics, antibiotics, and vaginal microbiota transplantation are treatment technologies of gynecological cancers demonstrating considerable potential in restoring microbial balance and improving clinical outcomes. Furthermore, significant challenges persist in standardizing microbial biomarkers and translating research findings into precision therapies. Future studies should prioritize large-scale clinical validation and develop integrative strategies to harness the potential of the vaginal microbiome for cancer prevention and personalized treatment.},
}

Humans
Female
*Genital Neoplasms, Female/diagnosis/therapy/microbiology/etiology
*Microbiota
*Vagina/microbiology

@article {pmid42616025,
year = {2026},
author = {Sasaki, Y and Kozakai, T and Inoue, M and Sakanaka, M and Katoh, T and Kaneko, H and Imai, H and Odamaki, T and Fujita, K and Katayama, T},
title = {Adaptations of gummivorous primate gut-associated bifidobacteria to type-II arabinogalactan utilization.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42616025},
issn = {1751-7370},
support = {//Kyoto University EHUB Cooperative Research Program/ ; Y-2023-2-026//Grants-in-Aid from the Institute for Fermentation, Osaka/ ; 22KJ1778//JSPS Research Fellowship/ ; },
mesh = {Animals ; *Galactans/metabolism ; *Bifidobacterium/metabolism/genetics/enzymology/classification ; *Primates/microbiology ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract/microbiology ; Diet ; Phylogeny ; },
abstract = {Bifidobacteria inhabiting the primate gut exhibit host-dependent genetic diversification, particularly in their gene repertoire related to carbohydrate metabolism, suggesting adaptation to host diets. However, these diverse genetic traits remain poorly associated with specific dietary components. Here, through enzymatic and genetic analyses, we demonstrate that several Bifidobacterium species residing in the gut of gummivorous primates, such as marmosets, possess previously uncharacterized pathways for the efficient utilization of type-II arabinogalactan (AG), the major polysaccharide component of tree gums. The assimilation pathways comprises two key components: a bifunctional β-1,3-galactanase that cleaves the AG backbone via both endo- and exo-mode actions and/or an ATP-binding cassette transporter that internalizes the released arabinogalactan oligosaccharides (AGOs) into cells. Data mining of deposited metagenomic datasets suggested that the endo/exo-β-1,3-galactanase and the AGO transporter contribute to cross-feeding interactions within Bifidobacterium communities in the gut of gummivorous primates. Our study not only highlights molecular strategies employed by certain Bifidobacterium species to adapt to the dietary habits of a host but may also inform probiotic intervention strategies for the health and welfare of these primates in captive settings.},
}

Animals
*Galactans/metabolism
*Bifidobacterium/metabolism/genetics/enzymology/classification
*Primates/microbiology
*Gastrointestinal Microbiome
*Gastrointestinal Tract/microbiology
Diet
Phylogeny

@article {pmid42721830,
year = {2026},
author = {Męcik, M and Stefaniak, K and Harnisz, M and Czatzkowska, M and Felis, E and Bajkacz, S and Sawicki, J and Krawczyk, K and Paukszto, Ł and Korzeniewska, E},
title = {From regionalization to homogenization: Nationwide metagenomic assessment of priority pathogens and the resistome in Polish hospital wastewater.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143526},
doi = {10.1016/j.jhazmat.2026.143526},
pmid = {42721830},
issn = {1873-3336},
mesh = {Poland ; *Wastewater/microbiology ; Hospitals ; Metagenomics ; *Bacteria/genetics/isolation & purification ; Seasons ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Metagenome ; Microbiota ; },
abstract = {Hospital wastewater (HWW) is a critical hotspot for the dissemination of antibiotic resistance genes (ARGs) and pathogens. This study provides the first comprehensive metagenomic characterization of HWW across Poland, analyzing 64 medical facilities across two seasons via Nanopore long-read sequencing (total of 128 HWW samples). The HWW microbiome was mostly dominated by Proteobacteria, Bacteroidota, and Firmicutes. Multivariate analysis confirmed a significant seasonal shift in the resistome. Winter samples exhibited geographic regionalization, with localized hotspots of specific ARGs, including vancomycin resistance (operon van) and carbapenemase genes (blaOXA, blaNDM). Conversely, summer samples showed a significant trend toward nationwide homogenization, characterized by a uniform distribution of ESBL genes (blaTEM, blaCTX-M) and multidrug resistance (MDR) determinants, alongside the persistence of localized clinical hotspots. Klebsiella pneumoniae emerged as a central network hub, particularly in summer, showing strong correlations with ESBLs. Quantitative genomic co-occurrence analysis revealed a functional division within dominant taxa: while environmental species like Acinetobacter johnsonii comprised the general background microbiome, clinical pathogens such as Acinetobacter baumannii served as primary vectors, showing frequent associations with high-risk ARGs. Environmental and opportunistic bacteria, such as Aeromonas spp. and Citrobacter spp., were identified as putative 'bridge hosts' associated with mobile resistance determinants and potentially contributing to HGT. The findings indicate that seasonal factors, such as increased temperature and sub-inhibitory antibiotic concentrations, may contribute to the transition from regionalized to homogenized resistance profiles, demonstrating that background resistome convergence can coexist with point-source clinical outbreaks. This seasonal "blurring" of regional boundaries positions HWW as an active vector for large-scale antimicrobial resistance (AMR) dissemination. These results underscore the urgent need for nationwide metagenomic surveillance and advanced wastewater treatment strategies within the "One Health" framework to mitigate the environmental spread of WHO priority pathogens.},
}

Poland
*Wastewater/microbiology
Hospitals
Metagenomics
*Bacteria/genetics/isolation & purification
Seasons
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Metagenome
Microbiota

@article {pmid42735627,
year = {2026},
author = {Meng, N and Zhu, J and Yan, J and Zhao, Y and Liu, J and Li, G and Zhang, J and Wu, M and Zhou, H and Ma, Q},
title = {Unraveling anaerobic indole degradation in an acclimated sludge consortium: Candidate pathways and microbial division of labor inferred from metagenomic and metatranscriptomic analyses.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143606},
doi = {10.1016/j.jhazmat.2026.143606},
pmid = {42735627},
issn = {1873-3336},
mesh = {*Indoles/metabolism ; *Sewage/microbiology ; Metagenomics ; Anaerobiosis ; Biodegradation, Environmental ; Transcriptome ; Microbial Consortia ; Bacteria/metabolism/genetics ; Gene Expression Profiling ; },
abstract = {Indole is a widespread nitrogen-containing heterocyclic compound in manure, sludge, and wastewater systems, yet the enzymes and microbial populations involved in its anaerobic transformation remain poorly resolved. Here, we established a long-term acclimated anaerobic sludge consortium and combined degradation assays, metabolite profiling, metatranscriptomics, and genome-resolved metagenomics to investigate the functional basis of anaerobic indole degradation. After 120 days of acclimation, the consortium stably degraded 100 mg/L indole, whereas skatole was not effectively removed under the same strategy, indicating substrate-specific adaptation of the microbial community. Metabolite profiling detected oxindole, dioxindole, isatin, and anthranilic acid, supporting a putative transformation route involving pyrrole-ring oxidation and ring cleavage toward anthranilate-like intermediates. Metatranscriptomic analysis identified 16,660 differentially expressed genes after indole addition, with strong transcriptional responses involving oxidoreductases, hydrolases, cofactor-dependent redox metabolism, aromatic-CoA-related metabolism, and methane metabolism-associated pathways. Transcriptional responses highlighted the xanthine dehydrogenase-like molybdenum-enzyme system and isatin hydrolase as candidate contributors to upstream indole transformation, whereas those of abmG-like, bcrC, and oah genes were consistent with possible anthranilic acid activation and downstream CoA-type processing. MAG-resolved analysis further suggested that these candidate functions may be distributed among populations affiliated with Bacteroidota, Chloroflexota, Desulfobacterota, and Methanobacterium. Together, these findings establish a stable anaerobic indole-degrading consortium and provide a testable functional framework for syntrophic interactions linking upstream indole transformation, aromatic-CoA metabolism, and methanogenesis-associated carbon flow.},
}

*Indoles/metabolism
*Sewage/microbiology
Metagenomics
Anaerobiosis
Biodegradation, Environmental
Transcriptome
Microbial Consortia
Bacteria/metabolism/genetics
Gene Expression Profiling

@article {pmid42765606,
year = {2026},
author = {Zhang, J and Xu, S and Chen, C and Wang, Z and Du, W and Hong, L and Asiegbu, FO and Wang, K},
title = {Synthetic microbial community promotes seedling growth of Chinese fir via dissolving phosphorus and modifying rhizosphere microbial community.},
journal = {Tree physiology},
volume = {46},
number = {10},
pages = {},
pmid = {42765606},
issn = {1758-4469},
support = {32572041//General Program of National Natural Science Foundation of China/ ; },
mesh = {*Cunninghamia/growth & development/microbiology/metabolism ; *Rhizosphere ; *Phosphorus/metabolism ; *Seedlings/growth & development/microbiology ; *Soil Microbiology ; Bacteria/metabolism ; Plant Roots/microbiology/growth & development ; *Microbiota ; Phosphates/metabolism ; Soil/chemistry ; },
abstract = {Phosphorus (P) is an essential nutrient for plant growth, yet its availability in soil is severely constrained by fixation into insoluble forms that plants cannot directly utilize. Although phosphate-solubilizing microorganisms (PSM) represent a promising strategy to mobilize soil phosphorus, the functional potential of endophytic PSM and their synthetic consortia in promoting tree growth remains largely underexplored. In this study, endophytic bacteria were isolated from the roots of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.). Among them, 42 isolates were screened for phosphate-solubilizing activity on media containing calcium phosphate, iron phosphate, aluminum phosphate and organic phosphorus. Six strains with strong solubilizing capacity and no antagonistic interactions were selected to construct a synthetic microbial community (SynCom-P6), which was then applied to local soil and Chinese fir seedlings. Soil available phosphorus content initially decreased but subsequently increased from day 7 to day 21 after SynCom-P6 inoculation, indicating effective mobilization of insoluble phosphorus in soil. Inoculation with SynCom-P6 significantly enhanced root elongation and biomass accumulation, with both root fresh and dry weights showing marked increases compared with the control. Absolute quantification 16S amplicon and metagenomic sequencing revealed that SynCom-P6 reshaped the rhizosphere bacterial community, enriching beneficial genera such as Massilia and Dyadobacter, and altered functional profiles, including upregulation of hormone signaling and nitrogen fixation-related genes. These results demonstrated that the synthetic community not only improved soil phosphorus availability but also promoted root growth and modified the rhizosphere microbiome in a beneficial direction. Our findings highlight the potential of endophytic phosphate-solubilizing SynCom-P6 as a promising bio-inoculant for sustainable forestry, reducing the need for chemical P fertilizers while enhancing Chinese fir productivity. Future research should focus on field validation and mechanistic exploration of microbial interactions and functional gene expression.},
}

*Cunninghamia/growth & development/microbiology/metabolism
*Rhizosphere
*Phosphorus/metabolism
*Seedlings/growth & development/microbiology
*Soil Microbiology
Bacteria/metabolism
Plant Roots/microbiology/growth & development
*Microbiota
Phosphates/metabolism
Soil/chemistry

@article {pmid42847700,
year = {2026},
author = {Singh, VY and Gadekar, VP and Sasikumar, S and Lokshanan, RMR and Senthamizhan, V and Prithiviraj, B and Sinha, H and Raman, K},
title = {Microbial communities on station and train surfaces in Chennai Metro: insights into urban transit microbiome.},
journal = {mSphere},
volume = {11},
number = {10},
pages = {e0043326},
pmid = {42847700},
issn = {2379-5042},
mesh = {*Microbiota/genetics ; India ; *Bacteria/classification/genetics/isolation & purification ; Metagenomics ; *Railroads ; Humans ; Metagenome ; Cities ; *Environmental Microbiology ; Shotgun Sequencing ; Transportation ; },
abstract = {UNLABELLED: Urban public transport systems, particularly metro networks, serve as key hubs for microbial transmission, yet the urban microbiome in densely populated regions like India remains poorly characterized. Understanding these environments is crucial for public health, especially in light of the COVID-19 pandemic and growing concerns about antimicrobial resistance (AMR). This study is the first of its kind to investigate the microbial communities and the presence of AMR genes in the Chennai Metro system. We collected 96 surface swabs from 12 metro stations across two lines, focusing on surfaces that people frequently touch, such as handrails, kiosks, banisters, and ticket counters. Of the collected samples, 47 met quality control standards and were subjected to shotgun metagenomic sequencing, and 41 samples with more than 1 million reads were included in our analysis. Our findings indicate that surface type significantly influences microbial community structure, with kiosks exhibiting the highest microbial diversity. Comparative analysis with global urban data sets revealed unique microbial patterns specific to Chennai, including nine species that were notably more prevalent in our samples than in other urban transit systems worldwide. Furthermore, through pangenome analysis, we generated high-quality metagenome-assembled genomes that elucidated the adaptive strategies of dominant microbial species in this urban environment. Despite their relatively low abundance, several AMR families were widely distributed across the data set, with over 80% of samples containing at least one associated AMR gene, including families linked to rifamycins, multidrug resistance, and sulfonamides. This study lays a foundation for understanding the urban microbiome in India, emphasizing distinct regional characteristics and underscoring the need for sustained monitoring to mitigate disease transmission risks in high-density transit settings.

IMPORTANCE: Densely populated urban transit systems are critical hubs for microbial exchange, yet the mass transit microbiomes of Indian cities remain largely uncharacterized, representing a significant gap in global surveillance. Our study provides the first comprehensive metagenomic analysis of the Chennai Metro, a high-traffic transit network serving millions. Our findings highlight the unique environmental drivers shaping urban microbiota in India. Chennai, with over 12 million residents and a metro system serving over 105 million passengers annually, is an ideal yet uncharacterized environment for studying microbial dynamics, surface-microbe interactions, and environmental antimicrobial resistance reservoirs.},
}

*Microbiota/genetics
India
*Bacteria/classification/genetics/isolation & purification
Metagenomics
*Railroads
Humans
Metagenome
Cities
*Environmental Microbiology
Shotgun Sequencing
Transportation

@article {pmid42925342,
year = {2026},
author = {Hercouët, K and Tardy, F and Marois-Créhan, C},
title = {The Palatine Tonsil Bacterial Microbiota in Pigs: Diverse, Underexplored, Yet Functionally Relevant.},
journal = {Current microbiology},
volume = {83},
number = {12},
pages = {},
pmid = {42925342},
issn = {1432-0991},
mesh = {Animals ; *Palatine Tonsil/microbiology ; *Microbiota ; Swine/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Swine Diseases/microbiology ; Metagenomics ; },
abstract = {The palatine tonsils play a pivotal role in porcine upper respiratory tract immunity by acting as an interface between the host and the external environment. As such, the tonsillar microbiota represents a critical yet insufficiently characterized microbial ecosystem. This review provides an overview of current knowledge on the porcine tonsillar microbiota, beginning with a description of sampling strategies and laboratory approaches, including metabarcoding, shotgun metagenomics, and culturomics. The development of the tonsillar microbiota over time and the main environmental, host-related, and management factors shaping its composition are examined. Particular emphasis is placed on the core bacterial communities commonly identified in the palatine tonsils, which are largely dominated by members of the Pasteurellaceae, Streptococcaceae, and Moraxellaceae families. The review further discusses how infectious and non-infectious diseases can disrupt tonsillar microbial homeostasis, as well as the effects of antimicrobial treatments, vaccination, and other prophylactic interventions on microbial structure and function. Finally, methodological biases inherent to current studies are highlighted, key knowledge gaps are identified, and future research directions are proposed to advance metagenomic investigations and better elucidate the role of the tonsillar microbiota in swine health and disease.},
}

Animals
*Palatine Tonsil/microbiology
*Microbiota
Swine/microbiology
*Bacteria/classification/genetics/isolation & purification
Swine Diseases/microbiology
Metagenomics

@article {pmid42930741,
year = {2026},
author = {Wang, H and Che, Y and Liu, H and Yu, X and Liu, B and Shu, F and Zhou, J and Wu, M},
title = {Arbuscular Mycorrhizal Fungi Inoculation Promotes Growth and Alleviates Fusarium tricinctum-Induced Growth Inhibition in Quercus variabilis Seedlings.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {10},
pages = {},
pmid = {42930741},
issn = {2309-608X},
support = {No. 42430702//National Natural Science Foundation of China/ ; },
abstract = {Quercus variabilis is a key species for reforestation in East Asia, yet the mechanisms by which arbuscular mycorrhizal fungi (AMF) influence seedling growth and responses to soil-borne fungal challenge remain incompletely understood. This study combined physiological and metagenomic approaches to address this gap. Among seven rhizosphere fungal isolates, Fusarium tricinctum (F15) exerted the strongest growth-inhibitory effect on Q. variabilis seedlings and was therefore selected for subsequent experiments. Inoculation with the AMF Rhizophagus intraradices significantly promoted seedling growth (p < 0.05), increasing root length by 4.94% relative to the uninoculated control and increasing ground diameter and aboveground fresh weight by 28.57% and 117.07%, respectively, relative to F15-treated seedlings. AMF inoculation also significantly altered substrate nutrient status (p < 0.05), particularly nitrogen, phosphorus, and potassium, and enhanced the activity of antioxidant enzymes, including peroxidase and catalase (p < 0.05). Metagenomic analysis revealed that AMF significantly reshaped rhizosphere microbial community composition and bacterial α-diversity (p < 0.05), enriching beneficial taxa such as Mesorhizobium. Functional profiling showed differences in predicted microbial functional profiles between AMF-inoculated and F15-treated groups. Together, these results indicate that AMF enhances seedling growth and mitigates the negative effects associated with F15 challenge, potentially through altered substrate nutrient dynamics, enhanced antioxidant capacity, and modulation of the rhizosphere microbial community.},
}

@article {pmid42934169,
year = {2026},
author = {Chasapi, IN and Aplakidou, E and Chasapi, MN and Lamari, E and Galaras, A and Diplari, S and Iliopoulos, I and Emiris, IZ and Georgakopoulos-Soares, I and Patalano, S and Stravopodis, DJ and Karatzas, E and Baltoumas, FA and Kyrpides, NC and Pavlopoulos, GA},
title = {ArthroVerse: mapping protein family diversity across arthropod-associated microbiomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag1067},
pmid = {42934169},
issn = {1362-4962},
support = {23592-EMISSION//Hellenic Foundation for Research and Innovation/ ; 28787-VIROMINE//Hellenic Foundation for Research and Innovation/ ; //Penn State College of Medicine and the University of Texas at Austin/ ; //US Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//US Department of Energy Office of Science user facilities/ ; 7832-YGIAMEL//Postdoctoral Researcher/ ; //HEAL-Link/ ; },
abstract = {Metagenomic studies of arthropod-associated microbiomes have generated vast amounts of sequence data, yet the functional and structural organization of these proteins remains largely unexplored. Here, we present ArthroVerse, the first comprehensive database of protein families derived from arthropod-associated metagenomes. Non-redundant protein families were generated after rigorous filtering, deduplication, and clustering. The protein families were further annotated with microbial taxonomy, host associations, protein structural information, and carbohydrate-active enzymes predictions. The resulting dataset integrates both metagenomic and reference genome-derived proteins, enabling systematic exploration of functional diversity, evolutionary relationships, and host-microbe interactions in insect microbiomes. ArthroVerse provides a valuable resource for the study of microbial ecology and arthropod physiology, offering unprecedented insight into the protein landscape of insect-associated microbial communities. ArthroVerse is publicly accessible at https://envofams.org/arthroverse/.},
}

@article {pmid42934259,
year = {2026},
author = {Serra Moncadas, L and Ruscheweyh, HJ and Woodhouse, J and Salcher, MM and Okazaki, Y and Ngugi, DK and Pester, M and Posch, T and Ghai, R and Grossart, HP and Sunagawa, S and Pernthaler, J and Andrei, AS},
title = {A global mitochondrial genomic atlas illuminates freshwater microeukaryote diversity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42934259},
issn = {2041-1723},
support = {PZ00P3_193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; PZ00P3_193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_182489//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; GR1540/51_1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GR1540/51_1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 20-12496X//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 20-12496X//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; },
mesh = {Phylogeny ; *Genome, Mitochondrial/genetics ; *Fresh Water/microbiology ; *Biodiversity ; *Eukaryota/genetics/classification ; Metagenome ; },
abstract = {Environmental genomics has transformed our view of the microbial world, yet progress remains largely prokaryote-centric. Among microbial eukaryotes, inconsistent marker choice and limited species-level resolution blunt diversity estimates and hinder cross-study synthesis. Consequently, regional‑to‑global gradients in richness, turnover, and phylogenetic structure remain poorly resolved. Here we establish a global mitogenome-based framework that converts shotgun metagenomes into species‑resolved, phylogeny‑anchored inventories. From 3,400 metagenomes spanning 362 lakes on seven continents, we reconstruct ~20,000 mitochondrial metagenome-assembled genomes (mitoMAGs), densely populating previously sparse branches of the eukaryotic tree-notably SAR (Stramenopiles-Alveolata-Rhizaria), Cryptophyceae, and Haptista. An empirically calibrated 98.1% mitoMAG‑identity threshold delineates species and tethers community profiles to an evolutionary backbone. On this backbone, coverage‑standardized inventories recover canonical ecological patterns: mesotrophic richness peaks, surface-layer expansion of phylogenetic breadth, and spring maxima with the strongest surface-deep coupling at vernal mixing; supporting the framework. Treating mitoMAGs as primer‑free barcodes yields a single, species‑level, phylogeny‑aware currency that renders richness, evenness, and phylogenetic breadth directly comparable across datasets, depths, seasons, and regions. By placing microbial eukaryotes on an analytical footing comparable to prokaryotes, the resulting atlas brings their diversity into reach and lays the groundwork for future high-throughput, species-aware monitoring and ecological forecasting.},
}

Phylogeny
*Genome, Mitochondrial/genetics
*Fresh Water/microbiology
*Biodiversity
*Eukaryota/genetics/classification
Metagenome

@article {pmid42934712,
year = {2026},
author = {Gu, C and Zhang, R and Rao, YZ and Zhang, X and Zhou, Z and Liu, Y and Dong, X and Wang, L and Wang, Y and Hua, ZS and Krupovic, M and Li, M},
title = {Expansion of the Asgard archaeal virome and defensome provides insights into virus-host interactions.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42934712},
issn = {2049-2618},
mesh = {*Archaeal Viruses/genetics/classification/physiology/isolation & purification ; *Archaea/virology/genetics/classification ; *Virome/genetics ; Metagenomics/methods ; Genome, Viral ; Phylogeny ; *Host Microbial Interactions ; Host-Pathogen Interactions ; },
abstract = {BACKGROUND: Asgard archaea, broadly considered as a group of archaea that exhibit the closest evolutionary relationship with eukaryotes, encode diverse defense systems and are infected by distinct viruses. However, the diversity of Asgard archaeal viruses and their interactions with the hosts remain poorly explored.

RESULTS: Here, using CRISPR spacer-protospacer matching, we predict 23 viruses associated with Asgard archaea from various habitats. Apart from clusters with known viruses, we report three previously undescribed groups of Asgard viruses with predicted head-tailed virions of the realm Duplodnaviria and filamentous virions characteristic of the archaea-specific realm Adnaviria. Mapping of metagenomic reads to viral and host genomes suggested that most Asgard viruses display relatively low virus-to-host ratios, typically below 10. In addition, we considerably expanded the known defensome of Asgard archaea, among others, detecting putative PARIS and Prometheus defense systems. Finally, the diversity of anti-defense proteins and putative archaeal type IV pilins encoded by some Asgard viruses provide additional insights into the interactions between Asgard archaea and their viruses.

CONCLUSIONS: Overall, this work sheds new light on the Asgard archaeal virome and defensome, and virus-host interactions. Video Abstract.},
}

*Archaeal Viruses/genetics/classification/physiology/isolation & purification
*Archaea/virology/genetics/classification
*Virome/genetics
Metagenomics/methods
Genome, Viral
Phylogeny
*Host Microbial Interactions
Host-Pathogen Interactions

@article {pmid42934726,
year = {2026},
author = {Auguste, M and Bosi, E and Saad, J and Oliveri, C and Doni, L and Marchese, A and Travers, MA and Toulza, E and Boulo, V and Courtay, G and Petton, B and Koechlin, H and Montagnani, C and Di Cesare, A and Corno, G and Andree, KB and Gairin, I and Furones, D and Broquard, C and Wegner, KM and Destoumieux-Garzón, D and Vezzulli, L},
title = {The resistome of European coastal environments revealed by high-resolution targeted metagenomics in oysters.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42934726},
issn = {2049-2618},
mesh = {Animals ; *Metagenomics/methods ; Europe ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Ostreidae/microbiology ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Microbiota ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Antimicrobial resistance is a major global health threat, and the environment is increasingly recognised as a key reservoir of antibiotic resistance genes (ARGs). In marine ecosystems, filter-feeding organisms such as oysters are sentinel species that reflect the microbiological diversity of their environment. Here, we investigated the ARG content of the Pacific oyster Magallana gigas across four European coastal sites, contrasting anthropogenically impacted aquaculture sites (Bay of Brest, Ebro Delta, Thau lagoon) with natural oyster reefs (Sylt island). ARGs sequencing was enriched using a targeted probe-and-capture metagenomic approach employing 37,826 RNA baits covering over 2000 ARG sequences. Moreover, a novel bioinformatic pipeline ARGifier was specifically designed for sensitive, high-resolution detection and classification of ARGs in metagenomic samples dominated by host DNA.

RESULTS: This strategy was able to overcome limitations of cultivation-based methods and whole metagenomic sequencing, enabling the detection of more than 33,000 ARG sequences in the oyster resistome spanning over 450 genes distributed over 23 resistance classes. Reads assigned to ARGs represented 0.23% of all raw reads and 25.02% of host-depleted reads. Accordingly, comparison of targeted metagenomics and pool-seq analysis of cultured isolates (culturomics) in specific pathogen-free oysters revealed that metagenomics captured dominant, community-wide resistance determinants, whereas culturomics recovered a broader diversity of ARGs due to their presence in genomes of cultivable strains. The oyster resistome across the four farming sites was dominated by multidrug efflux systems associated with intrinsic and housekeeping-related mechanisms, suggesting an environmentally shaped resistance profile. Clinically relevant ARGs, including extended-spectrum Beta-Lactamase, carbapenem, colistin, and vancomycin resistance genes, were detected in low abundance at all sites, with higher enrichment in anthropogenically impacted areas. In addition, several ARGs were associated with plasmids, indicating mobilization potential. Taxonomic analysis revealed that a limited subset of bacteria, particularly Betaproteobacteria and Actinomycetes, carried a disproportionately high number of ARGs despite their low relative abundance in the oyster microbiome.

CONCLUSIONS: Overall, this study delivers a comprehensive inventory of ecologically and clinically relevant ARGs in European coastal environments, positioning farmed and wild oysters as sentinel organisms for monitoring antimicrobial resistance in coastal waters. Our findings highlight the circulation of ARGs within coastal marine ecosystems, which may act as reservoirs and potential sources of mobilisable antimicrobial resistance. Video Abstract.},
}

Animals
*Metagenomics/methods
Europe
*Bacteria/genetics/classification/drug effects/isolation & purification
*Ostreidae/microbiology
Metagenome
Anti-Bacterial Agents/pharmacology
Microbiota
Sequence Analysis, DNA

@article {pmid42934727,
year = {2026},
author = {Liu, Y and Wu, X and Guo, Y and Mei, W and Gao, R and Wang, F and Chen, C and Wang, L and Hao, Y and Wu, T and Yao, X},
title = {Multi-omics analysis reveals that sleep deprivation exacerbates intestinal barrier injury via the microbiota-dependent taurodeoxycholic acid/group 3 innate lymphoid/IL-22 axis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42934727},
issn = {1479-5876},
support = {82403215//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Sleep Deprivation/microbiology/immunology/pathology ; Interleukin-22 ; *Interleukins/metabolism ; *Multiomics ; *Intestinal Barrier Function ; *Lymphocytes/metabolism ; *Immunity, Innate ; Mice, Inbred C57BL ; Male ; *Intestines/pathology ; Fecal Microbiota Transplantation ; Mice ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {BACKGROUND: Clinical studies demonstrated a correlation between sleep dysfunction and intestinal diseases. However, the detailed interactions and underlying mechanisms linking sleep disruption to intestinal microenvironment remain poorly understood.

METHODS: We employed the Curling Prevention by Water (CPW) paradigm to establish a mouse model of sleep deprivation (SD) for durations ranging from 0 to 96 h. The dynamic changes in the intestinal microenvironment were systematically profiled using multi-omics approaches, including metagenomic sequencing, untargeted metabolomics and RNA sequencing. The causal role of microbial dysbiosis and the underlying mechanisms were further investigated using germ-free mice, fecal microbiota transplantation (FMT), flow cytometry, and targeted intervention.

RESULTS: The intestinal microenvironment was highly sensitive to SD. Distinct microbial communities and metabolite profiles were observed among brief SD (< 24 h of SD), prolonged SD (24-96 h of SD) and control. Brief SD triggered a self-regulatory response of the gut microbiota, characterized by an increase in certain beneficial bacteria (e.g., Parabacteroides goldsteinii). In contrast, prolonged SD shaped a pro-inflammatory microbial structure, characterized by reduced Akkermansia muciniphila and enriched Pseudomonadota. Multi-omics analysis revealed that SD significantly inhibited microbial bile acid metabolism, particularly taurodeoxycholic acid (TDCA), and impaired intestinal barrier function while suppressing the intestinal immune response to bacteria antigens. Mechanistically, SD exacerbated intestinal barrier damage by inhibiting the TDCA/group 3 innate lymphoid cells (ILC3)/IL-22 axis. Supplementation with TDCA effectively restored ILC3 function, IL-22 production, and barrier integrity in SD mice. Furthermore, FMT from patients with sleep dysfunction significantly disturbed intestinal microenvironment and increased serum cortisol by regulating gut microbiota and inhibiting TDCA/ILC3/IL-22 axis.

CONCLUSION: This study dynamically delineates how SD disrupts intestinal homeostasis by reshaping the gut microbiota and suppressing the TDCA/ILC3/IL-22 axis. These findings provide novel mechanistic insights and identify potential therapeutic targets for sleep dysfunction-associated intestinal complications.},
}

Animals
*Sleep Deprivation/microbiology/immunology/pathology
Interleukin-22
*Interleukins/metabolism
*Multiomics
*Intestinal Barrier Function
*Lymphocytes/metabolism
*Immunity, Innate
Mice, Inbred C57BL
Male
*Intestines/pathology
Fecal Microbiota Transplantation
Mice
*Gastrointestinal Microbiome
*Microbiota

@article {pmid42937679,
year = {2026},
author = {Ran, J and Qiu, G and Jin, J and Zhang, P and Hu, H and Liu, Y and Liu, X and Li, C and Xi, Y},
title = {Clinicopathologic Features of Stress-Associated Sudden Death in Three Captive Crested Ibis (Nipponia nippon).},
journal = {Avian diseases},
volume = {70},
number = {3},
pages = {349-358},
doi = {10.1637/aviandiseases-D-26-00005},
pmid = {42937679},
issn = {1938-4351},
mesh = {Animals ; *Death, Sudden/veterinary/etiology ; *Stress, Physiological ; *Birds ; *Bird Diseases/pathology/etiology ; Female ; Male ; Endangered Species ; Animals, Zoo ; Corticosterone/analysis ; },
abstract = {The endangered crested ibis (Nipponia nippon), once reduced to just seven individuals in the wild worldwide in 1981, has rebounded to more than 10,000 through intensive conservation. Yet the species remains highly vulnerable to acute environmental disturbance, with stress-induced sudden death (SISD) posing persistent challenges for captive management and reintroduction programs. We investigated three SISD cases, integrating behavioral context with necropsy and histopathology in all cases, and computed tomography/magnetic resonance imaging neuroimaging and metagenomic pathogen screening in a subset. Major organs showed no diagnostic lesions, with only mild, nonspecific digestive tract changes. Neuroimaging identified localized subdural hemorrhage without diffuse parenchymal damage. Metagenomic screening detected no high-pathogenicity avian viruses, fungi, or parasites and only trace environmental bacteria. Using published datasets, we also compared baseline corticosterone (CORT) from feathers and blood across five avian species; crested ibis occupied the lower end of baseline CORT distributions, consistent with reduced endocrine buffering capacity. These observations suggest that peracute death may occur in association with acute disturbance even in the absence of overt infectious or major degenerative lesions, with panic flight and collision trauma likely contributing to the terminal events. Framing SISD as a failure of physiological tolerance thresholds highlights actionable management: minimizing startle stimuli, reducing predator cues and human disturbance during sensitive periods, carefully staging transfers to new enclosures, managing group dynamics to limit social transmission of stress, designing for safe flight, and early-warning monitoring. Taken as case-based evidence, this work may help refine captive husbandry and reintroduction protocols aimed at improving survival and long-term population resilience.},
}

Animals
*Death, Sudden/veterinary/etiology
*Stress, Physiological
*Birds
*Bird Diseases/pathology/etiology
Female
Male
Endangered Species
Animals, Zoo
Corticosterone/analysis

@article {pmid42937876,
year = {2026},
author = {Hioki, Y and Klapper, M and Ibrahim, A and Hübner, A and Steinacker, M and Willing, K and Nachawati, R and Hildebrandt, D and Reimer, L and Zimmermann, A and Mantke, J and Sato, M and Warinner, C and Stallforth, P},
title = {Reconstruction of a 30,000-Year-Old Biosynthetic Gene Cluster Reveals Lasso Peptides Formed by a Highly Tolerant Cyclase.},
journal = {Journal of the American Chemical Society},
volume = {148},
number = {38},
pages = {40629-40635},
pmid = {42937876},
issn = {1520-5126},
support = {NA//Werner Siemens-Stiftung/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; JP24KJ1884//Japan Society for the Promotion of Science/ ; NA//Astellas Foundation for Research on Metabolic Disorders/ ; },
mesh = {*Multigene Family ; *Peptides/chemistry/genetics/metabolism ; Humans ; *Actinomyces/genetics/enzymology ; Amino Acid Sequence ; Phylogeny ; },
abstract = {Microbial metagenomes preserved in prehistoric dental calculus samples provide access to past bacterial biodiversity and evolutionary dynamics across archeological time scales. Consequently, this sequence space represents a largely unexplored resource for natural product discovery. Phylogeny-guided genome mining of human dental calculus metagenomes spanning recent times to the Middle and Upper Paleolithic revealed a distinct lasso cyclase lineage associated with oral Actinomyces species. Heterologous expression of a biosynthetic gene cluster reconstructed from an approximately 30,000-year-old sample yielded two lasso peptides, palassoptides A1 and A2. Structure analyses established a canonical class II lasso topology with an eight-residue macrolactam ring. Notably, both palassoptides feature an unprecedented amino acid composition for lasso peptides. Mutational analysis of the PalA2 precursor further showed that PalC accepts all possible substitutions at core position 1 except for Pro, revealing the broadest respective tolerance reported for a lasso cyclase to date. Homologous gene clusters with highly conserved yet variable precursor sequences are widespread among modern oral Actinomyces, indicating long-term preservation of this biosynthetic lineage within the human oral microbiome. The two palassoptides exhibited combination-dependent antibacterial activity against selected Gram-positive bacteria. These findings demonstrate that ancient metagenomes can reveal chemically uncharacterized natural products and expand the known structural diversity of natural products.},
}

*Multigene Family
*Peptides/chemistry/genetics/metabolism
Humans
*Actinomyces/genetics/enzymology
Amino Acid Sequence
Phylogeny

@article {pmid42939670,
year = {2026},
author = {Dawson, ZD and Martin, T and Ji, E and Lee, KE and Chen, X and Zhou, X and St Jean, S and Li, Y and Ma, J},
title = {PAD2 Deficiency Reveals Sex-Divergent Colonic Homeostasis, β-Catenin Remodeling, and Antibiotic-Sensitive Phenotypes.},
journal = {Biomolecules},
volume = {16},
number = {10},
pages = {},
pmid = {42939670},
issn = {2218-273X},
support = {R01AG071676/AG/NIA NIH HHS/United States ; R01AG072430/AG/NIA NIH HHS/United States ; R01EY036243/EY/NEI NIH HHS/United States ; R01HL157215//National Heart Lung and Blood Institute/ ; },
mesh = {Animals ; *beta Catenin/metabolism ; Female ; Male ; Mice ; Colitis/chemically induced/metabolism/genetics/pathology ; *Anti-Bacterial Agents/pharmacology ; Humans ; Homeostasis/drug effects ; *Protein-Arginine Deiminase Type 2/deficiency/genetics/metabolism ; Mice, Knockout ; *Colon/metabolism/pathology/drug effects ; Phenotype ; Intestinal Mucosa/metabolism ; Dextran Sulfate ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Peptidylarginine deiminase 2 (PAD2) catalyzes protein citrullination and is implicated in inflammatory bowel disease and colorectal cancer. However, its role in regulating the intestinal epithelium and the influence of biological sex and the microbiome remain poorly defined. This study investigated the relationships among PAD2 deficiency, sex-divergent epithelial states, β-catenin regulation, and the intestinal microbiome. Global PAD2 knockout and wild-type littermate mice of both sexes were characterized under basal conditions and following dextran sodium sulfate-induced colitis. Intestinal epithelial phenotypes were assessed by histology, immunofluorescence, immunoblotting, quantitative RT-PCR, and immunoprecipitation. Gut microbial communities were evaluated by shotgun metagenomics, while broad-spectrum antibiotic treatment, fecal protein immunoblotting, and recombinant human PAD2 exposure in vitro were used to examine relationships among antibiotic-sensitive factors, β-catenin regulation, and epithelial phenotypes. PAD2 deficiency was associated with distinct epithelial states in male and female colons before injury. Male KO mice displayed increased β-catenin phosphorylation and increased susceptibility to DSS colitis, whereas female KO mice demonstrated increased total β-catenin abundance and preservation of structural epithelial features following injury. Female KO microbiota exhibited genotype-associated differences in microbial community composition by exploratory Bray-Curtis PERMANOVA. Broad-spectrum antibiotic treatment altered the female epithelial phenotype, reduced active β-catenin, and progressively depleted luminal PAD2-immunoreactive proteins. Exogenous recombinant human PAD2 increased epithelial protein citrullination and altered active β-catenin abundance in HT29 cells. Collectively, these findings demonstrate both sex-specific and sex-divergent colonic phenotypes while supporting a framework connecting PAD2 biology, epithelial architecture, and the microbial environment during intestinal maintenance and injury.},
}

Animals
*beta Catenin/metabolism
Female
Male
Mice
Colitis/chemically induced/metabolism/genetics/pathology
*Anti-Bacterial Agents/pharmacology
Humans
Homeostasis/drug effects
*Protein-Arginine Deiminase Type 2/deficiency/genetics/metabolism
Mice, Knockout
*Colon/metabolism/pathology/drug effects
Phenotype
Intestinal Mucosa/metabolism
Dextran Sulfate
Gastrointestinal Microbiome/drug effects

@article {pmid42939710,
year = {2026},
author = {Ascari, F and Baldelli, L and Scicchitano, D and Pellegrini, C and Ravaioli, F and De Fanti, S and Esposito, E and Porru, E and Di Laudo, F and Lodi, R and Bacalini, MG and Candela, M and Provini, F and Fiori, J and Interino, N},
title = {Exploratory Metabolomic and Metagenomic Profiling of Fecal Samples in Isolated REM Sleep Behavior Disorder.},
journal = {Biomolecules},
volume = {16},
number = {10},
pages = {},
pmid = {42939710},
issn = {2218-273X},
support = {//Ministero della Salute/ ; 2024.0058//Fondazione Del monte di Bologna e di Ravenna/ ; },
mesh = {Humans ; *REM Sleep Behavior Disorder/metabolism/microbiology/genetics ; *Feces/chemistry/microbiology ; *Metabolomics/methods ; Female ; Male ; Cross-Sectional Studies ; *Metabolome ; Middle Aged ; *Metagenomics/methods ; Multiomics ; Gastrointestinal Microbiome ; Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Isolated REM sleep behavior disorder (iRBD) is among the most reliable prodromal markers of α-synucleinopathies. Under the body-first (gut-first) model of α-synuclein pathology, in which pathology may originate in the enteric nervous system and ascend to the brain, the gut is a biologically plausible compartment in which early and accessible molecular alterations might be detectable; however, the fecal metabolome remains poorly investigated in this population. In this exploratory, cross-sectional study of 21 iRBD patients and 15 healthy controls, we characterized fecal samples through an integrated multi-omics framework. The fecal metabolome was profiled on two complementary mass spectrometry platforms: HS-SPME GC-EI-high-resolution MS, used for both untargeted volatilomics and targeted quantification of linear and branched short-chain fatty acids, and untargeted LC-MS/MS for the non-volatile fraction. Gut microbial community composition was characterized on the same material by 16S rRNA gene sequencing, and the metabolomic and microbial layers were combined by DIABLO multi-omics integration. Linear short-chain fatty acids were preserved, whereas branched-chain fatty acids were selectively increased in iRBD, indicating a shift toward proteolytic fermentation. Volatile indole was reduced, while p-cresol and 2-octanone were increased, paralleled at the LC-MS/MS level by attenuation of the tryptophan-indole axis, class-level bile acid depletion, and increased acylcarnitines. The microbiome was depleted of Blautia and Faecalibacterium and enriched in Oscillospirales. Integration resolved a coherent host-microbe signature that discriminated iRBD patients from controls within this discovery cohort (84.8% cross-validated accuracy). These cross-sectional findings characterize candidate fecal signatures associated with iRBD; given the exploratory design and the limited sample size, they are hypothesis-generating, and their value for predicting phenoconversion remains to be established in prospective studies.},
}

Humans
*REM Sleep Behavior Disorder/metabolism/microbiology/genetics
*Feces/chemistry/microbiology
*Metabolomics/methods
Female
Male
Cross-Sectional Studies
*Metabolome
Middle Aged
*Metagenomics/methods
Multiomics
Gastrointestinal Microbiome
Aged
RNA, Ribosomal, 16S/genetics

@article {pmid42940926,
year = {2026},
author = {Kuprin, A and Baklanova, V and Rechits, A},
title = {First Shotgun Metagenomic Characterization of the Gut Microbiome of the Endangered Longhorn Beetle Callipogon relictus (Coleoptera: Cerambycidae).},
journal = {Insects},
volume = {17},
number = {10},
pages = {},
pmid = {42940926},
issn = {2075-4450},
abstract = {The gut microbiome of Callipogon relictus, a rare member of the family Cerambycidae, was characterized for the first time using shotgun metagenomic sequencing. The aim of this study was to compare the taxonomic diversity and structure of the gut microbial communities in larvae and adults. Bacteria dominated the metagenomic profiles, accounting for 92.47% of the taxonomic composition in adults and 85.31% in larvae. Proteobacteria predominated in the bacterial component of both pooled profiles, accounting for 87.88% and 89.43%, respectively. The pooled adult profile had the highest relative abundances of Gammaproteobacteria and Enterobacterales, whereas the pooled larval profile had higher relative abundances of Alphaproteobacteria and Rickettsiales. In the pooled samples analyzed, 155 bacterial and 69 fungal genera were detected in the larval profile, compared with 85 and 17 genera, respectively, in the adult profile; the fungal component accounted for 10.46% of the larval profile and 0.18% of the adult profile. The two profiles shared 77 bacterial, 17 fungal, and 15 protist genera. The virus-like/retroelement sequence fraction was dominated by sequences related to Errantivirus, a member of the family Metaviridae. Because Metaviridae comprise LTR retrotransposons, this signal was interpreted as endogenous retroelement DNA rather than evidence of a free-virus gut virome. These results provide a preliminary description of a shared bacterial core accompanied by differences between the pooled profiles in lower-rank bacterial composition and in the structure of the fungal and protist components of the C. relictus microbiome.},
}

@article {pmid42941936,
year = {2026},
author = {Vacaras, C and Vacaras, V and Nistor, C and Vesa, SC and Jucan, C and Furdui, IM and Strilciuc, S and Stefanescu, E and Chira, D and Rafila, A and Muresanu, DF},
title = {Limited Gut Microbiome Differences Between Relapsing-Remitting and Secondary Progressive Multiple Sclerosis: A Shotgun Metagenomic Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {20},
pages = {},
pmid = {42941936},
issn = {1422-0067},
support = {//Foundation for the Study of Nanoneurosciences and Neuroregeneration and by the Romanian Society of Microbiology./ ; },
mesh = {Humans ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; *Multiple Sclerosis, Chronic Progressive/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Adult ; Biomarkers/blood ; Cross-Sectional Studies ; Shotgun Sequencing ; },
abstract = {The gut microbiome may contribute to multiple sclerosis (MS) pathophysiology, but its relationship with disease phenotype and progression remains unclear. To characterize taxonomic and functional gut microbiome differences between relapsing-remitting MS (RRMS) and secondary progressive MS (SPMS) and their associations with neurological disability and circulating biomarkers. This cross-sectional study included 89 participants (30 healthy controls, 29 RRMS, and 30 SPMS). Shotgun metagenomic sequencing was used to assess microbial diversity, taxonomic profiles, and predefined short-chain fatty acid (SCFA)-related pathways, integrated with disability measures and serum GFAP, NfL, and S100B. SPMS participants were substantially older than those with RRMS (median 49.0 vs. 31.0 years), prompting age-adjusted analyses and an age-overlap sensitivity analysis. Alpha diversity and overall microbial community composition were similar across groups. SPMS showed greater interindividual microbial community dispersion than RRMS in the full cohort, with a similar direction and magnitude but attenuated statistical significance in the age-overlap sensitivity analysis. Exploratory taxonomic signals were not confirmed by FDR-controlled analyses. No robust phenotype-specific differences in predicted SCFA-related pathways or associations of taxonomic or functional features with disability or circulating biomarkers were identified. Greater microbial community dispersion in SPMS was observed in the full cohort, but this finding was attenuated in the age-overlap sensitivity analysis and should be considered preliminary. Overall, these findings do not support a distinct SPMS-associated gut microbiome signature, although potential phenotype-related differences cannot be excluded.},
}

Humans
*Multiple Sclerosis, Relapsing-Remitting/microbiology
*Multiple Sclerosis, Chronic Progressive/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Female
Male
Middle Aged
Adult
Biomarkers/blood
Cross-Sectional Studies
Shotgun Sequencing

@article {pmid42942900,
year = {2026},
author = {Pătru, O and Luca, S and Păunescu, A and Enache, B and Văcărescu, C and Cozma, D and Crișan, S and Bena, A},
title = {The Gut Microbiome-Estrogen Axis in Menopause: Implications for Body Composition, Cardiometabolic Health and Nutrition.},
journal = {Nutrients},
volume = {18},
number = {20},
pages = {},
pmid = {42942900},
issn = {2072-6643},
mesh = {Humans ; *Menopause/physiology/metabolism ; Female ; *Estrogens/metabolism ; *Gastrointestinal Microbiome/physiology ; *Body Composition/physiology ; *Nutritional Status ; Aging ; Cardiometabolic Risk Factors ; },
abstract = {Background/Objectives: Menopause is associated with profound endocrine, metabolic, immune, and microbial changes that may contribute to accelerated biological aging and increased cardiometabolic risk. The gut microbiome represents a potential interface between estrogen biology, host metabolism, inflammation, and systemic organ function. This narrative review examines the role of menopause-associated gut microbiome remodeling in microbiome-mediated metabolic aging, focusing on the estrobolome, microbial metabolites, organ crosstalk, and microbiome-targeted interventions. Methods: Relevant literature was identified through searches of PubMed/MEDLINE, Scopus, and Web of Science, supplemented by reference-list screening. Human observational and clinical studies, mechanistic investigations, systematic reviews, meta-analyses, and relevant guidelines were critically evaluated and synthesized narratively. No formal meta-analysis was performed. Results: Menopause-associated changes in gut microbial composition and function may influence estrogen metabolism through the estrobolome and modify the production of short-chain fatty acids, lipopolysaccharides, trimethylamine N-oxide, and bile acid metabolites. These pathways may contribute to chronic low-grade inflammation, insulin resistance, endothelial dysfunction, dyslipidemia, hepatic metabolic dysfunction, adipose tissue inflammation, adverse changes in body composition, sarcopenia, neuroinflammation, and urogenital microbial instability. Dietary patterns, fermentable fiber, physical activity, probiotics, synbiotics, phytoestrogens, and menopausal hormone therapy may influence components of this network, although the strength of evidence remains variable. Current data do not support the use of microbiome characteristics to select or dose hormone therapy. Conclusions: The gut microbiome may act as a dynamic mediator linking estrogen decline with metabolic and systemic aging after menopause. However, causality, individual variability, and clinical translation remain insufficiently established. Longitudinal studies integrating shotgun metagenomics, metabolomics, hormone measurements, standardized hormone therapy exposure, and clinical outcomes are needed to determine whether microbiome-derived biomarkers can support risk stratification and personalized interventions for healthier aging in postmenopausal women.},
}

Humans
*Menopause/physiology/metabolism
Female
*Estrogens/metabolism
*Gastrointestinal Microbiome/physiology
*Body Composition/physiology
*Nutritional Status
Aging
Cardiometabolic Risk Factors

@article {pmid42943856,
year = {2026},
author = {Yao, P and Huang, J and Liu, W and Yuan, Q and Lv, J},
title = {Astragalus Polysaccharides Alleviate Inflammatory Damage in Murine Rheumatoid Arthritis by Modulating Th17/Treg Balance via the Gut-Joint Axis.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {20},
pages = {},
pmid = {42943856},
issn = {1420-3049},
support = {CSTB2022NSCQ-MSX0199//Natural Science Foundation of Chongqing/ ; 81903888//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Th17 Cells/drug effects/immunology/metabolism ; *T-Lymphocytes, Regulatory/drug effects/immunology/metabolism ; *Polysaccharides/pharmacology/chemistry ; *Arthritis, Rheumatoid/drug therapy/pathology/immunology/metabolism ; Mice ; *Astragalus Plant/chemistry ; Gastrointestinal Microbiome/drug effects ; Cytokines/metabolism ; *Arthritis, Experimental/drug therapy/pathology/immunology ; *Joints/drug effects/pathology ; Inflammation/drug therapy ; Disease Models, Animal ; Male ; },
abstract = {Astragalus polysaccharides (APSs) have demonstrated protective effects in RA models; however, the underlying microbe-host crosstalk remains unclear. In this study, collagen-induced arthritis (CIA) was established in mice, followed by prophylactic and therapeutic APS administration. The following were then assessed: articular histopathology, splenic Th17/Treg frequencies via flow cytometry, serum and joint cytokine profiles via ELISA and immunohistochemistry, gut microbial metagenomes, and bone erosion via Safranin O-fast green staining. It was found that APS treatment significantly attenuated joint inflammation and bone destruction, rebalanced the Th17/Treg ratio, and reduced pro-inflammatory cytokines (TNF-α and IL-17) while elevating anti-inflammatory IL-10 both systemically and locally. Subsequently, fecal microbiota from APS-treated donor mice was transplanted via oral gavage into CIA recipient mice. APS reversed RA-associated gut dysbiosis by enriching Ligilactobacillus, Lactobacillus, Limosilactobacillus, and Bacteroides, and these microbial shifts closely paralleled diminished articular inflammation and preserved bone architecture. Collectively, these findings indicate that APS mitigates RA progression by reconfiguring the gut microbial ecosystem-favoring beneficial taxa while curbing pathobionts-thereby restoring intestinal homeostasis, normalizing the Th17/Treg axis, and suppressing systemic and articular inflammatory responses.},
}

Animals
*Th17 Cells/drug effects/immunology/metabolism
*T-Lymphocytes, Regulatory/drug effects/immunology/metabolism
*Polysaccharides/pharmacology/chemistry
*Arthritis, Rheumatoid/drug therapy/pathology/immunology/metabolism
Mice
*Astragalus Plant/chemistry
Gastrointestinal Microbiome/drug effects
Cytokines/metabolism
*Arthritis, Experimental/drug therapy/pathology/immunology
*Joints/drug effects/pathology
Inflammation/drug therapy
Disease Models, Animal
Male

@article {pmid42944051,
year = {2026},
author = {Ghidini, M and Sberna, G and Guerrera, LP and Maggi, F and Novazzi, F},
title = {The Gut Virome in Gastrointestinal Cancers: Mechanisms, Biomarkers, and Translational Opportunities.},
journal = {Viruses},
volume = {18},
number = {10},
pages = {},
pmid = {42944051},
issn = {1999-4915},
mesh = {Humans ; *Gastrointestinal Neoplasms/virology/therapy ; *Virome ; *Gastrointestinal Microbiome ; Animals ; Bacteriophages ; Gastrointestinal Tract/virology ; Translational Research, Biomedical ; Biomarkers, Tumor ; Oncogenic Viruses ; Bacteria/virology ; },
abstract = {The gastrointestinal tract contains a dense multi-kingdom ecosystem in which bacteria, fungi, archaea, viruses, the mucosa, and the immune system interact. Although cancer microbiome research has focused mainly on bacteria, the gut virome dominated by bacteriophages may influence gastrointestinal carcinogenesis by reshaping bacterial communities, transferring functional genes, modulating inflammation, and altering treatment response. The strongest evidence comes from colorectal cancer, where multiple cohorts show altered phage diversity, temperate-phage enrichment, disrupted phage-bacteria networks, and reproducible stool-based diagnostic signals. Emerging studies in pancreatic cancer, esophageal adenocarcinoma, hepatocellular carcinoma, and precursor lesions suggest that virome disruption extends beyond colorectal cancer, although evidence remains uneven. Classic oncogenic viruses, including Epstein-Barr virus and hepatitis viruses, provide complementary examples of direct viral carcinogenesis in digestive organs. Anelloviruses are widespread in healthy individuals and are not established causes of cancer, but their abundance and composition may reflect immune status, inflammation, tissue injury, and altered host viral ecology. Virome-related interventions remain clinically immature: fecal microbiota transplantation has reached small phase I/II studies in gastrointestinal cancers, whereas phage, fecal-filtrate, and fecal virome approaches remain preclinical or non-oncology; direct oncolytic viruses have reached late-phase testing. Major barriers include viral dark matter, specimen and assay heterogeneity, disease-related confounding, limited external validation, and weak causal evidence. Standardized, mechanistically anchored, multi-kingdom studies are needed to establish clinical utility.},
}

Humans
*Gastrointestinal Neoplasms/virology/therapy
*Virome
*Gastrointestinal Microbiome
Animals
Bacteriophages
Gastrointestinal Tract/virology
Translational Research, Biomedical
Biomarkers, Tumor
Oncogenic Viruses
Bacteria/virology

@article {pmid42944646,
year = {2026},
author = {Lynggaard, C and Bodawatta, KH and de Fraga, R and Martins, VCC and Aleixo, A and Tavares, VDC and Trevelin, LC and Gastauer, M and Bohmann, K},
title = {Active Filtration of Airborne eDNA for Vertebrate Surveys in Tropical Caves.},
journal = {Molecular ecology resources},
volume = {26},
number = {8},
pages = {},
doi = {10.1111/1755-0998.70218},
pmid = {42944646},
issn = {1755-0998},
support = {CF21-0411//Carlsbergfondet/ ; R100603.NNL.04//Instituto Tecnológico Vale/ ; R100603.CR.04//Instituto Tecnológico Vale/ ; VIL41390//Villum Fonden/ ; 309243/2023-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 313429/2025-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 310865/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 441201/2023-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; *Caves ; Brazil ; *Vertebrates/classification/genetics ; *DNA, Environmental/genetics/isolation & purification ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Extrachromosomal DNA ; *Filtration/methods ; Tropical Climate ; *Metagenomics/methods ; },
abstract = {Hidden from sunlight, caves are remarkable subterraneous ecosystems that host a wide range of animals, including unique species. Conventional cave biodiversity surveys can be physically challenging, disturb sensitive vertebrate communities, or require animal collection. Here we evaluate the use of metabarcoding of airborne environmental DNA (eDNA) as a non-invasive method for surveying cave vertebrates. We collected 55 samples by filtering air for 24 h at three light zones (outside, and in twilight and dark zones inside the cave) in three tropical caves in Amazonian Brazil. Using two metabarcoding primer sets targeting mammal and vertebrate DNA, we detected 123 wild vertebrate taxa encompassing mammals, birds, amphibians, and a reptile, of which 74 were identified to genus level. Genus richness in the twilight zone was significantly higher than outside the caves. Vertebrate diversity was also highest in the twilight zone, and community composition differed significantly between light zones and caves. Mammals and amphibians were mostly detected in the twilight and dark zones, whereas birds were more frequently detected outside the cave and in the twilight zone. While preliminary, our results show that caves with smaller entrances yielded more homogeneous communities in the twilight and dark zones. We detected eight of the 13 bat species and one of the four amphibian species recorded in previous surveys, while also detecting taxa not previously recorded in the caves, demonstrating complementarity with conventional surveys. As airborne eDNA requires minimal human presence in cave interiors, it reduces disturbance to sensitive fauna, lowers safety risks to surveyors, and offers a scalable method to complement conventional cave biodiversity surveys in tropical regions.},
}

Animals
*Caves
Brazil
*Vertebrates/classification/genetics
*DNA, Environmental/genetics/isolation & purification
*DNA Barcoding, Taxonomic/methods
Biodiversity
Extrachromosomal DNA
*Filtration/methods
Tropical Climate
*Metagenomics/methods

@article {pmid42945246,
year = {2026},
author = {Wang, Y and Qu, G and Huang, ZYX and Zhang, X and Li, H and Wei, X and Hu, L and Xu, S and Becker, DJ and Wei, F and Xu, Y},
title = {Viral metagenomics reveals heterogeneity in mammalian virus hosting, sharing, and spillover.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {44},
pages = {e2610672123},
doi = {10.1073/pnas.2610672123},
pmid = {42945246},
issn = {1091-6490},
mesh = {Animals ; *Metagenomics/methods ; Humans ; *Mammals/virology ; Phylogeny ; Zoonoses/virology ; *Virome/genetics ; *Viruses/genetics/classification ; Chiroptera/virology ; },
abstract = {Zoonotic viruses originating from mammals pose a persistent threat to global health. While rodents and bats are often considered "special reservoirs," it is debated if spillover risk is driven by specific taxa or merely reflects mammalian species richness. However, most tests have focused on published host-virus association datasets, which can reflect systematic biases in host and virus sampling effort. To address this limitation, we analyzed a comprehensive repository of 4,685 metagenomic datasets, minimizing bias toward any one viral taxon and spanning 296 species across 14 mammalian orders. We characterized the global mammalian virome and found substantial heterogeneity in the capacity of different mammalian orders to harbor and share human-associated viruses. Counter to conventional wisdom, carnivores exhibited significantly higher propensities to carry human-associated viruses, with bats ranked lower in this metric of zoonotic risk. Network analyses of viral sharing further revealed higher cross-order virus sharing among specific mammalian orders (e.g., carnivores and artiodactyls). Phylogenetic comparative analyses revealed that host life-history traits (e.g., longevity) and anthropogenic factors (e.g., urban land use) were key ecological drivers of both virus richness and transmission centrality. Our study provides a data-driven framework that challenges prevailing narratives of zoonotic risk and offers a refined strategy for prioritizing surveillance and mitigating emerging zoonotic threats.},
}

Animals
*Metagenomics/methods
Humans
*Mammals/virology
Phylogeny
Zoonoses/virology
*Virome/genetics
*Viruses/genetics/classification
Chiroptera/virology

@article {pmid42786310,
year = {2026},
author = {Chen, J and Ren, Y and Zhou, Y and Wang, Z and Li, J and Guo, X and Xu, H and Wang, Y and Tang, H and Han, JJ},
title = {Multi-modality profiling identifies Neisseria flavescens as a central geroprotective oral commensal in humans.},
journal = {Nature aging},
volume = {6},
number = {10},
pages = {2202-2217},
pmid = {42786310},
issn = {2662-8465},
support = {32330017//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82361148130//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2025YFA1805300//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2024YFF0729200//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2025YFC3409300//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; L2604004//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; GZC20230084//China Postdoctoral Science Foundation/ ; },
mesh = {*Neisseria/physiology ; Humans ; *Aging/physiology ; Animals ; Mice ; Caenorhabditis elegans/physiology ; *Mouth/microbiology ; Multiomics ; Metagenome ; *Senotherapeutics ; Gastrointestinal Microbiome ; Biosynthetic Pathways ; Liver/metabolism ; Probiotics/administration & dosage ; Akkermansia/physiology ; Bifidobacterium/physiology ; Lactobacillaceae/physiology ; Random Allocation ; Male ; Mice, Inbred C57BL ; Tongue/microbiology ; },
abstract = {Aging is accompanied by progressive physiological decline, yet the microbiome determinants that modulate aging remain unclear. Here, we identify Neisseria flavescens (Nf) as an oral commensal associated with decelerated aging in humans. Using AURORA, a generative multi-modality framework, we developed multi-modality aging clocks, performed in silico screening for age-gap-reducing interventions and predicted Nf as a top hit. In silico perturbations linked increased Nf abundance to favorable physiological signatures, beneficial gut taxa and biosynthesis of beneficial metabolites. We isolated two Nf strains and validated their production of beneficial metabolites. Functional assays demonstrated that live Nf extended lifespan and healthspan in Caenorhabditis elegans. In aged mice, heat-killed Nf supplementation restored the serum metabolome, liver transcriptome and gut microbiome toward younger states. By establishing an AI-driven intervention discovery engine and identifying Nf as a geroprotective microorganism, these findings highlight the oral microbiome as an underestimated axis of systemic aging and a candidate for geroprotective interventions.},
}

*Neisseria/physiology
Humans
*Aging/physiology
Animals
Mice
Caenorhabditis elegans/physiology
*Mouth/microbiology
Multiomics
Metagenome
*Senotherapeutics
Gastrointestinal Microbiome
Biosynthetic Pathways
Liver/metabolism
Probiotics/administration & dosage
Akkermansia/physiology
Bifidobacterium/physiology
Lactobacillaceae/physiology
Random Allocation
Male
Mice, Inbred C57BL
Tongue/microbiology

@article {pmid42858690,
year = {2026},
author = {Guler Cekic, S and Vatansever, C and Akpinar, A and Belge, S and Shahrokhi, G and Unal, C and Altintas, A and Aydin, S and Can, F},
title = {Interactions between vaginal, periurethral and urinary microbiota in genitourinary syndrome of menopause and the effects of local estrogen therapy.},
journal = {Maturitas},
volume = {214},
number = {},
pages = {109146},
doi = {10.1016/j.maturitas.2026.109146},
pmid = {42858690},
issn = {1873-4111},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota/drug effects ; Middle Aged ; *Estriol/pharmacology/therapeutic use ; Prospective Studies ; *Estrogens/pharmacology/therapeutic use ; *Urethra/microbiology ; Syndrome ; *Estrogen Replacement Therapy ; Atrophy/microbiology ; *Urinary Bladder/microbiology ; Postmenopause ; *Female Urogenital Diseases/microbiology/drug therapy ; Menopause ; Lactobacillus ; },
abstract = {OBJECTIVES: Alterations to the vaginal microbiota have been investigated in genitourinary syndrome of menopause but data regarding periurethral and urinary microbiota remain limited. We aimed to characterize vaginal, periurethral, and urinary microbiota in clinically stratified postmenopausal women and to evaluate the effects of estrogen therapy.

STUDY DESIGN: In this prospective study, postmenopausal women were categorized as controls without atrophy or symptoms, women with clinical atrophy without symptoms, symptomatic women, and symptomatic women receiving 12 weeks of vaginal estriol. Vaginal, periurethral, and bladder samples were collected.

MAIN OUTCOME MEASURES: Microbiota composition and diversity (alpha diversity - Shannon index; and beta diversity - Bray-Curtis dissimilarity) across urogenital niches and changes in these following estrogen therapy.

RESULTS: Vaginal and periurethral alpha diversity was higher in women with asymptomatic atrophy and symptomatic women at baseline than in controls and estrogen-treated women. Beta diversity analyses demonstrated separation of controls and estrogen-treated women from the atrophy groups at baseline. Controls exhibited Lactobacillus-enriched periurethral communities and Klebsiella-dominant urinary profiles. Women with asymptomatic atrophy and symptomatic women showed reduced Lactobacillus and increased anaerobic taxa in vaginal and periurethral niches, while urinary samples were characterized by Escherichia predominance. Notably, in women with asymptomatic atrophy, Lactobacillus abundance was higher in periurethral than vaginal samples. Estrogen therapy increased Lactobacillus abundance in vaginal and periurethral compartments and shifted urinary microbiota toward a control-like composition. Periurethral Streptococcus abundance correlated with sexual symptom scores.

CONCLUSIONS: Microbial alterations in genitourinary syndrome of menopause are compartment-specific and extend beyond the vagina. Periurethral microbiota may contribute to symptom expression, while local estrogen therapy promotes restoration of Lactobacillus-dominant urogenital microbiota.

CLINICALTRIALS: gov registration: NCT06633705.},
}

Humans
Female
*Vagina/microbiology
*Microbiota/drug effects
Middle Aged
*Estriol/pharmacology/therapeutic use
Prospective Studies
*Estrogens/pharmacology/therapeutic use
*Urethra/microbiology
Syndrome
*Estrogen Replacement Therapy
Atrophy/microbiology
*Urinary Bladder/microbiology
Postmenopause
*Female Urogenital Diseases/microbiology/drug therapy
Menopause
Lactobacillus

@article {pmid42861590,
year = {2026},
author = {Deng, LR and Zhong, YM and Zhu, SF and Wu, ZY and Chen, FJ and Huang, CY and Wu, QY and Tomlinson, B and Tan, HE and Li, YH},
title = {Anemoside B4 from Pulsatilla chinensis Ameliorates Ulcerative Colitis by Inhibiting Inflammatory Responses via the Modulation of the Gut Microbiota-Immune Interplay.},
journal = {The American journal of Chinese medicine},
volume = {54},
number = {7},
pages = {2297-2325},
doi = {10.1142/S0192415X26500849},
pmid = {42861590},
issn = {1793-6853},
mesh = {Animals ; *Colitis, Ulcerative/immunology/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects/immunology ; Disease Models, Animal ; *Saponins/isolation & purification/pharmacology/administration & dosage/therapeutic use ; *Pulsatilla/chemistry ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; *Phytotherapy ; Mice ; CD4-Positive T-Lymphocytes/immunology ; Adoptive Transfer ; Homeodomain Proteins ; },
abstract = {We previously demonstrated that anemoside B4 (AB4) exerts a beneficial effect in a dextran sulfate sodium (DSS)-induced murine model of ulcerative colitis (UC). In this study, we further explored the mechanism of AB4 against UC from the perspective of gut microbiota-immune interplay. The gut microbiota was depleted in two DSS-induced colitis models to investigate the modulatory effects of the gut microbiome on immune responses and the activity of AB4. In parallel, adoptive transfer of CD4[Formula: see text]CD62L[Formula: see text] T cells into Rag1-deficient (Rag1[-/-]) mice was used to elucidate the alterations in the gut microbiota associated with immune-mediated colitis as well as the modulation by AB4. qPCR, ELISA and western blotting were used to determine the inflammatory responses of mice with colitis, while immunohistochemistry and flow cytometry were employed to determine the CD4[Formula: see text] T cell function and the underlying mechanism. Metagenomic sequencing analysis was used to detect changes in the intestinal microbiota. The depletion of the gut microbiota attenuated disease severity and immune responses in mice with DSS-induced acute and chronic colitis. Notably, the inhibitory effects of orally administered AB4 on colitis progression and immune responses were abrogated. In addition, colitis induced by adoptive transfer of CD4[Formula: see text]CD62L[Formula: see text] T cells into Rag1[-/-] mice was accompanied by CD4[Formula: see text] T cell engraftment and alterations in gut microbiota. Remarkably, all these pathological changes were significantly attenuated by AB4. Crucially, we found that AB4 suppresses the proliferation, migration, and differentiation of CD4[Formula: see text] T cells, which provides a mechanistic basis for its immunosuppressive effects. Collectively, these findings indicate that the gut microbiota and the immune system, particularly CD4[Formula: see text] T cells, interact with each other in the initiation of colitis. We show that, by targeting this gut microbiota-immune interplay, AB4 is a promising therapeutic strategy for UC.},
}

Animals
*Colitis, Ulcerative/immunology/drug therapy/microbiology
*Gastrointestinal Microbiome/drug effects/immunology
Disease Models, Animal
*Saponins/isolation & purification/pharmacology/administration & dosage/therapeutic use
*Pulsatilla/chemistry
Mice, Inbred C57BL
Dextran Sulfate
Male
*Phytotherapy
Mice
CD4-Positive T-Lymphocytes/immunology
Adoptive Transfer
Homeodomain Proteins

@article {pmid42878705,
year = {2026},
author = {Keuschnig, C and Feord, HK and Broadwell, ELM and Zervas, A and Tranter, M and Anesio, AM and Benning, LG},
title = {Aerobic anoxygenic phototrophs are widespread and active members of Greenland Ice Sheet microbiomes.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {11},
pages = {},
doi = {10.1093/femsec/fiag116},
pmid = {42878705},
issn = {1574-6941},
support = {856416/ERC_/European Research Council/International ; I-044-16-01//Helmholtz Recruiting Initiative/ ; 101108340//European Union/ ; },
mesh = {*Ice Cover/microbiology ; Greenland ; Metagenome ; *Microbiota ; *Phototrophic Processes ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Ecosystem ; Cyanobacteria/genetics ; },
abstract = {The Greenland Ice Sheet (GrIS) hosts diverse microbial communities where glacier ice algae, snow algae, and cyanobacteria act as key primary producers across bare ice, snow, and cryoconite habitats, yet the ecological roles of associated heterotrophic prokaryotes remain poorly understood. Aerobic anoxygenic phototrophs (AAPs) are known to couple light harvesting to heterotrophy and enter trophic relationships with algae in marine systems, suggesting they may represent an important but underexplored functional group in supraglacial ecosystems. Using genome-resolved analyses of supraglacial metagenomes and metatranscriptomes from Greenland, we recovered nine AAP metagenome-assembled genomes (MAGs) (4% of the 229 recovered MAGs) consistently enriched in bare ice and cryoconite communities, but nearly absent in snow. A meta-analysis of 2 451 public metagenomes supported this cryospheric habitat association. AAP_MAGs were disproportionally enriched in thiosulfate oxidation and bicarbonate-dependent carbon assimilation pathways relative to other MAGs. Iron and CO oxidation pathways were broadly distributed across the GrIS microbiome, including in AAPs, together suggesting adaptation strategies in supraglacial ecosystems. Genomic evidence for algal coupling via sulfoquinovose degradation was limited. Overall, we document that AAPs are active and widespread in weathering crust habitats, highlighting their potential contributions to biogeochemical cycling in supraglacial ecosystems.},
}

*Ice Cover/microbiology
Greenland
Metagenome
*Microbiota
*Phototrophic Processes
*Bacteria/genetics/classification/metabolism/isolation & purification
Ecosystem
Cyanobacteria/genetics

@article {pmid42923064,
year = {2026},
author = {Galaras, A and Chasapi, IN and Aplakidou, E and Chasapi, MN and Lamari, E and Diplari, S and Georgakopoulos-Soares, I and Karatzas, E and Baltoumas, FA and Kyrpides, NC and Pavlopoulos, GA},
title = {WasteFams: a database of protein families from global wastewater microbiomes.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {4},
pages = {lqag127},
pmid = {42923064},
issn = {2631-9268},
mesh = {*Wastewater/microbiology ; *Microbiota/genetics ; Metagenome ; Metagenomics ; *Databases, Protein ; *Bacterial Proteins/genetics ; },
abstract = {Wastewater surveillance has emerged as a critical tool for global epidemiology, yet the functional diversity of wastewater microbiomes remains poorly characterized at the protein level. Here, we present WasteFams, the first comprehensive database dedicated to the systematic exploration of protein families in wastewater metagenomic and metatranscriptomic studies worldwide. Integrating data from 580 metagenomes, 132 metatranscriptomes, and 1709 reference genomes (504 metagenomes, 129 metatranscriptomes, and 1151 reference genomes after filtering), WasteFams catalogs 3887 non-redundant protein families (containing ⪰100 members) derived from over 105 million predicted proteins. Each protein family is enriched with multi-layered annotations, including AlphaFold3 structural predictions, taxonomic classifications, and biome-specific metadata. To further expand their functional annotation, we integrated deep genomic context analysis to link protein families to mobile genetic elements, biosynthetic gene clusters, antibiotic resistance genes, and CRISPR elements. Accessible through the EnvoFams portal, WasteFams provides a user-friendly interface featuring advanced search capabilities, sequence and structural similarity tools, and interactive visualization modules. As global initiatives increasingly leverage wastewater for public health and environmental insights, WasteFams can serve as a critical resource for discovering novel microbial functions, monitoring resistance mechanisms, and exploring the biotechnological potential of secondary metabolites within wastewater-engineered ecosystems.},
}

*Wastewater/microbiology
*Microbiota/genetics
Metagenome
Metagenomics
*Databases, Protein
*Bacterial Proteins/genetics

@article {pmid41845557,
year = {2026},
author = {Dormiente, A and Mancabelli, L and Ventura, M and Longhi, G and Mergoni, G and Manfredi, M},
title = {Metagenomic Evaluation of Oral Microbiota in Patients Affected by Oral Lichen Planus: A Pilot Study.},
journal = {Oral diseases},
volume = {32},
number = {8},
pages = {2323-2333},
pmid = {41845557},
issn = {1601-0825},
support = {//Bando di Ateneo per la Ricerca 2023- Azione B/ ; },
mesh = {Humans ; Pilot Projects ; *Lichen Planus, Oral/microbiology/drug therapy ; Female ; Male ; *Microbiota ; Metagenomics ; Middle Aged ; Adult ; *Candidiasis, Oral/microbiology ; *Mouth/microbiology ; Saliva/microbiology ; Aged ; },
abstract = {OBJECTIVE: To characterize the oral bacterial and fungal microbiota of symptomatic oral lichen planus patients undergoing topical corticosteroid therapy and to explore microbial patterns potentially associated with subsequent oral candidiasis.

METHODS: Twelve patients with clinically and histologically confirmed OLP were enrolled. Unstimulated saliva and tongue dorsum swabs were collected at baseline and weekly for three weeks during betamethasone therapy. Bacterial communities were profiled using shallow shotgun metagenomics analyzed with METAnnotatorX2, and fungal communities through ITS sequencing and QIIME 2 workflows. Beta-diversity analyses assessed the effects of time, clinical variables, and later candidiasis development. Associations between bacterial taxa and Candida abundance were evaluated using Spearman correlations.

RESULTS: Oral candidiasis developed in three patients (25%). Microbiota composition showed marked inter-individual variability but high intra-subject stability, with no consistent shifts linked to corticosteroid therapy. Commensal taxa such as Streptococcus, Rothia, and Actinomyces were negatively associated with candidiasis and Candida abundance, whereas anaerobic species including Porphyromonas gingivalis, Prevotella multiformis, and Lachnoanaerobaculum gingivalis displayed positive correlations with fungal proliferation.

CONCLUSIONS: Despite overall stability of the oral microbiota during therapy, specific bacterial signatures were associated with subsequent Candida overgrowth. These findings suggest that cross-kingdom interactions may influence susceptibility to corticosteroid-associated candidiasis and warrant validation in larger cohorts.},
}

Humans
Pilot Projects
*Lichen Planus, Oral/microbiology/drug therapy
Female
Male
*Microbiota
Metagenomics
Middle Aged
Adult
*Candidiasis, Oral/microbiology
*Mouth/microbiology
Saliva/microbiology
Aged

@article {pmid42530605,
year = {2026},
author = {Yasuda, K and Iida, N and Takeshita, Y and Masuo, Y and Honda, M and Takamura, T and Yamashita, T},
title = {Tofogliflozin alters amino acid metabolism in gut microbiota linked to hepatic transcriptomic signatures in MASLD.},
journal = {Journal of gastroenterology},
volume = {61},
number = {11},
pages = {1606-1619},
pmid = {42530605},
issn = {1435-5922},
mesh = {Humans ; *Amino Acids/metabolism ; *Gastrointestinal Microbiome/drug effects ; Liver/metabolism/pathology ; *Glucosides/pharmacology/therapeutic use ; Diabetes Mellitus, Type 2/drug therapy/complications ; Transcriptome/drug effects ; *Sodium-Glucose Transporter 2 Inhibitors/therapeutic use/pharmacology ; Male ; Female ; *Fatty Liver/drug therapy/microbiology/metabolism ; Benzhydryl Compounds ; },
abstract = {BACKGROUND: A deeper understanding of the relationship between dysbiotic gut microbiota and liver tissue-level molecular and histopathological phenotypes in metabolic dysfunction-associated steatotic liver disease (MASLD) remains needed. We aimed to characterize the associations between gut microbial metabolic functions and treatment responses in participants with MASLD.

METHODS: We performed a prespecified sub-analysis of a randomized controlled trial comparing the sodium-glucose cotransporter 2 inhibitor (SGLT2i) tofogliflozin and the sulfonylurea (SU) glimepiride in participants with MASLD and type 2 diabetes (ClinicalTrials.gov NCT02649465). Fecal whole-genome shotgun metagenomics, liver RNA sequencing, serum profiling, and histopathological assessments were integrated to investigate microbiota-host interactions.

RESULTS: Microbial metabolic pathways, rather than taxonomic composition, differed significantly between participants with MASLD and healthy controls. Among the altered microbial pathways, amino acid metabolism emerged as a prominent functional category and was selected for further investigation. Pathways related to amino acid metabolism, particularly phenylalanine metabolism, exhibited opposing patterns: phenylalanine degradation was enriched in MASLD and positively correlated with liver fibrosis scores, whereas phenylalanine biosynthesis inversely correlated with fibrosis severity. Microbial phenylalanine degradation was positively associated with 28 hepatic pathways, including the non-alcoholic fatty liver disease (NAFLD) pathway, in which mitochondria-associated genes were core-enriched. Both SGLT2i and SU treatments improved NAFLD activity scores and altered microbial metabolic pathways without significantly changing microbial species composition. Notably, SGLT2i increased phenylalanine biosynthesis pathways, which were inversely associated with liver fibrosis.

CONCLUSIONS: Gut microbial amino acid metabolism, particularly phenylalanine metabolism, is closely linked to liver fibrosis and molecular pathways in MASLD. Modulation of microbial metabolic functions may represent a promising therapeutic strategy beyond changes in microbial composition.},
}

Humans
*Amino Acids/metabolism
*Gastrointestinal Microbiome/drug effects
Liver/metabolism/pathology
*Glucosides/pharmacology/therapeutic use
Diabetes Mellitus, Type 2/drug therapy/complications
Transcriptome/drug effects
*Sodium-Glucose Transporter 2 Inhibitors/therapeutic use/pharmacology
Male
Female
*Fatty Liver/drug therapy/microbiology/metabolism
Benzhydryl Compounds

@article {pmid42598885,
year = {2026},
author = {Baidya, AK and Aich, P},
title = {Serum-Cecal Metabolome Integration Predicts Gut Microbial Communities and Reveals Pathway-Level Host-Microbe Crosstalk Under Disease-Induced Dysbiosis.},
journal = {Omics : a journal of integrative biology},
volume = {30},
number = {12},
pages = {710-717},
doi = {10.1177/15578100261479266},
pmid = {42598885},
issn = {1557-8100},
mesh = {Animals ; *Metabolome ; *Dysbiosis/microbiology/metabolism/blood ; Multiomics ; *Gastrointestinal Microbiome ; Metabolomics/methods ; RNA, Ribosomal, 16S/genetics ; *Cecum/microbiology/metabolism ; *Host Microbial Interactions ; Mice ; Metabolic Networks and Pathways ; },
abstract = {The gut microbiome shapes systemic physiology through metabolites that enter circulation, yet most computational approaches focus on predicting metabolite profiles from microbial features rather than inferring microbial composition from host metabolomes. Here, we investigate whether host-derived metabolomic profiles can be leveraged to predict gut microbial community structure and to determine how disease-associated dysbiosis reshapes metabolite-microbe interactions and gut-to-systemic metabolic communication. We developed an integrative multi-omics framework combining serum and cecal metabolomics with 16S rRNA-based microbiome profiling. Supervised learning models demonstrated that cecal metabolites carry predictive signals for microbial abundances across conditions. Regularized canonical correlation analysis (rCCA) revealed cross-compartment metabolite-microbe networks. These analyses showed both conserved and condition-specific interaction patterns, indicating substantial network reorganization under disease-associated dysbiosis. Pathway-level integration further identified metabolic pathways linking the gut microbiome, the cecal environment, and the systemic circulation, representing coordinated gut-to-systemic communication axes. Together, our results establish a multi-omics strategy for predictive inference of gut microbial composition from host metabolomes and provide a framework for identifying pathway-level mechanisms underlying host-microbe metabolic crosstalk.},
}

Animals
*Metabolome
*Dysbiosis/microbiology/metabolism/blood
Multiomics
*Gastrointestinal Microbiome
Metabolomics/methods
RNA, Ribosomal, 16S/genetics
*Cecum/microbiology/metabolism
*Host Microbial Interactions
Mice
Metabolic Networks and Pathways

@article {pmid42914410,
year = {2026},
author = {Zhang, Y and Li, Z and Yang, H and Chen, A and Chen, Y and Luo, Y and Zheng, C and She, L and Tang, P},
title = {Comparative characterization of physicochemical properties, microbial communities, and volatile flavor compounds during the fermentation of high-temperature Daqu produced from two different wheat raw materials.},
journal = {Food research international (Ottawa, Ont.)},
volume = {245},
number = {Pt 2},
pages = {120679},
doi = {10.1016/j.foodres.2026.120679},
pmid = {42914410},
issn = {1873-7145},
mesh = {*Triticum/microbiology/chemistry ; *Fermentation ; *Volatile Organic Compounds/analysis ; Hot Temperature ; *Microbiota ; *Alcoholic Beverages/analysis/microbiology ; Bacteria/metabolism/classification ; Taste ; *Food Microbiology ; Odorants/analysis ; },
abstract = {Soft wheat (Sy) and mixed wheat (My; a 7:3 blend of soft and hard wheat) are used to produce high-temperature Daqu (HTD) for reducing production costs in certain baijiu enterprises. However, the differences between single-wheat HTD (S-HTD) and mixed-wheat HTD (M-HTD) remain unclear. This study aimed to compare the physicochemical properties, microbial succession, and flavor metabolism during fermentation of HTD produced from two different wheat raw materials. Although all monitored properties followed the same trends, differences existed between the two types of HTD during fermentation. At the end of fermentation, M-HTD had higher relative contents of key aroma contributors, such as pyrazines, esters, and acids. Metagenomic sequencing revealed Bacillus, Saccharopolyspora, and Kroppenstedtia (bacteria) and Aspergillus, Lichtheimia, Paecilomyces, and Monascus (fungi) as the dominant genera. Different HTD exhibited distinct patterns of microbial relative abundance during fermentation. The correlations of dominant microorganisms with differential flavor compounds were also illustrated. Moreover, microbial functional prediction revealed a higher relative abundance of many enzymes related to flavor production in M-HTD. Gene function prediction also confirmed immense potential for metabolism in M-HTD. These results indicated that HTD produced from the mixed wheat was associated with higher relative contents of key flavor compounds. Our findings may help enterprises select wheat raw materials and provide a theoretical basis for promoting the high-quality production of HTD.},
}

*Triticum/microbiology/chemistry
*Fermentation
*Volatile Organic Compounds/analysis
Hot Temperature
*Microbiota
*Alcoholic Beverages/analysis/microbiology
Bacteria/metabolism/classification
Taste
*Food Microbiology
Odorants/analysis

@article {pmid42916222,
year = {2026},
author = {Cai, J and Shen, Y and Jiang, L and Li, S and Li, C and Li, H and Zhou, S and Liang, X and Jiang, C and He, N},
title = {Scale-Dependent Drivers Shape Airborne Microbiomes across the Shanghai Subway Network.},
journal = {Environmental science & technology},
volume = {60},
number = {37},
pages = {26060-26072},
doi = {10.1021/acs.est.6c00174},
pmid = {42916222},
issn = {1520-5851},
support = {DGF201001//Shanghai Municipal Education Commission/ ; DGF201003//Shanghai Municipal Education Commission/ ; DGF201004//Shanghai Municipal Education Commission/ ; DGF201006//Shanghai Municipal Education Commission/ ; },
mesh = {China ; *Microbiota ; *Air Microbiology ; Particulate Matter ; Railroads ; Particle Size ; Bacteria ; },
abstract = {Urban subway systems represent important yet understudied environments for human exposure to airborne microorganisms. Therefore, we conducted an investigation of air microbiome across 43 underground stations spanning 13 lines of the Shanghai subway. Using stratified cluster sampling, we simultaneously collected total suspended particles (TSP, aerodynamic diameter ≤ 100 μm) and fine particulate matter (PM2.5, aerodynamic diameter ≤ 2.5 μm) at station entrances, halls, and platforms, integrating microbial taxonomy, transcriptional potential, PM2.5 chemical composition, microclimate, and network topology. We found bacteria dominated both particle-size fractions and accounted for the majority of transcriptional signals, whereas eukaryotic taxa were strongly enriched in TSP, reflecting pronounced particle-size filtering. Although transcriptional potential generally increased with abundance, dominant taxa such as Staphylococcus and Bacillus exhibited weak abundance-transcription coupling, indicating functional decoupling between numerical dominance and transcriptional contribution in subway air microbiomes. Microbial diversity and community composition remained broadly homogeneous across the subway network, consistent with extensive passenger mobility and high network connectivity. In contrast, finer-scale heterogeneity emerged within stations, particularly for eukaryotic communities, which declined from entrances to enclosed platform environments. Environmental associated factors exhibited kingdom-specific patterns: bacterial and viral diversity were primarily associated with local microclimatic conditions, especially temperature, whereas eukaryotic diversity was more strongly linked to urbanization and externally derived aerosol inputs. Overall, these findings demonstrate that subway airborne microbiomes are shaped by interacting effects of particle-size filtering, environmental selection, and network-driven microbial mixing.},
}

China
*Microbiota
*Air Microbiology
Particulate Matter
Railroads
Particle Size
Bacteria

@article {pmid42918750,
year = {2026},
author = {Xiao, L and Liu, J and Tanentzap, AJ and Duarte, CM and Fu, C and Zhou, L and Dang, R and Zhou, M and Luo, M and Zhang, P and Yu, J and Xu, Y and Rosentreter, J and Spencer, RGM and Lichtfouse, E and Luo, Y and Han, G},
title = {Resilience of blue carbon microbiomes in response to ecological and anthropogenic filtering.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42918750},
issn = {2041-1723},
support = {U2106209//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42077025//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42277236//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991330//National Natural Science Foundation of China (National Science Foundation of China)/ ; U2106209//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2021213//Youth Innovation Promotion Association of the Chinese Academy of Sciences (Youth Innovation Promotion Association CAS)/ ; },
mesh = {Phylogeny ; *Carbon/metabolism ; *Microbiota/genetics ; *Ecosystem ; Metagenome ; *Anthropogenic Effects ; Bacteria/genetics/classification/metabolism ; Carbon Cycle ; },
abstract = {Global change is threatening the microbial consortia that sustain the services and functions of blue carbon ecosystems (BCEs), but little is known about how the composition and functioning of these consortia will respond to ecological and anthropogenic stressors. Here, we construct a continental-scale microbial genome catalog from 116 representative habitats, including mangrove forests, saltmarshes, and seagrass meadows, and recover 1954 non-redundant metagenome-assembled genomes (MAGs). We find that BCE microbiomes are taxonomically distinct from terrestrial, marine, and marginal sea ecosystems, with ecosystem type and spatial distribution further differentiating community composition. Environmental filtering constrains taxonomic composition, yet functional composition is largely invariant to taxonomic turnover. Specialist KEGG orthologues underpin over 90% of metabolic functions conserved across all BCEs. Notably, for carbon fixation, phylogenetically divergent functional lineages provide functional redundancy that can mitigate the effects of species replacement. Collectively, our study quantifies the vulnerability of BCEs to future species loss while providing a scientific basis for confidence that blue carbon ecosystems, supported by phylogenetic redundancy, may sustain functional stability despite environmental change.},
}

Phylogeny
*Carbon/metabolism
*Microbiota/genetics
*Ecosystem
Metagenome
*Anthropogenic Effects
Bacteria/genetics/classification/metabolism
Carbon Cycle

@article {pmid42918805,
year = {2026},
author = {Liu, P and Lv, Y and Zhang, Y and Wang, Y and Zhu, K and Cao, Z and Dong, L and Xiao, X and Pan, Y and Li, J},
title = {Extensive horizontal gene transfer drives microbial adaptation and diversification in Kermadec Trench hadal microbiomes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42918805},
issn = {2041-1723},
support = {42225402//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gene Transfer, Horizontal ; Phylogeny ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Metagenome ; *Adaptation, Physiological/genetics ; *Geologic Sediments/microbiology ; Metagenomics ; },
abstract = {Hadal trenches, plunging beyond six kilometers depth, harbor a dynamic yet enigmatic microbial biosphere. From ~10 km depth Kermadec Trench sediments, we integrated metagenomics, in situ metatranscriptomics, and phylogenetics to reconstruct 300 prokaryotic species and 186,496 viral populations. In hadal sediment metagenomes analyzed here, we detect distant horizontal gene transfer (DHGT) across phyla/domains and estimate that it contributes on average ~13% of each genome and accounting for >46.7% of multi-copy gene expansions, with four phyla acquiring more than 30% of their genes via DHGT. These DHGT genes encode critical adaptations, including reactive oxygen species detoxification, aromatic compound degradation, and fatty acid/heme biosynthesis, which help microbes survive extreme pressure, low temperatures, and oligotrophy. While classical mechanisms such as conjugation (~0.27%), transduction (~2.1%), and transformation account for a fraction of events, additional potential gene flow conduits are proposed: magnetotaxis-mediated encounters by magnetotactic bacteria (~17.4% of DHGT events), possibly increasing opportunities for gene exchange. These findings suggest that DHGT can contribute substantially to metabolic diversification in the hadal genomes, representing an evolutionary mode distinct from gradualist Darwinian inheritance and consistent with the idea that episodic acquisition of functional modules can contribute to rapid metabolic diversification.},
}

*Gene Transfer, Horizontal
Phylogeny
*Microbiota/genetics
*Bacteria/genetics/classification
Metagenome
*Adaptation, Physiological/genetics
*Geologic Sediments/microbiology
Metagenomics

@article {pmid42919172,
year = {2026},
author = {Jorquera, R and Ejsmentewicz, T and Lagos, R and Bravo, N and Issotta, F and Hernández-Oliveras, A and Villarroel-Espíndola, F and González-Stegmaier, R},
title = {Evaluating 16S metagenomics data analysis pipelines using an Ion Torrent sequencer for human gut microbiome research.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42919172},
issn = {1471-2180},
support = {internal grant ID FALP-LMT-2021//Fundacion Arturo Lopez Perez/ ; internal grant ID FALP-LMT-2022//Fundacion Arturo Lopez Perez/ ; },
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Software ; *High-Throughput Nucleotide Sequencing/methods ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: High-throughput 16S rRNA gene amplicon sequencing is essential for characterizing gut dysbiosis in translational research. However, microbiome profiles vary widely across sequencing platforms, library preparation protocols, targeted hypervariable regions (HVRs), and bioinformatics workflows. For users of the Ion Torrent S5 platform, there is currently no consensus methodology for performing open-source analyses as an alternative to proprietary frameworks. This study evaluates the proprietary Ion Reporter™ software against eight open-source pipelines based on QIIME2 and the SILVA database, accounting for data compositionality. Benchmarking was performed using a commercial human fecal reference material (ZymoBIOMICS™ D6323) characterized via DNA-shotgun sequencing (the ZB-Shotgun profile), as the reference standard.

RESULTS: Poisson regression modeling showed that using two primer sets for library preparation yielded a 30 % lower expected read count than a single primer set (IRR = 0.6986, p < 0.001). Across all configurations, the choice of denoising algorithm (DADA2 vs. Deblur) significantly affected alpha diversity calculations. At the phylum level, hierarchical clustering of Bayes factors (BFs) indicated that multi-region Ion Reporter workflows produced stable consensus predictions. Conversely, at the species level, single-HVR open-source pipelines significantly outperformed multi-region approaches.

CONCLUSIONS: Open-source pipelines that combine targeted HVR2 or HVR4 inputs with state-of-the-art denoisers outperform proprietary Ion Reporter options, providing superior taxonomic resolution and precision for species-level microbiome profiling. This study establishes a traceable, reproducible, and cost-effective framework that empowers independent researchers to maximize the utility of Ion Torrent 16S rRNA data in healthcare and gastrointestinal research without relying on restrictive software ecosystems.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Software
*High-Throughput Nucleotide Sequencing/methods
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Bacteria/genetics/classification/isolation & purification
Computational Biology/methods
Sequence Analysis, DNA/methods
DNA, Bacterial/genetics

@article {pmid42919413,
year = {2026},
author = {Moreno, ML and Taft, DH and Tompkins, TA and Dahl, WJ},
title = {Efficacy of yeast mannan supplementation on increasing stool frequency in adults: a randomized controlled trial.},
journal = {Trials},
volume = {27},
number = {1},
pages = {},
pmid = {42919413},
issn = {1745-6215},
support = {PRO00067834//Lallemand/ ; },
mesh = {Humans ; *Mannans/administration & dosage/adverse effects ; Double-Blind Method ; Feces/microbiology ; *Dietary Supplements ; *Defecation/drug effects ; *Saccharomyces cerevisiae/chemistry ; Gastrointestinal Transit/drug effects ; Treatment Outcome ; Adult ; Time Factors ; Quality of Life ; *Gastrointestinal Microbiome/drug effects ; },
abstract = {BACKGROUND: Yeast mannans are microbial-available substrates that may improve laxation and specifically modulate gut microbiota composition. The aim of this study is to determine the effect of yeast mannan supplementation on stool frequency in adults. Secondary aims will assess gastrointestinal tolerance and quality of life, whole gut transit time, fecal microbiota composition, and fecal and urinary levels of microbial-generated metabolites.

METHODS: A 6-week, double-blinded, parallel, randomized trial will evaluate the effect of 12 g of yeast mannan (Saccharomyces cerevisiae cell wall fraction containing mannan-oligosaccharides and mannoproteins) or control (maltodextrin and yeast protein) supplementation on mean daily stool frequency in adults (n = 60). Participants will complete a daily survey of stool frequency, gastrointestinal symptoms, and quality of life, any adverse events, and compliance with supplement intake during the 2-week baseline and 4-week intervention periods; gastrointestinal tolerance will be assessed weekly. Capsules containing radiopaque markers will be administered, and all stools will be collected during the last 3 days of baseline and intervention. Whole gut transit time will be estimated using the 80% recovery of radiopaque markers method. Per period, 24-h urine will be collected, and metabolomics will be determined by LC-MS/MS. For the primary outcome, change from baseline daily stool frequency between groups will be compared, and between-group comparisons of secondary outcomes using appropriate generalized linear regression models, and for those outcomes with repeated measures, linear mixed effect models. Fecal microbiome using whole metagenome sequencing data will be processed using metaphlan4, Braken, or another tool appropriate for estimating the relative abundance of microbial species. Additional analysis using tools such as humann3 will enable functional assignment of reads. Resulting relative abundance and normalized functional data will be further analyzed using a combination of tools in R software, including phyloseq and vegan packages.

DISCUSSION: In accordance with our pilot open-label study, the hypothesis is that yeast mannans will increase daily stool frequency, be highly tolerable, and demonstrate specific modulation of the microbiota, supporting its prebiotic properties. Additionally, yeast mannan supplementation may decrease whole gut transit time and mitigate the microbial production of inflammatory microbial-generated metabolites.

TRIAL REGISTRATION: NCT ID NCT06911177. Registered on 04 April 2025.},
}

Humans
*Mannans/administration & dosage/adverse effects
Double-Blind Method
Feces/microbiology
*Dietary Supplements
*Defecation/drug effects
*Saccharomyces cerevisiae/chemistry
Gastrointestinal Transit/drug effects
Treatment Outcome
Adult
Time Factors
Quality of Life
*Gastrointestinal Microbiome/drug effects

@article {pmid42919998,
year = {2026},
author = {Chen, K and Li, J and Zhou, L and Ge, R and Zheng, K and Xu, C and Su, Y and Sun, S and Liang, Y and Xing, J and Wang, M},
title = {Isolation and genomic characterization of a Teetrevirus phage infecting Klebsiella quasipneumoniae with a putative SAMase gene.},
journal = {Archives of virology},
volume = {171},
number = {11},
pages = {},
pmid = {42919998},
issn = {1432-8798},
support = {LSKJ202203201//the National Key Research and Development Program of China/ ; 42120104006 and 42176111//the National Natural Science Foundation of China/ ; 202172002//the Fundamental Research Funds for the Central Universities/ ; },
mesh = {Phylogeny ; *Genome, Viral ; *Bacteriophages/genetics/isolation & purification/classification/enzymology ; *Klebsiella/virology ; *Viral Proteins/genetics/metabolism/chemistry ; Wastewater/virology/microbiology ; Genomics ; Models, Molecular ; Molecular Docking Simulation ; },
abstract = {Phages regulate bacterial populations in engineered ecosystems. However, wastewater associated phage lineages remain uncultured and poorly characterized. Here, we describe vB_KquP_T1, a bacteriophage infecting Klebsiella quasipneumoniae and exhibiting a lytic growth phenotype, isolated from urban wastewater. Genome-based phylogenomic analyses revealed that vB_KquP_T1 represents a distinct species-level lineage within the Teetrevirus of the Autotranscriptaviridae, closely related to uncultured viral genomes. Metagenomic recruitment from 234 global wastewater datasets reveals that vB_KquP_T1-like phages are widespread, with pronounced regional variation. Notably, the vB_KquP_T1 genome encodes a putative S-adenosyl-L-methionine hydrolase (SAMase)-like protein. Structural modeling and comparative analysis revealed a conserved structural architecture, while molecular docking predicted potential interactions with SAM-related ligands. These findings link an uncultured viral lineage to a cultivated representative and support the conservation of SAM metabolism-related auxiliary genes across tailed phages.},
}

Phylogeny
*Genome, Viral
*Bacteriophages/genetics/isolation & purification/classification/enzymology
*Klebsiella/virology
*Viral Proteins/genetics/metabolism/chemistry
Wastewater/virology/microbiology
Genomics
Models, Molecular
Molecular Docking Simulation

@article {pmid42923033,
year = {2026},
author = {Zhang, C and Chen, Q and Sun, Z and Wu, T and Zhang, Y and Huang, B and Huang, S and Zhang, Y and Han, M},
title = {Tripterygium wilfordii ameliorates complete freund adjuvant-induced rheumatoid arthritis through modulating the gut-joint axis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1828110},
pmid = {42923033},
issn = {1664-3224},
mesh = {Animals ; *Tripterygium/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Arthritis, Rheumatoid/drug therapy/chemically induced/immunology/metabolism ; Rats ; *Arthritis, Experimental/drug therapy/immunology/metabolism ; Cytokines/metabolism/blood ; *Joints/drug effects/metabolism/immunology ; Male ; *Plant Extracts/pharmacology ; Synovial Membrane/metabolism ; *Drugs, Chinese Herbal/pharmacology ; Signal Transduction/drug effects ; Metabolomics ; },
abstract = {INTRODUCTION: Although Tripterygium wilfordii (TW) is a classical Chinese herbal medicine for the treatment of rheumatoid arthritis (RA), the mechanism by which it alleviates inflammation through modulation of the gut microbiota remains unclear.

METHODS: To elucidate the mechanism underlying the therapeutic effects of TW on RA, we first employed network pharmacology to predict the relevant pathways and core targets. Subsequently, an integrative multi-omics approach was applied, including gut metagenomics, gut metabolomics, serum metabolomics, and synovial transcriptomics, to investigate the alterations in gut microbiota, intestinal and serum metabolites, and synovial gene expression in a rat model of RA.

RESULTS: Our findings revealed that TW supplementation lowered serum concentrations of IL-6, IL-1β, TNF-α, and IL-10 and modulated the Th17/Treg balance in intestinal tissue. TW treatment altered gut microbiota (GM) composition, marked by increased abundance of Prevotella sp PCJ2 and Psychrobacter pasteurii, and decreased Adlercreutzia equolifaciens and Schaedlerella arabinosiphila, synergizing with keystone species (Bifidobacterium animalis, Phocaeicola sartorii, Blautia faecis) to promote gut health. Concurrently, TW elevated tryptophan metabolites (tryptophol, tryptamine, 5-hydroxykynurenamine) while reducing 4-(2-aminophenyl)-2,4-dioxobutanoic acid, restoring tryptophan metabolism. This regulation coincided with upregulated Inmt mRNA in synovium, activating the tryptophan pathway. Correlation and mediation analyses indicated that gut-derived circulating metabolites such as N-myristoyl arginine and lauramidoxide were positively correlated with synovial Jun expression, potentially participating in the modulation of the IL-17-NF-κB cascade. Consistently, upregulated synovial Socs3 may exert negative feedback suppression on JAK-STAT signaling to alleviate inflammatory responses.

DISCUSSION: These findings point to the gut microbiome and tryptophan pathway as a new therapeutic avenue for RA.},
}

Animals
*Tripterygium/chemistry
*Gastrointestinal Microbiome/drug effects
*Arthritis, Rheumatoid/drug therapy/chemically induced/immunology/metabolism
Rats
*Arthritis, Experimental/drug therapy/immunology/metabolism
Cytokines/metabolism/blood
*Joints/drug effects/metabolism/immunology
Male
*Plant Extracts/pharmacology
Synovial Membrane/metabolism
*Drugs, Chinese Herbal/pharmacology
Signal Transduction/drug effects
Metabolomics

@article {pmid42479812,
year = {2026},
author = {Jia, Y and Yan, Y and Chen, B and Shu, WS and Lu, H},
title = {Revealing Dual Synergistic Strategies in Sulfate-Reducing Microbiomes for Sulfamethoxazole Biodegradation via DNA-SIP and Metagenomics.},
journal = {Environmental science & technology},
volume = {60},
number = {36},
pages = {25622-25634},
doi = {10.1021/acs.est.6c05921},
pmid = {42479812},
issn = {1520-5851},
support = {52000186//National Natural Science Foundation of China/ ; 52131001//National Natural Science Foundation of China/ ; },
mesh = {*Sulfamethoxazole/metabolism ; Metagenomics ; *Microbiota ; Biodegradation, Environmental ; Sulfates/metabolism ; Bioreactors ; },
abstract = {Sulfate-reducing microbiomes (SRMs) have shown strong potential for antibiotic remediation, yet the active microorganisms and community-level strategies associated with sulfamethoxazole (SMX) biotransformation remain poorly understood. In this study, long-term bioreactor operation (269 days; 500-1500 μg/L SMX), DNA-stable isotope probing (DNA-SIP), and metagenomic analyses were integrated to investigate the microbial contributors and functional organization underlying SRM-driven SMX biotransformation. Desulfobacterium, a key SRM member, was co-enriched with Geobacter and Leptolinea in the 13C-labeled heavy fraction, suggesting potential metabolic complementarity during community-level SMX biotransformation. Genome-resolved analyses further revealed structured patterns of inferred horizontal gene transfer (HGT) and predicted metabolite exchange among keystone taxa. The transferred genes were mainly associated with energy conservation, transport, sulfur-associated metabolism, and stress-response functions, whereas the predicted exchanged metabolites included carbon metabolites, amino acid-related sulfur compounds, purine-related intermediates, and cofactor-associated metabolites. Together, these findings suggest that HGT-associated functional redistribution and metabolic complementarity may contribute to the persistence and coordinated activity of sulfate-reducing microbiomes under high SMX stress. This study links SIP-identified active populations with genome-inferred interaction patterns in a sulfate-reducing system and provides new insight into microbiome-based anaerobic strategies for antibiotic-containing wastewater treatment.},
}

*Sulfamethoxazole/metabolism
Metagenomics
*Microbiota
Biodegradation, Environmental
Sulfates/metabolism
Bioreactors

@article {pmid42710654,
year = {2026},
author = {Chen, Y and Li, Y and Chen, Y and Gou, C and Li, H and He, X and Zeng, N and Du, E and Chen, X and Gui, F},
title = {Host detoxification and gut microbiota are associated with chlorantraniliprole resistance in Spodoptera frugiperda.},
journal = {Journal of insect physiology},
volume = {174},
number = {},
pages = {105062},
doi = {10.1016/j.jinsphys.2026.105062},
pmid = {42710654},
issn = {1879-1611},
mesh = {Animals ; *Spodoptera/microbiology/drug effects/metabolism/genetics ; *Insecticide Resistance/genetics ; *ortho-Aminobenzoates/pharmacology ; *Insecticides/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Inactivation, Metabolic ; },
abstract = {Spodoptera frugiperda is a major agricultural pest that causes severe damage in China. Chlorantraniliprole (CAP) is the primary insecticide used for control; however, it is yet unknown how much the intrinsic detoxification system and gut microbiota of the host contribute to resistance. In this study, we used a resistant strain (CR) with a 71.85-fold resistance ratio after 10 generations of CAP selection. The molecular and microbial changes associated with CAP resistance in S. frugiperda were systematically analyzed by integrating phenotypic and multi-omics data. Results demonstrated that detoxification enzyme activities were markedly increased in the CR strain. Host-mediated metabolic pathways driven by Cytochrome P450 and glutathione S-transferase were significantly upregulated. Furthermore, transcriptome evidence indicated that CAP-induced calcium dysregulation was mitigated via enhanced calcium sequestration and endoplasmic reticulum chaperone responses, suggesting physiological tolerance of insects to this insecticide. Continuous CAP stress also significantly reshaped the gut microbial community structure of S. frugiperda, with Enterococcus emerging as the dominant genus. According to metagenomic annotation, the gut microbiome was enriched in candidate genes associated with CAP degradation, including dehalogenases and amidases, that could potentially break the chemical bonds in CAP and thereby contribute to resistance. Enterococcus mundtii was the most prominently contributor in terms of gene abundance. Phylogenetic analysis revealed sequence similarities and conserved domains between candidate microbial degradation genes and host metabolic detoxification genes, suggesting potential functional similarity. The integrative analyses suggested that S. frugiperda resistance may arise from correlated changes in host endogenous metabolism, calcium homeostasis, and gut-microbiota-mediated degradation potential. The gut microbiota may form a coordinated adaptive regulatory system by encoding candidate degrading enzymes and exhibiting correlative coupling with host genes, which requires further functional validation. These findings highlight the potential synergy between host detoxification and gut microbiota as a contributing factor to CAP resistance in S. frugiperda.},
}

Animals
*Spodoptera/microbiology/drug effects/metabolism/genetics
*Insecticide Resistance/genetics
*ortho-Aminobenzoates/pharmacology
*Insecticides/pharmacology
*Gastrointestinal Microbiome/drug effects
Inactivation, Metabolic

@article {pmid42742264,
year = {2026},
author = {Keller-Costa, T and Tignat-Perrier, R and Marques, M and Ferrier-Pagès, C and Pogoreutz, C},
title = {Symbiotic interactions and climate change implications of the octocoral microbiome.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42742264},
issn = {1751-7370},
support = {10.54499/2024.14436.PEX//Portuguese Foundation for Science and Technology/ ; SFRH/BD/151376/2021//Portuguese Foundation for Science and Technology/ ; },
mesh = {Animals ; *Anthozoa/microbiology/physiology ; *Climate Change ; *Symbiosis ; *Microbiota ; Bacteria/classification/genetics ; Ecosystem ; },
abstract = {Octocorals are vital components of tropical, temperate, and cold-water benthic marine ecosystems. Their associated microbiomes, comprising microeukaryotes, prokaryotes, and viruses, are increasingly recognized as central to host health, nutrient cycling, and chemical defense. Metagenomics and amplicon sequencing have uncovered taxonomic and functional complexity within these microbial communities, revealing patterns of host specificity and health status, along with seasonality and geographic structuring. However, anthropogenic stressors, particularly those associated with global climate change, exert intense pressure on coral-dominated ecosystems, leading to complex and poorly understood local and regional patterns of octocoral expansion and mortality. Microbial interactions may be a main driver of these contrasting outcomes by mediating the ecological resilience of octocorals to environmental stress. We synthesize the current state of research on the diversity, organization, and function of the octocoral microbiome, and identify critical knowledge gaps on octocoral holobionts relative to scleractinian corals. Our meta-analysis of 79 publicly available bacterial genomes from octocorals reveals group-specific specialization in denitrification and nitrate assimilation, along with widespread capacities for essential amino acid, cofactor, and vitamin production, suggesting important contributions to nutrient cycling in the holobiont. While sampling efforts between cultured and uncultured lineages are even, our genomic survey reveals strong sampling bias toward the Atlantic Ocean, temperate gorgonians, and healthy host states, whereas bacterial genomes representing the pathobiome, tropical and/or deep-sea regions, and other octocoral taxa remain underrepresented. Accordingly, we propose future research directions to advance understanding of octocoral microbiome ecology and its role in the resilience of tropical, temperate, and cold-water coral reefs.},
}

Animals
*Anthozoa/microbiology/physiology
*Climate Change
*Symbiosis
*Microbiota
Bacteria/classification/genetics
Ecosystem

@article {pmid42743804,
year = {2026},
author = {Chen, ZY and Gao, FZ and Li, P and Bai, H and He, LY and Liu, YS and Ying, GG},
title = {Multi-omics evidence reveals robust airborne-human resistome connectivity driven by high-risk ARGs and mediated by Staphylococcus.},
journal = {Environment international},
volume = {216},
number = {},
pages = {110525},
doi = {10.1016/j.envint.2026.110525},
pmid = {42743804},
issn = {1873-6750},
mesh = {Humans ; *Staphylococcus/genetics ; *Air Microbiology ; Multiomics ; Microbiota ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Occupational Exposure ; Dairying ; },
abstract = {Airborne microbiomes are considered an important source of human antimicrobial resistance (AMR) exposure, yet multi-omics evidence linking airborne and human nasal resistomes remains limited. Here, we integrated metagenomic sequencing and whole-genome sequencing of antibiotic-resistant Staphylococcus isolates to investigate the connectivity between air and human nasal resistomes in dairy farm environments. Metagenomic taxonomic profiling showed that Staphylococcus was prominent in total suspended particles (TSP) and consistently detected across all samples. Among environmental reservoirs, TSP resistomes exhibited the strongest similarity to human nasal resistomes. This connectivity was supported by multiple lines of evidence, including highly similar resistome profiles, extensive homologous antibiotic resistance gene (ARG) pairs, strain-level similarity of resistant Staphylococcus isolates, and conserved mobile ARG genetic contexts. Notably, this connectivity was primarily driven by high-risk ARGs, while Staphylococcus was frequently associated with mobile ARGs and represented the only shared pathogenic genomes carrying both ARGs and virulence factor genes between airborne and nasal samples. Although lower ARG diversity, nasal resistomes exhibited higher ARG burden, risk scores, antibiotic-resistant bacterial genome abundance, and prevalence of resistant Staphylococcus. Occupational exposure further increased total and high-risk ARG burdens among farm workers. Together, these findings indicate that TSP can serve as an important route of occupational AMR exposure, with high-risk ARGs and Staphylococcus contributing to connectivity between airborne and nasal resistomes. Incorporating the host microbiome may therefore provide a more complete assessment of human-associated AMR exposure within a One Health framework.},
}

Humans
*Staphylococcus/genetics
*Air Microbiology
Multiomics
Microbiota
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Occupational Exposure
Dairying

@article {pmid42768105,
year = {2026},
author = {Dong, D and Walsh, AM and Vatanen, T and Weingart, G and Khdhiri, M and Stampfer, MJ and Vehik, K and Franzosa, EA and Huttenhower, C and Wang, DD and , },
title = {Gut microbiome maturation in early childhood interacts with host genetics to predict type 1 diabetes risk.},
journal = {Nature metabolism},
volume = {8},
number = {10},
pages = {2133-2151},
pmid = {42768105},
issn = {2522-5812},
mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/microbiology ; *Gastrointestinal Microbiome ; Genetic Predisposition to Disease ; Child, Preschool ; Female ; Child ; Male ; Infant ; Metagenome ; },
abstract = {Prospective evidence linking early-life microbiome development and host genetics with type 1 diabetes (T1D) risk is limited. Here, we describe how gut microbiome maturation and host genetics influence T1D risk in the TEDDY study. We analysed 12,151 longitudinal metagenomes and host genetic data from 887 children at high genetic risk for T1D followed for up to 6 years. We identify three microbiome maturational patterns: Early Matured, Late Matured and Early Plateaued, driven primarily by non-linear changes in species from the Bifidobacterium and Ruminococcus genera. The Early Matured pattern is enriched in galactose metabolism and exhibits higher production of aromatic amino acids and B-group vitamins at early follow-ups, whereas the Early Plateaued pattern has increased microbial production of branched-chain amino acids. Notably, the Early Plateaued pattern is associated with a threefold elevated risk of T1D, whereas other patterns are not associated with T1D risk. Furthermore, we find that host genetic variants related to antimicrobial and antiviral immune responses modify the association between the Late Matured pattern and T1D risk. These findings highlight the role of early microbial exposures and host genetics in T1D susceptibility.},
}

Humans
*Diabetes Mellitus, Type 1/genetics/microbiology
*Gastrointestinal Microbiome
Genetic Predisposition to Disease
Child, Preschool
Female
Child
Male
Infant
Metagenome

@article {pmid42907460,
year = {2026},
author = {Khatib, L and Oles, R and Hernández, AR and Myers, T and Zhao, J and Kumar, M and Laroya, A and Tolosa-Enguis, V and Matsunami, N and Suzuki, D and Chiba, N and Gilbert, KE and Das, P and Sanders, JG and Patel, L and Litwin, N and Nowinski, B and Birmingham, A and Farmer, S and Brennan, C and Bryant, M and Tribelhorn, C and Sanders-Bodai, K and Cowart, C and Nizet, O and Diaz, EA and Veiga, P and Shetty, SA and Knol, J and Lay, C and Koutnikova, H and Chaumont, S and Tap, J and Cotillard, A and Derrien, M and Laiola, M and González, A and Tovar, AR and Torres, N and Sanz, Y and Yamada, T and McDonald, D and Song, SJ and Bartko, A and Knight, R},
title = {Five-country analysis of geographic and dietary drivers of gut microbiome composition and genomic variation.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42907460},
issn = {2041-1723},
support = {T32 GM154642/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Mexico ; *Diet ; *Gastrointestinal Microbiome/genetics ; United States ; Japan ; Spain ; United Kingdom ; Metagenomics ; Geography ; Genetic Variation ; Female ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Male ; },
abstract = {Human diet and lifestyle vary widely across cultures, shaping global diversity in gut microbiome composition and function. However, comparable cross-population studies have been limited by methodological heterogeneity. The Human Diets and Microbiome Initiative (THDMI) integrates standardized recruitment, dietary assessment, and shotgun metagenomics across 1,976 participants from the United States, United Kingdom, Spain, Mexico, and Japan to disentangle biological from technical variation. We observed pronounced geographic differences in nutrient intake, food consumption, and microbial composition, with both shared and country-specific features linked to diet. Sparse canonical correlation and machine-learning analyses revealed that microbiome-diet associations were largely population-specific, with limited cross-country generalization. Strain-level analyses further uncovered significant genomic differentiation of gut microbes, consistent with localized dietary and ecological differences. Together, these results show that while core microbial responses to healthy eating exist, the structure and function of the human gut microbiome varies strongly with culture, geography, and long-term dietary practices.},
}

Humans
Mexico
*Diet
*Gastrointestinal Microbiome/genetics
United States
Japan
Spain
United Kingdom
Metagenomics
Geography
Genetic Variation
Female
Bacteria/classification/genetics/isolation & purification
Metagenome
Male

@article {pmid42907919,
year = {2026},
author = {Danthanarayana, N and O'Dwyer, J and Goi, J and Latimore, S and Stevens, V and Pal, M and McSharry, BP and Hernandez-Jover, M and Pomat, W and Karl, S and Roby, JA and Forwood, JK and Neave, MJ and Williams, DT},
title = {Diversity of insect-specific viruses in Culex mosquitoes from Papua New Guinea.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {42907919},
issn = {1743-422X},
mesh = {Animals ; *Culex/virology ; Papua New Guinea ; Genome, Viral ; Female ; Phylogeny ; *Insect Viruses/genetics/classification/isolation & purification ; Virome ; Metagenomics ; Biodiversity ; *Mosquito Vectors/virology ; Genetic Variation ; Metagenome ; RNA Viruses/genetics/classification/isolation & purification ; },
abstract = {Insect-specific viruses (ISVs) are integral components of mosquito viromes, influencing virus evolution, vector competence, and arbovirus ecology. Papua New Guinea (PNG) is a region of exceptional biodiversity, yet ISVs in local mosquito populations remain poorly characterized. Here, we present the first comprehensive metagenomic survey of ISVs in Culex mosquitoes collected across five provinces of PNG between 2019 and 2021. Using unbiased shotgun metagenomic sequencing, 13,871 female Culex mosquitoes representing five species were analyzed across 86 samples. Approximately 1.6 billion paired-end reads were generated, yielding ∼20 million viral read pairs. Overall, 231 viral species representing 38 viral families were detected. Of these, 120 were ISV species spanning 25 viral families, and ISVs accounted for 93.8% of species-assigned viral reads, with RNA viruses predominating. The most abundant families included Partitiviridae, Birnaviridae, Rhabdoviridae, and Iflaviridae. Approximately 40% of viral reads corresponded to viruses that are not currently assigned to recognized ICTV families. More than 150 complete viral genomes or genome segments were recovered, including divergent sequences that share <90% amino acid identity with known references. Phylogenetic analyses revealed several divergent viral lineages across major ISV groups. Within the Partitiviridae, previously unrecognized RNA-dependent RNA polymerase (RdRP)-capsid pairings enabled reconstruction of complete genome architectures for Broome partiti-like virus 1 and Sonnbo virus for the first time, together with additional divergent partitivirus lineages. Cambodia Culex birnavirus sequences from PNG, clustered within the known lineage but formed a distinct regional clade. Rhabdovirus analyses identified host-restricted lineages, including Culex tritaeniorhynchus rhabdovirus-like sequences confined to Culex annulirostris. Within the Iflaviridae, several viruses were detected for the first time in PNG. Hubei virga-like virus 2 was the most abundant ISV detected and formed a PNG-specific clade, suggesting local diversification. ISVs were detected in both blood-fed and unfed mosquitoes, indicating that they are stable constituents of the mosquito virome. Multiple viral species from the same family were detected within pooled samples, consistent with either co-infection of individual mosquitoes or heterogeneous infections among pooled individuals. Overall, this study reveals a diverse ISV landscape in PNG Culex mosquitoes, expanding the known geographic range and genetic diversity of multiple viral groups and providing a baseline for future investigations into ISV ecology and evolution in the Indo-Pacific region and mosquito-virus interactions globally.},
}

Animals
*Culex/virology
Papua New Guinea
Genome, Viral
Female
Phylogeny
*Insect Viruses/genetics/classification/isolation & purification
Virome
Metagenomics
Biodiversity
*Mosquito Vectors/virology
Genetic Variation
Metagenome
RNA Viruses/genetics/classification/isolation & purification

@article {pmid42908401,
year = {2026},
author = {Alekhin, D and Alon, M and Sidi, T and Mazeh, SP and Carmi, G and Finkel, OM and Erez, A},
title = {Fast and accurate taxonomic domain assignment of short metagenomic reads using BBERT.},
journal = {Nucleic acids research},
volume = {54},
number = {19},
pages = {},
pmid = {42908401},
issn = {1362-4962},
support = {1001577560//Israel Ministry of Science and Technology/ ; 101077278/ERC_/European Research Council/International ; },
mesh = {*Metagenomics/methods ; *Metagenome ; Soil Microbiology ; Bacteria/classification/genetics ; Shotgun Sequencing ; *Software ; Algorithms ; },
abstract = {Shotgun metagenomes from complex environments such as soil uncover vast biodiversity. Yet most short reads produced by shotgun sequencing cannot be taxonomically or functionally annotated, as they lack a sufficiently comprehensive reference, obscuring the true structure and function of microbial communities. We introduce BBERT, a nucleotide large language model optimized for short reads. Testing on a large cohort of soil metagenomes, we found that BBERT identifies bacterial sequence syntax without relying on reference databases, enabling accurate assignment of taxonomic domain, coding potential, and reading frame directly from reads as short as 100 bp. BBERT is small and fast enough to analyze metagenomes using a modest GPU and can be used to convert short metagenomic reads directly to bacterial amino acid sequences for downstream applications. BBERT also improves de novo metagenomic assembly, reducing mismatches and gaps while accelerating runtime. Using metagenomes from wild legume nodules, we demonstrate that BBERT filtering improves bin quality while significantly accelerating de novo assembly. By providing fast, reference-free classification of short reads, BBERT unlocks large metagenomic archives for more accurate ecological and evolutionary analyses.},
}

*Metagenomics/methods
*Metagenome
Soil Microbiology
Bacteria/classification/genetics
Shotgun Sequencing
*Software
Algorithms

@article {pmid42912803,
year = {2026},
author = {Jiang, H and Peng, Y and Lam, B and Yang, K and Lin, Y and Mak, JWY and Tse, YK and Chan, FKL and Xu, Z and Ng, SC},
title = {Gut virome remodeling after fecal microbiota transplantation is associated with virus-bacteria co-variation and metabolic response in obesity and type 2 diabetes.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2746820},
doi = {10.1080/19490976.2026.2746820},
pmid = {42912803},
issn = {1949-0984},
mesh = {Humans ; *Diabetes Mellitus, Type 2/therapy/metabolism/microbiology/virology ; *Fecal Microbiota Transplantation ; *Obesity/therapy/metabolism/microbiology/virology ; *Virome ; Feces/microbiology/virology ; *Bacteria/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; *Viruses/classification/genetics/isolation & purification ; },
abstract = {Fecal microbiota transplantation (FMT) modifies gut bacterial composition and improves metabolic outcomes in subjects with obesity and type 2 diabetes (ObT2), but bacterial changes alone do not fully explain the heterogeneity in clinical response. We performed virus-like particle (VLP)-enriched metagenomic sequencing coupled with bulk-DNA metagenomic sequencing on longitudinal fecal samples from a randomized controlled FMT trial in ObT2. Using random forest classification, post-FMT virome changes showed accuracy comparable to bacteriome changes (84.8% vs 81.4%) in distinguishing LDL responders from non-responders. Donor-derived viral contig engraftment was detected in 64.7% (11/17) of recipients receiving FMT alone and 58.8% (10/17) receiving FMT with lifestyle intervention (LSI), versus 5.6% (1/18) in the sham with LSI group. FMT was associated with increased virome diversity, compositional shifts toward the donor virome, and coordinated virus-bacteria associations, with most responsive viral contigs classified as Caudoviricetes. FMT-responsive viral contigs that were shared between the two FMT groups were predicted to infect Roseburia and Bifidobacterium, while contigs associated with clinical responses were predicted to infect Escherichia, Roseburia, Blautia, and Enterococcus. These findings suggest that the gut virome is a complementary ecological component associated with FMT responses and metabolic outcomes in ObT2.},
}

Humans
*Diabetes Mellitus, Type 2/therapy/metabolism/microbiology/virology
*Fecal Microbiota Transplantation
*Obesity/therapy/metabolism/microbiology/virology
*Virome
Feces/microbiology/virology
*Bacteria/genetics/classification/isolation & purification
*Gastrointestinal Microbiome
*Viruses/classification/genetics/isolation & purification

@article {pmid42708586,
year = {2026},
author = {Solanki, R and Wiszniak, E and Yi, L and Cabria, G and Strous, M and Davila Aleman, FD},
title = {Genome mining of alkaliphilic cyanobacterial consortia: identification of biosynthetic gene clusters in Sodalinema and associated heterotrophs.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {10},
pages = {e0078026},
pmid = {42708586},
issn = {1098-5336},
support = {CRC-2020-00257//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Multigene Family ; *Lakes/microbiology ; *Cyanobacteria/genetics/metabolism/classification ; Phylogeny ; *Genome, Bacterial ; *Microbial Consortia ; Biosynthetic Pathways/genetics ; Hydrogen-Ion Concentration ; },
abstract = {Alkaline soda lakes are high-pH environments that host specialized microbial communities with potential for biotechnology and natural product discovery. We characterized three Sodalinema-dominated cyanobacterial consortia enriched from Canadian soda lakes over 510 days. Using hybrid metagenomic sequencing and metatranscriptomics across pH, alkalinity, and temperature gradients, we reconstructed high-quality metagenome-assembled genomes and assessed functional activity. All consortia converged toward cyanobacteria dominance and exhibited temperature optima between 21°C and 30°C. Phylogenetic analysis placed Sodalinema genomes within a distinct clade affiliated with Candidatus Sodalinema alkaliphilum. Genomic analysis indicated complete biosynthetic pathways for vitamin B5, vitamin B7, and the molybdenum cofactor, but incomplete pathways for vitamins B1, B9, and B12, consistent with patterns observed in Sodalinema yuhuli. Metatranscriptomic profiles showed increased expression of genes involved in phycocyanin and carotenoid biosynthesis at pH 10.2 relative to pH 8.5. Biosynthetic gene cluster analysis revealed that most secondary metabolic potential resided in heterotrophic community members. Roseinatronobacter encoded pathways for N-acyl homoserine lactones, osmoprotectants, betalactones, and prodigiosin, while Alkalimonas, Wenzhouxiangella, and members of the Kiloniellales encoded clusters for lanthipeptides, cyclodipeptides, hydrogen cyanide, and pyrroloquinoline quinone. These findings indicate functional partitioning within the consortia and highlight the contribution of heterotrophs to secondary metabolism.IMPORTANCEAlkaline soda lakes contain microbial communities adapted to high pH that remain underexplored for biotechnology. This study focuses on Sodalinema, a filamentous cyanobacterium that dominates enriched consortia from Canadian soda lakes, and its associated heterotrophic partners. We show that while Sodalinema drives primary productivity, heterotrophic bacteria encode most of the pathways for antimicrobial and signaling compounds. These interactions may support community stability and defense against competing microorganisms. By linking genomic potential with gene expression, this work identifies alkaline cyanobacterial consortia as a source of bioactive compounds and provides a framework for exploring extremophilic microbial communities for natural product discovery.},
}

*Multigene Family
*Lakes/microbiology
*Cyanobacteria/genetics/metabolism/classification
Phylogeny
*Genome, Bacterial
*Microbial Consortia
Biosynthetic Pathways/genetics
Hydrogen-Ion Concentration

@article {pmid42726488,
year = {2026},
author = {Tang, L-Y and Zhang, H and Zhao, J-X and Gao, Y-Q and Zhang, X and Xie, S-C and Zheng, Z and Zhu, X-Q and Zhang, X-X and Xia, C and Liu, R and Ma, H},
title = {Toxoplasma gondii infection disrupts secondary bile acid transformation in feline gut microbiota.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {10},
pages = {e0067426},
pmid = {42726488},
issn = {1098-5336},
support = {32172887//National Natural Science Foundation of China/ ; 2023YFF0724603//National Key Research and Development Program of China/ ; U2202201//National Natural Science Foundation of China-Yunnan Joint Fund/ ; 2021XG001//Special Research Fund of Shanxi Agricultural University for High-level Talents/ ; ZR2025MS501//Shandong Provincial Natural Science Foundation/ ; },
mesh = {Animals ; Cats ; *Bile Acids and Salts/metabolism ; *Toxoplasmosis, Animal/microbiology/metabolism/parasitology ; *Toxoplasma/physiology ; *Gastrointestinal Microbiome ; Bacteria/metabolism/genetics/classification/isolation & purification ; *Cat Diseases/parasitology/microbiology/metabolism ; },
abstract = {UNLABELLED: Bile acid (BA) transformation relies on gut microbiota and is vulnerable to Toxoplasma gondii infection, yet feline microbial BA-transforming capacity upon toxoplasmosis remains unclear. Here, we constructed a catalog of 2,474 nonredundant feline gut microbial genomes and integrated serum metabolomic data to verify BA transformation alterations. The results revealed that the feline gut microbiome harbored widespread genetic potential for BA transformation but lacked a complete 7α-dehydroxylation pathway due to the absence of the key gene baiE. The BA transformation-related genomes (2,045 in total) were predominantly from the phyla Bacillota_A and Actinomycetota, among which only 37 encoded baiB, all belonging to Bacillota_A. The distribution of BA transformation-related genes varied across intestinal regions: genes encoding 7α-HSDH were primarily enriched in the small intestine, whereas genes encoding 3α-HSDH, baiCD, and baiH were more abundant in the large intestine. Additionally, the abundance of genes encoding BSH and 3α-HSDH increased significantly in the small intestine on day 3 post-infection, accompanied by increases in the phylum Bacillota_C and genera such as Blautia_A, Enterococcus_E, and Ligilactobacillus. Serum metabolomics revealed a significant increase in cholesterol levels post-infection, supporting the impact of T. gondii infection on intestinal BA transformation. These findings illustrated that the feline gut microbiota played an important role in BA transformation and that T. gondii infection disrupted the microbial potential for secondary BA transformation. This study provided new insights into gut microbiota-associated metabolic perturbations during feline toxoplasmosis.

IMPORTANCE: Bile acid (BA) transformation plays a critical role in host metabolism and immune regulation. Although studies on BA transformation are increasing, the capacity for BA transformation within the feline gut microbiota and the impact of Toxoplasma gondii infection on this capacity remain unclear. To bridge this gap, we constructed a catalog of 2,474 nonredundant feline gut microbial genomes and integrated serum metabolomic data to verify BA transformation alterations. Our findings revealed that the feline gut microbiome lacked a complete 7α-dehydroxylation pathway, and the specific functions involved in BA transformation may differ between the small and large intestines. Furthermore, integrated metagenomic and serum metabolomic analyses suggested that T. gondii infection disrupted BA transformation capacity in the small intestine. This study provided new insights into gut microbiota-associated metabolic perturbations during feline toxoplasmosis.},
}

Animals
Cats
*Bile Acids and Salts/metabolism
*Toxoplasmosis, Animal/microbiology/metabolism/parasitology
*Toxoplasma/physiology
*Gastrointestinal Microbiome
Bacteria/metabolism/genetics/classification/isolation & purification
*Cat Diseases/parasitology/microbiology/metabolism

@article {pmid42731191,
year = {2026},
author = {Yang, MT and Bai, T and Zhao, JX and Zhang, M and Xie, SC and Ma, H and Chen, XT and Gao, YQ and Tang, LY and Zhu, XQ and Elsheikha, HM and Liu, R and Zhang, XX},
title = {Interkingdom remodeling of the intestinal bacteriome and virome during Toxoplasma gondii infection in rats.},
journal = {Veterinary parasitology},
volume = {348},
number = {},
pages = {110925},
doi = {10.1016/j.vetpar.2026.110925},
pmid = {42731191},
issn = {1873-2550},
mesh = {Animals ; *Toxoplasmosis, Animal/microbiology/virology/parasitology ; *Gastrointestinal Microbiome ; *Virome ; Toxoplasma/physiology ; Rats ; Rats, Sprague-Dawley ; Bacteria/classification/genetics ; Male ; Intestines/microbiology/virology ; Metagenome ; },
abstract = {Toxoplasma gondii infection is associated with intestinal microbiome disruption, but its effects on genome-resolved bacterial populations, the gut virome, and bacteriome-virome relationships remain poorly understood. Using previously generated shotgun metagenomic datasets from 36 intestinal samples collected from 18 Sprague-Dawley rats across control, acute, and chronic infection groups, we reconstructed 294 quality-filtered, non-redundant bacterial metagenome-assembled genomes (MAGs) and identified 899 medium-to-high-quality viral operational taxonomic units (vOTUs) from assembled metagenomic contigs. Infection was associated with reduced bacterial richness in the small intestine during both acute and chronic stages and lower Shannon diversity during chronic infection. In contrast, large-intestinal α-diversity remained stable despite significant compositional reorganization. Taxonomic changes included increased Lactobacillus intestinalis, Limosilactobacillus reuteri, and Prevotella sp900547005, together with decreased Rothia sp002492045 and Akkermansia muciniphila. Functional profiling revealed region- and stage-specific changes in predicted bacterial metabolic potential, including reduced energy-related pathways and carbohydrate-active enzyme abundance. The virome also showed significant compositional changes in both intestinal regions. Quimbyviridae and Podoviridae_crAss-like viruses decreased in the small intestine during chronic infection, while Quimbyviridae, Flandersviridae, and Podoviridae_crAss-like viruses showed stage-specific decreases in the large intestine. Predicted bacterial hosts were assigned to 48.39% of vOTUs, with Lachnospiraceae and Ruminococcaceae being the most frequently linked families. Trans-kingdom networks further revealed region-specific positive and negative abundance correlations between bacterial and viral taxa. These findings extend previous microbiota-metabolome observations by integrating genome-resolved bacteriome analysis with contig-based virome profiling, providing a foundation for future mechanistic studies of toxoplasmosis-associated microbiome remodeling.},
}

Animals
*Toxoplasmosis, Animal/microbiology/virology/parasitology
*Gastrointestinal Microbiome
*Virome
Toxoplasma/physiology
Rats
Rats, Sprague-Dawley
Bacteria/classification/genetics
Male
Intestines/microbiology/virology
Metagenome

@article {pmid42753294,
year = {2026},
author = {Saleh, ZH and El Enbaawy, MI and Kamal, MA and Mahmoud, H and Hassan, M},
title = {Heat stress, respiratory dysbiosis, and poultry pathobiome: A comprehensive review of chronic respiratory disease in chickens.},
journal = {Veterinary microbiology},
volume = {322},
number = {},
pages = {111225},
doi = {10.1016/j.vetmic.2026.111225},
pmid = {42753294},
issn = {1873-2542},
mesh = {Animals ; *Chickens/microbiology ; *Poultry Diseases/microbiology ; *Dysbiosis/veterinary/microbiology ; Microbiota ; Respiratory System/microbiology ; Chronic Disease ; *Heat-Shock Response ; *Respiratory Tract Diseases/veterinary/microbiology ; Mycoplasma gallisepticum ; Climate Change ; },
abstract = {The poultry respiratory microbiome is increasingly recognized as a critical determinant of poultry health, mucosal immunity, and host resistance to opportunistic pathogens. Chronic Respiratory Disease (CRD) exerts a severe economic toll on the global broiler industry. While conventionally attributed to specific etiological agents such as Mycoplasma gallisepticum, disease progression is fundamentally tied to broad ecological dysbiosis within the respiratory tract. This comprehensive review synthesizes current knowledge on the functional roles and compositional dynamics of the poultry respiratory microbiome in both healthy and diseased states. Notably, we acknowledge the emerging threat of climate change, elucidating how heat stress physically and immunologically disrupts the respiratory mucosal microenvironment, acting as a primary catalyst for microbiome destabilization and CRD susceptibility. By shifting the paradigm from a single-pathogen model to a comprehensive pathobiome perspective, we detail the microbial shifts that characterize CRD. Furthermore, because investigating this low-biomass environment presents unique analytical challenges, we critically evaluate current technical methodologies. We address critical bottlenecks in sample collection, DNA extraction biases, and the comparative efficacy of 16S rRNA amplicon versus shotgun metagenomic sequencing. Ultimately, this synthesis provides a foundational framework for optimizing diagnostic methodologies and developing microbiome-targeted interventions -such as next-generation probiotics- to mitigate CRD in an era of escalating environmental stressors.},
}

Animals
*Chickens/microbiology
*Poultry Diseases/microbiology
*Dysbiosis/veterinary/microbiology
Microbiota
Respiratory System/microbiology
Chronic Disease
*Heat-Shock Response
*Respiratory Tract Diseases/veterinary/microbiology
Mycoplasma gallisepticum
Climate Change

@article {pmid42765918,
year = {2026},
author = {Gregory, CL and Radja, K and Haak, DC and Bradford, EL and Fell, RD and Walke, JB and Belden, LK},
title = {A metagenomic survey reveals widespread antibiotic resistance genes in honey bee (Apis mellifera) gut bacteria across the United States.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {10},
pages = {e0075526},
pmid = {42765918},
issn = {1098-5336},
support = {1817717//Division of Molecular and Cellular Biosciences/ ; 1817736//Division of Molecular and Cellular Biosciences/ ; },
mesh = {Animals ; Bees/microbiology ; *Bacteria/genetics/drug effects/isolation & purification/classification ; *Anti-Bacterial Agents/pharmacology ; Metagenomics ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Bacterial/genetics ; *Genes, Bacterial ; United States ; Virginia ; },
abstract = {Antibiotic use has contributed to antibiotic resistance genes (ARGs) accumulating in many environments, including host-associated microbiomes. Managed honey bee gut bacteria may accumulate ARGs, as honey bees are sometimes treated with antibiotics and often live in agricultural landscapes contaminated with antibiotics. We describe the occurrence and distribution of ARGs in honey bee bacterial gut symbionts from 13 apiaries in a transect across the USA from Washington to Virginia. Using metagenomic sequencing, we detected 55 unique ARGs conferring resistance to 14 classes of antibiotics. Of these, 11 ARGs encoded multidrug resistance. ARGs varied among sites, and ARG composition in hives shifted across the transect. Among honey bee gut bacterial genera, ARG occurrence varied, with Gilliamella and Frischella containing the highest proportions of ARGs despite their low relative abundance in the gut community, suggesting specific genera may serve as ARG reservoirs. As tetracycline is the most used antibiotic in beekeeping, we compared the frequency and abundance of tetracycline resistance genes across apiaries. All hives contained tetracycline resistance genes, with tetB and tetM present at all apiaries. Based on qPCR, tetB and tetM abundance varied significantly among apiaries. TetB was higher overall and declined in abundance from Washington to Virginia. We demonstrate that honey bee gut bacteria possess a diversity of ARGs, not all of which are consistent with antibiotic use in beekeeping, ARG frequency varies among bacterial genera in the honey bee gut, and certain ARGs are associated with hive geographic location.IMPORTANCEThe spread of antibiotic resistance genes (ARGs) to bacterial pathogens is a critical issue facing global health. Gut bacterial symbionts of managed honey bees make good bioindicators for ARGs because honey bees interact with potential environmental reservoirs of ARGs and are broadly distributed across the USA, including in both urban and rural environments. Based on our transect across the USA, ARGs were diverse and widely distributed among honey bee gut symbionts, although certain bacterial genera had a higher propensity for accumulating ARGs. Tetracycline resistance genes were most common, and varied in occurrence and abundance across the transect. The abundance of tetB, in particular, increased from east to west along the sampled transect. These large-scale patterns of ARG distribution within a widely dispersed host-associated microbiome system provide a foundation from which to examine the underlying factors driving differences in ARG occurrence and abundance.},
}

Animals
Bees/microbiology
*Bacteria/genetics/drug effects/isolation & purification/classification
*Anti-Bacterial Agents/pharmacology
Metagenomics
*Gastrointestinal Microbiome/genetics
*Drug Resistance, Bacterial/genetics
*Genes, Bacterial
United States
Virginia

@article {pmid42772353,
year = {2026},
author = {Yu, M and Hou, D and Wang, Z and Cui, Y and Wang, Y and Lou, Y and Han, G and Zhang, X and Gregorini, P},
title = {Precipitation gradients restructure rhizosphere and bulk soil microbial communities and potential nitrogen-cycling gene profiles in a desert steppe.},
journal = {Environmental research},
volume = {309},
number = {Pt 2},
pages = {125706},
doi = {10.1016/j.envres.2026.125706},
pmid = {42772353},
issn = {1096-0953},
mesh = {*Soil Microbiology ; *Rhizosphere ; Desert Climate ; *Nitrogen Cycle/genetics ; *Rain ; Soil/chemistry ; *Microbiota ; *Grassland ; Nitrogen/metabolism ; China ; Bacteria/genetics ; },
abstract = {Precipitation change can restructure microbially mediated soil nitrogen (N) cycling in water-limited grasslands, yet whether rhizosphere and bulk soils respond differently remains unclear. An in situ precipitation-gradient experiment in the desert steppe of Inner Mongolia combined soil physicochemical measurements, shotgun metagenomic sequencing, and piecewise structural equation modelling. Treatments included 50% reduced precipitation (W-50%), ambient precipitation (CK), 50% increased precipitation (W+50%), and 100% increased precipitation (W+100%). Soil water content was 37.2% higher under W+100% than under W-50%, whereas NO3[-]-N was 55.5% lower under W+50% than under W-50%. Microbial α-diversity showed a significant treatment × soil compartment interaction, whereas N-cycling functional α-diversity did not differ significantly among precipitation treatments or soil compartments. Precipitation treatment explained 48.35% of microbial community variation and 38.41% of N-cycling gene variation, while soil compartment explained 8.88% and 11.16%, respectively. From W-50% to W+50%, Sphingomonas increased from 2.93% to 13.66% in bulk soil and from 5.14% to 16.87% in rhizosphere soil. Relative to CK, W-50% increased the relative abundances of narZ and norB by 152.5% and 46.6% but decreased those of nrfC and gltD by 27.2% and 7.9%. W+50% increased the relative abundance of ureC by 23.1% while decreasing those of amoB, nirD, and nirK by 56.9%, 31.3%, and 17.8%, respectively. Compared with bulk soil, rhizosphere soil had higher relative abundances of nrfA, ureB, gltB, and nifD. Piecewise SEM explained 86.8% of the variation in N-cycling functional profiles, with microbial community composition showing the strongest association (β = 0.710, P < 0.001). These findings show that precipitation gradients primarily reorganize microbial community composition and potential N-cycling functions, with distinct N-cycling gene profiles between rhizosphere and bulk soils.},
}

*Soil Microbiology
*Rhizosphere
Desert Climate
*Nitrogen Cycle/genetics
*Rain
Soil/chemistry
*Microbiota
*Grassland
Nitrogen/metabolism
China
Bacteria/genetics