@article {pmid42593076,
year = {2026},
author = {Romano, ALR and Coutouné, N and Rego-Costa, A and Desai, MM and Carazzolle, MF and Gombert, AK},
title = {Dynamics of contaminant microbes in bioethanol production from sugarcane.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {53},
number = {},
pages = {},
doi = {10.1093/jimb/kuag020},
pmid = {42593076},
issn = {1476-5535},
support = {2018/04962-5//FAPESP/ ; 306190/2022-2//CNPq/ ; 130582/2021-2//CNPq/ ; },
mesh = {*Saccharum/microbiology/metabolism ; *Ethanol/metabolism ; Brazil ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fermentation ; *Biofuels ; Industrial Microbiology ; Metagenomics ; Microbiota ; },
abstract = {The dynamics and impact of microbial contaminants in industrial sugarcane bioethanol production in Brazil were investigated through a 2-year metagenomic study across two biorefineries. Shotgun metagenomic sequencing revealed that temporal shifts in the contaminant microbiome dynamics within production seasons were more pronounced than inter-annual or inter-mill variations. While Saccharomyces spp. dominated, bacterial communities, primarily within the Firmicutes phylum and dominated by the genera Lactobacillus, Limosilactobacillus, and Bacillus, exhibited dynamic changes. Correlation analyses with industrial process parameters revealed a complex interplay: lower Lactobacillus levels in one mill were associated with increased ethanol yield, whereas higher levels in another mill correlated with reduced yeast viability and increased flocculation. The presence of Limosilactobacillus was linked to decreased yeast viability, whereas Bacillus showed potential for inhibiting both Lactobacillus and Limosilactobacillus. These findings highlight the nuanced and species-specific impacts of bacterial contaminants on bioethanol production, underscoring the need for strain-level functional studies and targeted interventions to optimize fermentation efficiency and stability in industrial settings. One-Sentence Summary The dynamics of contaminant bacterial populations during fuel ethanol production from sugarcane was unrevealed in two biorefineries and in two consecutive production years using shotgun metagenomics.},
}

*Saccharum/microbiology/metabolism
*Ethanol/metabolism
Brazil
*Bacteria/classification/genetics/isolation & purification/metabolism
Fermentation
*Biofuels
Industrial Microbiology
Metagenomics
Microbiota

@article {pmid42610965,
year = {2026},
author = {Liu, ZT and Zhao, XD and Li, JQ and Li, SX and Tang, X and Zhang, SY},
title = {High molecular weight dissolved organic matter drives soil resistome proliferation by enhancing microbial competition and viral carbon metabolism.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag212},
pmid = {42610965},
issn = {1751-7370},
support = {JYB2025XDXM904//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; 22522603//National Natural Science Foundation of China/ ; 425B2046//National Natural Science Foundation of China/ ; 22522603//National Natural Science Foundation of China/ ; 425B2046//National Natural Science Foundation of China/ ; JYB2025XDXM904//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism ; Molecular Weight ; *Soil/chemistry ; *Dissolved Organic Matter/chemistry/metabolism/analysis ; *Bacteria/genetics/metabolism ; China ; *Drug Resistance, Microbial/genetics ; Metagenomics ; *Microbiota ; },
abstract = {Soil organic carbon is a key determinant of microbial community structure and function, yet the role of dissolved organic matter (DOM) bioavailability in shaping the soil antibiotic resistome remains poorly understood. Here, we combined previous continental-scale field sampling across 18 provinces in China (n = 141) with additional microcosm experiments to investigate how DOM molecular weight influences soil antibiotic resistance gene (ARG) proliferation. Using Fourier transform ion cyclotron resonance mass spectrometry and metagenomic analyses, we found that soils enriched in high molecular weight (HMW) DOM harbored significantly greater ARG abundance and diversity compared to low molecular weight DOM soils. HMW DOM intensified microbial competition, as evidenced by a higher proportion of negative correlations in the co-occurrence network and lower niche breadth, favoring the enrichment of co-hosts that simultaneously carried ARGs, carbon metabolism genes, and biosynthetic gene clusters for antimicrobial compounds. Microcosm experiments confirmed that HMW DOM (lignin) addition significantly increased ARG transcript abundance (2.4-fold) and co-host relative abundance (2.3-fold), accompanied by a concurrent increase in transcribed viral auxiliary metabolic genes (2.5-fold) involved in complex carbon degradation. Structural equation modeling revealed that HMW DOM abundance and chemodiversity exerted the strongest positive effects on ARG abundance, primarily by shaping microbial community competition and metabolic potential. Collectively, our findings establish DOM bioavailability, particularly its molecular weight, as a critical yet previously overlooked driver of soil resistome development, challenging the conventional focus on total carbon content and highlighting the potential for molecular-level organic matter management to mitigate the spread of ARGs.},
}

*Soil Microbiology
*Carbon/metabolism
Molecular Weight
*Soil/chemistry
*Dissolved Organic Matter/chemistry/metabolism/analysis
*Bacteria/genetics/metabolism
China
*Drug Resistance, Microbial/genetics
Metagenomics
*Microbiota

@article {pmid42786178,
year = {2026},
author = {Zou, X and Ni, Y and Zhang, Q and Li, S and Zhang, Y and Wang, C and Yao, X and Chang, K and Lu, B and Guo, R and Xing, G and Yu, H and Yin, J and Gan, N and Wang, Z and Yan, Q and Cao, B},
title = {OAPGC: a high-quality oral and airway prokaryotic genome catalog for enhanced ecological resolution and disease inference.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42786178},
issn = {2055-5008},
support = {2025-NHLHCRF-JBGS-B-WZ-06//National High Level Hospital Clinical Research Funding/ ; BRWEP2024W114060104//Beijing Research Ward Excellence Program/ ; XLYC2403207//Young Top Talents Program of the Liaoning Revitalization Talents Initiative/ ; ZRJY2023-GG24//China-Japan Friendship Hospital elite program/ ; 2024RJ018//Dalian Outstanding Young Scientific and Technological Talents Program/ ; 2022YFA1304303//National Key R&D Program of China/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Mouth/microbiology ; Metagenome ; *Respiratory System/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Genome, Bacterial ; Metagenomics/methods ; Phylogeny ; Case-Control Studies ; },
abstract = {The human oral cavity and airway harbor diverse microbiomes that are implicated in oral and respiratory diseases, yet comprehensive genomic catalogs remain scarce. Here, we present the Oral and Airway Prokaryotic Genome Catalog (OAPGC), comprising 99,215 high-quality, non-redundant genomes reconstructed from public and newly sequenced metagenomes and isolates. OAPGC was clustered into 2474 species using refined, phylum-specific nucleotide identity thresholds, and 29.5% of them are uncultured. Habitat-driven divergence was evident across 15 oral and 8 airway sites, with airway microbiomes showing greater inter-individual variability and enriched antibiotic resistance genes. Across 25 case-control comparisons covering 12 diseases, disease status explained significant community shifts in 19 datasets, with classifiers achieving an AUC > 0.70 in 20 datasets. Shared microbial signatures were identified for diseases such as periodontitis and pneumonia, including uncultured taxa. We also detected 12.3% of OAPGC species in the gut, whose enrichment was linked to multiple diseases and improved cross-cohort classification performance. OAPGC establishes a foundational, disease-relevant genomic framework for oral and airway microbiome studies.},
}

Humans
*Microbiota/genetics
*Mouth/microbiology
Metagenome
*Respiratory System/microbiology
*Bacteria/classification/genetics/isolation & purification
*Genome, Bacterial
Metagenomics/methods
Phylogeny
Case-Control Studies

@article {pmid42789300,
year = {2026},
author = {Li, M and Mao, J and Liu, S and Yu, H and Qin, H and Liu, X and Tu, R and Chen, S and Liu, Z and Zhang, S and Mao, J},
title = {Ethanol exposure is associated with spatial and taxon-specific gut microbiota remodeling characterized by ecological adaptation rather than broad activation of microbial ethanol metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734657},
doi = {10.1080/19490976.2026.2734657},
pmid = {42789300},
issn = {1949-0984},
mesh = {Animals ; *Ethanol/metabolism ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Mice ; *Bacteria/classification/genetics/metabolism/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Adaptation, Physiological ; Acetaldehyde/metabolism ; Metagenomics ; },
abstract = {Alcohol-associated diseases are linked to gut microbiota disruption, but how ethanol intake is associated with microbial functional remodeling remains unclear. Here, using male C57BL/6J mice, we integrated spatiotemporal quantification of ethanol and acetaldehyde across the gastrointestinal tract with 16S rRNA sequencing, metagenomics, metaproteomics, and metabolomics. Our results showed that small-intestinal communities were enriched in taxa and functions related to bile acid tolerance/utilization, whereas cecal communities exhibited pronounced remodeling of multiple core functions associated with ecological adaptation. Although the abundance of several ethanol metabolism-related genes increased, this genetic potential was not broadly translated into detectable protein-level activation. Ethanol metabolism-related proteins were mainly derived from Lachnospiraceae, whose metabolic activity was suppressed. In contrast, Muribaculaceae, Desulfovibrionaceae, and Barnesiellaceae gained functional advantages in substrate acquisition, energy metabolism, oxidative stress defense, and proteostasis. These findings provide a region-resolved functional map indicating that ethanol-associated microbiota remodeling is characterized by ecological adaptation, rather than uniform activation of direct microbial ethanol metabolism.},
}

Animals
*Ethanol/metabolism
Male
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Mice
*Bacteria/classification/genetics/metabolism/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
Adaptation, Physiological
Acetaldehyde/metabolism
Metagenomics

@article {pmid42792947,
year = {2026},
author = {Du, Q and Xing, L and Zhu, C and Li, P},
title = {Gut Microbiota and Metabolic Pathway Signatures for Inflammatory Bowel Disease Identified via Subject-Stratified Random Forest Based on the Longitudinal HMP2 Cohort.},
journal = {Genes},
volume = {17},
number = {9},
pages = {},
doi = {10.3390/genes17091053},
pmid = {42792947},
issn = {2073-4425},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Random Forest ; *Metabolic Networks and Pathways/genetics ; *Gastrointestinal Microbiome/genetics ; Longitudinal Studies ; Feces/microbiology ; Female ; Machine Learning ; },
abstract = {Background: Inflammatory bowel disease (IBD) is characterised by severe intestinal microbial dysbiosis. Most machine learning diagnostic models built on the longitudinal HMP2 cohort suffer serious data leakage from random sample-level cross-validation splitting, which leads to artificially inflated AUC values. Additionally, incomplete reporting of microbial preprocessing, random forest hyperparameters and multi-dimensional evaluation metrics reduces the reproducibility of existing research. Methods: We re-analysed the public HMP2 (IBDMDB) longitudinal metagenomic dataset containing 130 unique subjects (103 IBD/27 healthy controls) and 1627 longitudinal faecal samples. Raw 585 species were filtered by a minimum relative abundance of 1 × 10[-5] and sample prevalence ≥20%, retaining 89 taxa; all 1135 metabolic pathways were retained. CLR transformation was applied to compositional abundance data. We performed Wilcoxon differential testing with Benjamini-Hochberg FDR correction, alpha/beta diversity analysis, and three random forest models (filtered species, all FDR-significant pathways, strictly filtered pathways). Critical improvements included subject-ID-stratified 5-fold cross-validation repeated 5 times, within-fold training-set-only feature importance calculation, and class weighting to balance unbalanced IBD/control samples. PERMANOVA with subject stratification and PERMDISP dispersion test were implemented with 999 fixed-seed permutations. Results: All four alpha diversity indices were significantly lower in IBD patients (all p < 0.0001). Subject-stratified PERMANOVA showed disease status only explained 1.18% of total Bray-Curtis community variance (R[2] = 0.0118, p = 1); PERMDISP detected significant group dispersion heterogeneity (p = 0.027). We identified 63 differentially abundant species and 695 perturbed pathways at FDR < 0.05. Canonical butyrate producers Faecalibacterium prausnitzii and Roseburia hominis showed no significant inter-group differences. Bootstrap 1000-resampling AUC 95% CIs indicated moderate classification performance: species model (0.626-0.705, mean AUC = 0.665), all-significant-pathway model (0.645-0.712, mean AUC = 0.679), strict-pathway model (0.620-0.685, mean AUC = 0.654). Alistipes putredinis and peptidoglycan biosynthesis I were the top taxonomic and pathway biomarkers, respectively. Conclusions: This study established a leakage-free machine learning pipeline for longitudinal microbiome cohorts via subject-level cross-validation splitting. The moderate AUC values eliminate false high performance caused by sample leakage, and we provide reliable candidate microbial and metabolic biomarkers for IBD. Restricted by single-cohort internal validation and unadjusted medication confounders, these markers still require independent multi-centre external verification before clinical translation.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/metabolism/genetics
Random Forest
*Metabolic Networks and Pathways/genetics
*Gastrointestinal Microbiome/genetics
Longitudinal Studies
Feces/microbiology
Female
Machine Learning

@article {pmid42794458,
year = {2026},
author = {Carini, F and Sorce, A and Ciuppa, ME and David, S and Giammanco, M and Di Carlo, P and Evola, S and Tomasello, G and Mulè, G and Carollo, C},
title = {Gut, Oral, and Fungal Microbiota in Hypertension: A Multi-Compartment Systematic Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188029},
pmid = {42794458},
issn = {1422-0067},
mesh = {Humans ; *Hypertension/microbiology ; *Mouth/microbiology ; *Gastrointestinal Microbiome ; *Mycobiome ; *Microbiota ; *Fungi ; },
abstract = {The gut microbiota is an established modulator of blood pressure, but the oral bacteriome and the fungal mycobiome have been examined largely in isolation from it and from each other. No previous synthesis has evaluated all three compartments within one analytical framework, or treated sex and ethnicity as primary analytical axes rather than adjustment covariates. Systematic review reported according to PRISMA 2020 and, for the synthesis, the SWiM guideline. PubMed/MEDLINE, Embase, Scopus, and Web of Science were searched from inception to 30 June 2026. Observational human studies in adults reporting gut, oral, or fungal microbiota data stratified by blood pressure status were eligible, together with Mendelian randomisation studies and studies with a nested experimental causal component. Two reviewers screened and extracted independently, with a third resolving disagreement. Risk of bias was assessed with the Newcastle-Ottawa Scale and certainty of evidence with GRADE adapted for exposure-outcome questions. Increased abundance of the Ruminococcus gnavus group was the most convergent taxon-level finding, replicated in three independent populations on two continents, including one prospective multi-ethnic cohort with full adjustment and correction for multiple comparisons (OR 1.07, 95% CI 1.01-1.14 for incident hypertension). In the oral compartment, depletion of the nitrate-reducing commensal Neisseria subflava converged across a United States prospective cohort and an Italian case-control study using unrelated methods, and salivary nitric oxide was approximately three-fold lower in hypertensive subjects. Depletion of the short-chain fatty acid producers Faecalibacterium and Roseburia and enrichment of Klebsiella were convergent but geographically restricted. Mycobiome evidence was contradictory: two studies reported fungal dysbiosis, one of them already at the pre-hypertensive stage, while a cross-cohort metagenome-wide study on two independent cohorts from Beijing and Dalian (N = 159 hypertensive patients, 101 healthy controls) identified 61 gut bacterial species with consistent altered abundance across both cohorts while finding no replicable mycobiome signal. Recurring across compartments and kingdoms was the collapse of microbial co-correlation networks in hypertension, alongside a dissociation between null alpha diversity and significant beta diversity. Associations differed by ethnicity within a single multi-ethnic cohort and were generally stronger in women. Certainty of evidence, assessed per individual convergent finding, was very low for every taxon-level finding and low for salivary nitric oxide; these ratings concern the attribution of hypertension to specific organisms, not the existence of a microbiota-hypertension association, which is supported at community level in every compartment examined and by experimental transfer models. That the microbiota differs in hypertension is well supported; which organisms are responsible is not. The most reproducible signal is structural rather than taxonomic, and conventional differential-abundance analysis is not designed to detect it. No individual microbial taxon is currently ready to serve as a marker of hypertension or to inform clinical practice.},
}

Humans
*Hypertension/microbiology
*Mouth/microbiology
*Gastrointestinal Microbiome
*Mycobiome
*Microbiota
*Fungi

@article {pmid42794824,
year = {2026},
author = {Kim, M and Song, WH and Ju, HJ and Koh, YK and Kim, SJ and Lee, YB and Lee, M},
title = {Shotgun Metagenomic Characterization of Skin Microbiome Shifts in Human Scabies Before and After Scabicidal Treatment.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188397},
pmid = {42794824},
issn = {1422-0067},
mesh = {Humans ; *Scabies/drug therapy/microbiology ; *Skin Microbiome ; *Metagenomics/methods ; Male ; Female ; *Skin/microbiology ; Shotgun Sequencing ; Sarcoptes scabiei ; Metagenome ; Adult ; *Microbiota ; },
abstract = {Scabies, caused by Sarcoptes scabiei, is a globally prevalent ectoparasitic infestation associated with intense pruritus and secondary bacterial infection, yet the molecular composition of the skin microbiome during active infestation remains poorly characterized. We performed shotgun metagenomic sequencing of 41 skin samples collected from 18 patients at dry and moist anatomical sites before and after scabicidal treatment. In exploratory group-level comparisons, pretreatment moist-site samples had lower alpha diversity and higher bacterial and viral read-based burdens than post-treatment moist-site samples. Pretreatment dry and moist samples did not differ significantly in diversity, and Staphylococcus was the predominant genus. No genus- or species-level taxon or predicted pathway remained statistically significant after Benjamini-Hochberg false discovery rate correction at a threshold of 0.05. Nominal differences in predicted purine biosynthesis pathways were interpreted as exploratory observations. These findings provide a shotgun metagenomic characterization of the skin microbiome during active scabies and describe exploratory treatment-associated patterns that require confirmation in larger, paired longitudinal studies.},
}

Humans
*Scabies/drug therapy/microbiology
*Skin Microbiome
*Metagenomics/methods
Male
Female
*Skin/microbiology
Shotgun Sequencing
Sarcoptes scabiei
Metagenome
Adult
*Microbiota

@article {pmid42795487,
year = {2026},
author = {Che, M and Zhang, J and Kudelaiti, K and Zhang, J and Liusui, Y and Dong, Z},
title = {Effects of Co-Application of γ-Polyglutamic Acid and Chemical Fertilizer on Rhizosphere Microbial Community Structure and Function of Cotton at Different Growth Stages in an Arid Cotton Field.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14091905},
pmid = {42795487},
issn = {2076-2607},
support = {2024D01A82//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
abstract = {Long-term excessive nitrogen application in arid cotton fields increases nitrate leaching risk during fallow and disrupts rhizosphere microecology. To clarify the cross-growth-stage regulatory effects of the biostimulant γ-polyglutamic acid (γ-PGA) combined with chemical fertilizer on rhizosphere microbial communities, we compared chemical fertilizer alone (NK) and γ-PGA plus chemical fertilizer (GT) using rhizosphere soils collected at boll-setting (August) and fallow (October), with physicochemical measurements and metagenomic sequencing technology. At boll-setting, GT lowered pH by 0.74 units compared with NK and increased NH4[+]-N, NO3[-]-N, and TN by 339.3%, 491.4%, and 23.0%, respectively. By fallow, GT increased TOC by 70.6% and maintained NH4[+]-N at 18.38 mg/kg, while NK accumulated 66.85 mg/kg NO3[-]-N. GT buffered post-harvest fungal community disturbance (Shannon: GT 4.06 vs. NK 2.80) and shifted bacterial communities toward oligotrophic taxa and archaea toward ammonium-preferring taxa. A metagenomic LEfSe analysis showed that GT was enriched in functional genes related to [Q]: Secondary metabolite biosynthesis, transport and catabolism, [T]: Signal transduction mechanisms, and [V]: Defense mechanisms, indicating a shift from resource acquisition to conservative maintenance. Mantel tests revealed that microbial functional profiles showed the strongest association with NH4[+]-N (r = 0.828 in August, r = 0.883 in October, p < 0.001). Thus, γ-PGA with chemical fertilizer stabilizes fallow rhizosphere microbial communities, reduces nutrient leaching, and promotes carbon-nitrogen co-retention.},
}

@article {pmid42795606,
year = {2026},
author = {Méndez-Rodríguez, A and Ledesma, J and López-González, C and Zarza, H and López-Wilchis, R and Labiod, N and Cuesta, I and Casas, I and Echevarría, JE and Vázquez, A and Juste, J},
title = {Virome Diversity in Three Bat Species in Different Environments in Southern Spain.},
journal = {Microorganisms},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/microorganisms14092025},
pmid = {42795606},
issn = {2076-2607},
support = {PLEC2021-007968//NEXTHREAT/ ; //European Union NextGeneration EU/PRTR funds/ ; },
abstract = {Viruses represent a major component of global biodiversity and are integral to ecological and evolutionary processes shaping host populations and communities. Bats, with high species richness and ecological diversity, provide a system to examine how host traits and environmental context structure viral communities. Here, we characterize viral diversity from three bat species (Pipistrellus kuhlii, Cnephaeus isabellinus, and Nyctalus lasiopterus) using samples across two environments in southern Spain: a well-preserved Mediterranean forest (Sierras de Cazorla, Segura, and Las Villas Natural Park, CSVNP) and a human-modified wetland-agrosystem mosaic (Doñana National Park, DNP). Metagenomics detected 72 eukaryotic virus species, including viruses reported in mammals, insects, arachnids, and plants. Viral richness and composition varied among samples, bat species, and environments. Samples of P. kuhlii exhibited the highest richness, driven by insect-associated viruses. C. isabellinus showed a higher contribution of vertebrate-related viruses, whereas N. lasiopterus exhibited the lowest richness. CSVNP samples showed higher viral richness and more exclusive taxa, whereas DNP samples exhibited lower richness, with a greater contribution of arthropod-associated viruses, potentially reflecting prey communities. Despite this, diversity metrics were similar between environments, indicating structurally comparable communities composed of distinct taxa. Bat viromes appear to be associated with host ecology, trophic behavior, and environmental context.},
}

@article {pmid42796698,
year = {2026},
author = {Huang, J and Zhao, H and Wang, F and Zeng, B and Ma, Z and Wang, R and Yang, Y and Amier, M and Yilihaer, B and Lu, Y},
title = {Whole-Genome Sequencing and Intestinal Metagenome Sequencing Revealed the Carriage and Transmission of Salmonella enterica in Xinjiang, China.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {9},
pages = {},
doi = {10.3390/pathogens15090930},
pmid = {42796698},
issn = {2076-0817},
mesh = {*Salmonella enterica/genetics/isolation & purification/classification ; Humans ; China/epidemiology ; Whole Genome Sequencing ; *Salmonella Infections/transmission/microbiology/epidemiology ; *Metagenome ; Phylogeny ; *Gastrointestinal Microbiome ; Feces/microbiology ; Virulence Factors/genetics ; *Carrier State/microbiology/epidemiology ; Metagenomics ; Genome, Bacterial ; },
abstract = {Background:Salmonella enterica, a major foodborne pathogen, poses a severe global public health threat. However, data regarding its carriage characteristics, transmission patterns, and association with intestinal microbiota in healthy populations of Xinjiang, China, remain insufficient, limiting the formulation of targeted salmonellosis prevention and control strategies. Methods: In this study, 31 Salmonella enterica strains isolated from more than 2000 healthy individuals in Urumqi were subjected to whole-genome sequencing to analyze serovars, antimicrobial resistance (AMR) genes, and virulence genes. Meanwhile, metagenomic sequencing was performed on 50 fecal samples (culture negative) from 2000 healthy individuals to investigate intestinal microbiota structure, Salmonella enterica prevalence, and related microbial taxa. Results: The results showed that 60% of samples (30/50) were positive by the read-based criterion (≥1000 Salmonella-specific reads), while the assembly-verified criterion (≥1000 reads and contigs > 1 kb) confirmed Salmonella-specific sequences in 12% (6/50). Among the 31 culture-confirmed isolates, Salmonella Typhimurium and Salmonella Paratyphi B were the dominant serovars, together accounting for 60%. All isolates harbored core virulence genes for Type III secretion system and adhesion factors, with low AMR gene carriage and no multidrug-resistant strains. Phylogenetic analysis showed that Urumqi-derived isolates were distributed across multiple genomic clusters, suggesting active inter-regional circulation of S. enterica within the available dataset. Salmonella enterica carriage did not affect gut microbial α-diversity but altered community composition, with Escherichia coli, Shigella flexneri, and Klebsiella pneumoniae as key associated taxa. Conclusions: This study found that Urumqi-derived isolates are widely distributed across genomic clusters in Xinjiang, with a unique local transmission chain identified, though definitive source attribution requires further geographically balanced sampling. Salmonella enterica carriage exhibited ecological niche synergy with intestinal Enterobacteriaceae, but did not significantly affect gut microbial diversity.},
}

*Salmonella enterica/genetics/isolation & purification/classification
Humans
China/epidemiology
Whole Genome Sequencing
*Salmonella Infections/transmission/microbiology/epidemiology
*Metagenome
Phylogeny
*Gastrointestinal Microbiome
Feces/microbiology
Virulence Factors/genetics
*Carrier State/microbiology/epidemiology
Metagenomics
Genome, Bacterial

@article {pmid42797815,
year = {2026},
author = {Moreira, G and Silva, E and Mourão, J and Mesquita, JR},
title = {First European Identification of a Partial Tacheng Tick Virus 8-like Underscores the Hidden Burden of Tick-Borne Flavivirus-like Viruses.},
journal = {Viruses},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/v18090984},
pmid = {42797815},
issn = {1999-4915},
support = {2025.05151.BD//Fundação para a Ciência e Tecnologia/ ; },
mesh = {Animals ; Phylogeny ; Genome, Viral ; *Flavivirus/genetics/classification/isolation & purification ; Portugal ; Dermacentor/virology ; *Ticks/virology ; },
abstract = {Tick-associated viruses are an underexplored component of global viromes, and highly divergent RNA viruses often remain undetected due to low abundance and sequence divergence. Tacheng tick virus 8 (TcTV8) is a poorly characterized RNA flavivirus-like virus originally reported from Dermacentor-associated ticks in China, with few subsequent reports and no confirmed detections outside Asia. Here, we report the detection and partial genomic characterization of a TcTV8-like virus in ticks collected from Portugal. Sequence-independent (SISPA) nanopore sequencing of individual ticks recovered three partial fragments (~2.7 kb, ~14% of the reference genome; ~30% of the reference covered at ≥1×), which shared high amino-acid identity with the TcTV8 polyprotein, including a methyltransferase-region domain. Phylogenetic analysis placed the Portuguese sequence within the TcTV8 lineage. Read-level classification and coverage analysis further support the presence of this virus in the positive sample. These findings represent, to our knowledge, the first detection of a TcTV8-like virus in European ticks, extending its known geographic range beyond Asia. The detection of this cryptic viral lineage highlights the need for broader tick virome surveillance to better understand the diversity, evolution, and ecology of flavivirus-like viruses.},
}

Animals
Phylogeny
Genome, Viral
*Flavivirus/genetics/classification/isolation & purification
Portugal
Dermacentor/virology
*Ticks/virology

@article {pmid42797867,
year = {2026},
author = {Kushugulova, A and Kamzayeva, N and Kozhakhmetov, S and Vinogradova, E and Jarmukhanov, Z and Mukhanbetzhanov, N and Kovenskiy, A and Kossumov, A and Rakhmankulova, A and Ukybassova, T},
title = {Cervicovaginal Virome Restructuring Associated with HPV Status, Bacterial Dysbiosis, and Cervical Cytological Abnormalities.},
journal = {Viruses},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/v18091036},
pmid = {42797867},
issn = {1999-4915},
support = {BR24992853//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; Female ; *Human Papillomavirus Viruses/genetics/isolation & purification/classification ; *Cervix Uteri/virology/pathology/microbiology ; *Vagina/virology/microbiology ; *Papillomavirus Infections/virology ; *Dysbiosis/virology/microbiology ; *Virome ; Bacteria/classification/genetics ; Bacteriophages/genetics ; Microbiota ; Metagenomics ; Papillomaviridae/genetics ; },
abstract = {The cervicovaginal virome remains poorly characterized in relation to human papillomavirus (HPV) infection and bacterial community structure. We performed shotgun metagenomic sequencing of 311 cervicovaginal specimens from a Kazakhstani cohort spanning seven groups defined by HPV status and cervical cytology. Viral community composition differed according to HPV status, with increasing representation of the oncogenic Alphapapillomavirus 9 clade across more abnormal cytological categories. Predicted phage functional profiles also differed between NILM HPV-positive and NILM HPV-negative women. Integrase, excisionase, transcriptional repressor, anti-repressor Ant, and amidase annotations showed differential prevalence after false-discovery-rate correction. Auxiliary metabolic and host-interaction genes associated with nucleotide metabolism, DNA modification, anti-restriction functions, and toxin-antitoxin systems were also differentially represented. Stratification by bacterial community state type revealed contrasting predicted functional repertoires, with toxin-antitoxin-associated annotations enriched in Lactobacillus crispatus-dominated communities and anti-restriction-associated annotations enriched in Gardnerella vaginalis-dominated communities. These findings identify associations between HPV status, bacterial community structure, and cervicovaginal viral composition and predicted phage functions. Longitudinal and experimental studies are required to determine the directionality and biological activity of these associations.},
}

Humans
Female
*Human Papillomavirus Viruses/genetics/isolation & purification/classification
*Cervix Uteri/virology/pathology/microbiology
*Vagina/virology/microbiology
*Papillomavirus Infections/virology
*Dysbiosis/virology/microbiology
*Virome
Bacteria/classification/genetics
Bacteriophages/genetics
Microbiota
Metagenomics
Papillomaviridae/genetics

@article {pmid42798402,
year = {2026},
author = {Ahn, J and Kim, M and Min, SH and Bae, HG and Bae, JY and Kwon, J and Yi, H and Park, DH},
title = {Fecal microbiota transplantation from duodenal light stimulation-conditioned donors is associated with improved glucose tolerance and intestinal incretin-related remodeling in diabetic Goto-Kakizaki rats.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1900693},
pmid = {42798402},
issn = {2235-2988},
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; Rats ; *Diabetes Mellitus, Type 2/therapy/metabolism ; *Incretins/metabolism ; *Gastrointestinal Microbiome ; *Duodenum/microbiology ; Male ; Glucose Tolerance Test ; Disease Models, Animal ; Blood Glucose ; Feces/microbiology ; },
abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is a complex metabolic disorder characterized by impaired glucose homeostasis and β-cell dysfunction. Emerging evidence suggests that the gut microbiota-incretin axis may contribute to metabolic regulation. However, whether microbiota from duodenal light stimulation (DLS)-conditioned donors can influence metabolic phenotypes via fecal microbiota transplantation (FMT) remains unclear.

METHODS: We evaluated whether FMT from DLS-conditioned donors was associated with metabolic and intestinal changes in diabetic GK (Goto-Kakizaki) rats. Recipients received FMT from week -2 to week 0 and were then followed for 7 weeks after the final FMT dose. Metabolic phenotyping, intestinal histology, short-chain fatty acid (SCFA) profiling, and shotgun metagenomic profiling of bacterial and viral communities were performed.

RESULTS: FMT recipients showed within-group improvement in OGTT glucose profiles, without significant changes in fasting glucose levels. Total glucose AUC0-120 was significantly reduced within the FMT group in the within-group (period) comparison; however, the group × period interaction was not significant, indicating no statistically significant longitudinal between-group treatment effect. Early GLP-1 responses showed a modest increasing trend in FMT recipients, whereas total GLP-1 AUC0-120 was not significantly changed. HOMA-β (homeostatic model assessment of β-cell function) increased within the FMT group, and pancreatic insulin-positive area was greater in FMT recipients than in controls at the study endpoint. Intestinal remodeling was evident, including an increased villus:crypt ratio and increased colonic GLP-1-positive cells. FMT was associated with fecal bacteriome differences, including one FDR-significant taxon and several nominally associated taxa, such as Akkermansia muciniphila and Xylanibacter rodentium. No significant global shift in fecal virome composition was observed, although selected viral taxa showed nominal group-associated differences that did not remain significant after FDR correction. Exploratory network analysis suggested group-specific bacteriome-virome association patterns after FMT.

CONCLUSION: FMT from DLS-conditioned donors was associated with improved glucose tolerance, intestinal incretin-related remodeling, increased pancreatic insulin-positive area, and fecal bacteriome differences in diabetic GK rats based on within-group longitudinal changes for the glucose- and β-cell-related outcomes, for which the group × period interactions were not significant, whereas the histological and microbiome differences reflect cross-sectional between-group comparisons at the study endpoint. These findings support a hypothesis-generating link between donor-conditioned FMT, intestinal remodeling, and microbiome-associated metabolic regulation, while further studies are required to define DLS-specific and donor-derived effects.},
}

Animals
*Fecal Microbiota Transplantation/methods
Rats
*Diabetes Mellitus, Type 2/therapy/metabolism
*Incretins/metabolism
*Gastrointestinal Microbiome
*Duodenum/microbiology
Male
Glucose Tolerance Test
Disease Models, Animal
Blood Glucose
Feces/microbiology

@article {pmid42798947,
year = {2026},
author = {Yin, Y and Ma, Y and Wang, Y and Gao, P and Jia, C and Li, C and Yang, Q and Zhang, F and Bo, H and Wang, R and Chen, J},
title = {Chemical heterogeneity and mixed pollution are associated with microbial functional potential across soils in a coal mining subsidence landscape.},
journal = {RSC advances},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6ra03694e},
pmid = {42798947},
issn = {2046-2069},
abstract = {Coal mining subsidence occurs when underground coal extraction removes structural support for overlying strata, causing ground deformation and localized surface collapse. However, it remains unclear whether soils across a subsidence landscape respond in a similar way, or whether different habitats develop distinct nutrient conditions and mixtures of heavy metals and PAHs that are associated with different microbial communities and carbon, nitrogen, and sulfur cycling potentials. Local ecological risks would be overlooked if the entire subsidence zone is generalized as one disturbed ecosystem. Here, we sampled surface soils (0-20 cm) in September 2024 from four ordered habitats along a local subsidence associated topographic habitat in Jining, China: subsidence soil (SS), ditch soil adjacent to the subsidence area (SL), ditch soil near farmland (SR), and farmland soil (SF). We quantified soil physicochemical properties, heavy metals, polycyclic aromatic hydrocarbons (PAHs), and enzyme activities, and characterized bacterial and fungal communities and functional genes using metagenomic sequencing and downstream multivariate analyses. Soil chemical conditions differed consistently across habitats, with clear separation along nutrient related gradients and distinct contaminant profiles among habitats. Microbial α-diversity and β-diversity showed specific habitat patterns, and community composition differed among habitats for both bacteria and fungi. Functional profiles related to carbon, nitrogen, and sulfur cycling also varied across habitats, indicating that chemical heterogeneity and mixed pollution coincided with reconfiguration of microbial metabolic potential at the pathway and gene levels. Ordination analyses further showed that microbial community structure and functional potential were strongly associated with soil physicochemical gradients and pollutant variables, while enzyme activities covaried with key soil properties and contaminants. Our results indicate that coal mining subsidence landscapes contain multiple habitat-specific chemical and contaminant filters rather than a single uniform "subsidence effect", supporting chemically informed, habitat-stratified assessment of soil condition and microbial functional potential in mining-affected ecosystems.},
}

@article {pmid42379362,
year = {2026},
author = {Piantoni, P and Sardi, MI and Aumiller, T and Khafipour, E and Roman-Garcia, Y and Chakrabarti, A and Dieho, K and Aubert, T and Schroeder, GF},
title = {Effects of increasing doses of a phytogenic product based on condensed tannins and spices on production performance and rumen microbiome of lactating dairy cows fed a low-protein diet.},
journal = {Journal of dairy science},
volume = {109},
number = {10},
pages = {10489-10505},
doi = {10.3168/jds.2025-28174},
pmid = {42379362},
issn = {1525-3198},
mesh = {Animals ; Female ; *Rumen/microbiology ; Cattle/physiology/microbiology ; *Lactation/drug effects ; Diet/veterinary ; *Proanthocyanidins/administration & dosage/metabolism ; Animal Feed/analysis ; *Spices/analysis ; Milk/chemistry/metabolism ; *Microbiota/drug effects ; Dietary Proteins/metabolism ; Animal Nutritional Physiological Phenomena ; Dose-Response Relationship, Drug ; },
abstract = {The objective of this experiment was to determine the effect of increasing doses of a phytogenic product based on condensed tannins and spices (CTS) on production performance of lactating dairy cows fed a low-protein diet. Eight rumen-cannulated Holstein Friesian dairy cows (140 ± 86 DIM; 39.0 ± 5 kg/d milk yield; mean ± SD) were used in a replicated 4 × 4 Latin square design experiment with 4-wk periods. Treatments were 0, 10, 20, and 30 g/d CTS (CTR, 10CTS, 20CTS, and 30CTS, respectively). The grass- and corn silage-based diet was 55.2% forage, 38.7% NDF, 21.0% total starch, and 14.6% CP. Orthogonal contrasts were used to evaluate the linear and quadratic effect of increasing doses of CTS. Results follow the order CTR, 10CTS, 20CTS, and 30CTS. Increasing doses of CTS quadratically increased DMI (25.4, 25.9, 26.1, and 25.1 kg/d) and milk yield (37.1, 38.5, 37.7, and 36.3 kg/d), tended to increase fat- and protein-corrected milk (36.9, 37.6, 37.4, and 36.1 kg/d), and did not affect feed or N efficiency (1.45% ± 0.2% and 32.0% ± 2.3%, respectively). Treatments did not affect milk fat yield (1.48 ± 0.2 kg/d) but increasing doses of CTS increased milk protein yield quadratically (1.22, 1.27, 1.26, and 1.20 kg/d). Intermediate doses of CTS tended to increase de novo fatty acid yield (352, 369, 373, and 356 g/d) and decrease trans-10 C18:1 (4.31, 4.05, 4.05, and 4.24 g/d) compared with CTR and 30CTS. Treatments did not affect milk urea concentration (17.8 ± 1.7 mg/dL) or milk CP (3.39% ± 0.2%) or fat (4.06% ± 0.2%) content. Rumen pH and time below rumen pH of 5.8 were not affected by level of CTS supplementation. A treatment by time interaction for rumen ammonia concentration indicated that 20CTS and 30CTS increased ammonia concentration 3 h after feeding compared with CTR and 10CTS (7.72, 7.94, 13.7, and 14.1 mg/dL). The 10CTS treatment decreased rumen propionate concentration only at 3 h after feeding compared with the other treatments. Apparent DM and NDF total-tract digestibility were not affected by treatments. Shotgun metagenomics were used to evaluate the effect of CTS supplementation on the solid- and liquid-associated rumen microbiome. Treatment effects were only observed in the solid-associated microbiome. Supplementation of CTS linearly decreased α diversity at both the taxa and functional levels, indicating promotion of a leaner microbial community with higher doses of CTS. Differential abundance analysis identified 26 species with large fold changes, including some species with a high presence of cellulases and significant correlations with phenotypic parameters such as DMI, N efficiency, and milk production. In conclusion, a mixture of CTS affected microbiome and rumen metabolism, increasing fat- and protein-corrected milk yield when fed at 10 and 20 g/d only. This experiment demonstrates the importance of in vivo dose-response experiments with phytogenic products to determine optimum dosage for improved rumen metabolism and performance.},
}

Animals
Female
*Rumen/microbiology
Cattle/physiology/microbiology
*Lactation/drug effects
Diet/veterinary
*Proanthocyanidins/administration & dosage/metabolism
Animal Feed/analysis
*Spices/analysis
Milk/chemistry/metabolism
*Microbiota/drug effects
Dietary Proteins/metabolism
Animal Nutritional Physiological Phenomena
Dose-Response Relationship, Drug

@article {pmid42442424,
year = {2026},
author = {Luo, Z and Zhang, K and Wang, L and Zhang, J and Huang, Y and Lu, X and Zhao, F and Cao, S and Li, J},
title = {Astragalus polysaccharides reshape gut resistome of postpartum dairy cows.},
journal = {Bioresource technology},
volume = {461},
number = {},
pages = {135399},
doi = {10.1016/j.biortech.2026.135399},
pmid = {42442424},
issn = {1873-2976},
mesh = {Animals ; *Polysaccharides/pharmacology ; Cattle ; *Astragalus Plant/chemistry ; Female ; *Postpartum Period ; Feces/microbiology ; Metagenome ; *Gastrointestinal Microbiome/drug effects/genetics ; Dairying ; Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics/drug effects ; Genes, Bacterial ; },
abstract = {Antibiotic resistance genes (ARGs) in livestock feces represent an important environmental reservoir of antimicrobial resistance. Natural product intervention is a potential strategy for regulating the gut microbiome of livestock; however, its effects on the gut resistome of postpartum dairy cows remain poorly understood. In this study, we investigated the effects of Astragalus polysaccharides (APS) supplementation on the fecal microbiome, ARGs, mobile genetic elements (MGEs), virulence factors (VFs), and ARG-carrying metagenome-assembled genomes (MAGs) in dairy cows during postpartum period. Alpha and beta diversity analyses showed that APS supplementation did not significantly alter the global resistome, mobilome, or virulome structure. The content of several ARGs and VFs, including AAC(6')-Iw, qacEdelta1, ast, PM_RS00425, and sdrF, significantly decreased in the APS group, and several plasmid-associated MGEs genes showed group-specific changes. Co-occurrence network analysis revealed complex associations between ARGs, VFs, and core bacterial taxa, with Paludibacter and Parabacteroides identified as potential microbial reservoirs of resistance- and virulence-associated genes. Furthermore, 101 metagenome-assembled genomes (MAGs) were recovered, 42 of which carried multiple ARGs. Bin.1, assigned to Scatovivens, had the highest ARG count. APS supplementation reduced the overall ARG load, particularly the ARG contribution in bin.1. However, APS utilization potential was not significantly correlated with ARG density or ARG load across MAGs. Thus, this study provides new insights into APS supplementation and nutritional strategies that can mitigate the fecal ARG burden in dairy production.},
}

Animals
*Polysaccharides/pharmacology
Cattle
*Astragalus Plant/chemistry
Female
*Postpartum Period
Feces/microbiology
Metagenome
*Gastrointestinal Microbiome/drug effects/genetics
Dairying
Virulence Factors/genetics
*Drug Resistance, Microbial/genetics/drug effects
Genes, Bacterial

@article {pmid42462831,
year = {2026},
author = {Qiang, H and Jing, Y and Xu, X and Heo, S and Liu, Z and Yue, X and Zhou, A and Fernández-Morales, FJ and Oleskowicz-Popiel, P},
title = {N-(3-oxohexanoyl)-homoserine lactone-assisted enrichment reshapes functional microbial consortia for chain elongation in electrofermentation.},
journal = {Bioresource technology},
volume = {461},
number = {},
pages = {135425},
doi = {10.1016/j.biortech.2026.135425},
pmid = {42462831},
issn = {1873-2976},
mesh = {*Fermentation/drug effects ; *4-Butyrolactone/analogs & derivatives/metabolism/pharmacology ; *Microbial Consortia/drug effects/physiology ; Bacteria/metabolism ; Caproates/metabolism ; Sewage/microbiology ; },
abstract = {The functional microbial consortia supporting chain elongation determine medium-chain carboxylate recovery from organic wastes, but how signal-molecule-assisted enrichment shapes chain-elongating bacteria (CEB), electroactive bacteria (EAB), and competing guilds in electrofermentation remains unclear. Here, three N-acyl-homoserine lactones: N-butyryl-homoserine lactone (C4-HSL), N-octanoyl-homoserine lactone (C8-HSL), and N-(3-oxohexanoyl)-homoserine lactone (3OC6-HSL), were supplied during microbial enrichment, and the subsequent electrofermentation was conducted fed with sludge fermentation broth. Compared with the Control (without signaling molecules), 3OC6-HSL had the strongest response, increasing caproate production by 94.0%, compared with 16.9% and 27.3% for C4-HSL and C8-HSL, respectively. It also increased the apparent caproate electron transfer efficiency by 20.7 percentage points, increased the abundance of CEB (44.9% vs. 33.2%) and EAB (14.3% vs. 6.6%), and reduced the abundance of homoacetogens (12.1% vs. 33.7%). Co-occurrence network analysis revealed more modular and compact inferred associations, with 25.0% more modules and a 34.7-49.3% shorter average path length. Metagenomic analysis revealed enhanced reverse β-oxidation, QS, chemotaxis, and flagellar assembly potentials, and the expression levels of acetyl-CoA acyltransferase (ACAT/fadA) and acyl-CoA dehydrogenase (ACADS/ACADM) increased by 162.1% and 96.6%, respectively. Clostridium kluyveri dominated the ACAT contribution (85.9%). Overall, enrichment-phase 3OC6-HSL supplementation was associated with a caproate-oriented microbial consortium and improved caproate recovery without continuous signal dosing.},
}

*Fermentation/drug effects
*4-Butyrolactone/analogs & derivatives/metabolism/pharmacology
*Microbial Consortia/drug effects/physiology
Bacteria/metabolism
Caproates/metabolism
Sewage/microbiology

@article {pmid42468699,
year = {2026},
author = {Qing, C and Zhou, Y and Wang, Y and Li, P and Hedlund, B},
title = {Arsenic detoxification mediated by mutualistic cross-feeding in a thermophilic microbial consortium.},
journal = {Bioresource technology},
volume = {461},
number = {},
pages = {135440},
doi = {10.1016/j.biortech.2026.135440},
pmid = {42468699},
issn = {1873-2976},
mesh = {*Arsenic/metabolism/toxicity ; *Microbial Consortia/physiology ; Biodegradation, Environmental ; Photosynthesis ; *Cyanobacteria/metabolism ; Hot Springs/microbiology ; *Symbiosis ; Inactivation, Metabolic ; Oxidation-Reduction ; Coculture Techniques ; },
abstract = {Cyanobacteria-dominated microbial mats thrive in arsenic (As)-rich hot springs, but how they cope with As stress remains unclear. This study explored the As detoxification strategy of a photosynthetic microbial mat from a high-As hot spring in Tibet. The photosynthetic mat oxidized arsenite [As(Ⅲ)] under light without external organic carbon sources or electron acceptors. However, As(Ⅲ) was not oxidized by a pure culture of the dominant cyanobacterium isolated from the mat, "Thermoleptolyngbya sichuanensis" XZ-Cy5. Instead, exposure of a growing culture to 5 mM As(Ⅲ) led to rapid loss of chlorophyll and photosynthetic activity. In contrast, a pure culture of the mat-derived heterotroph Chelatococcus sp. XZ-Ab1 could oxidize As(Ⅲ) quickly with the addition of organic carbon and oxygen. A co-culture system demonstrated mutualistic interactions where "T. sichuanensis" XZ-Cy5 secreted organic carbon to facilitate heterotrophic growth of Chelatococcus sp. XZ-Ab1, while Chelatococcus sp. XZ-Ab1 promoted growth of "T. sichuanensis" XZ-Cy5 by oxidizing toxic As(Ⅲ) to the less toxic arsenate. Following growth of the co-culture using [13]CO2, NanoSIMS isotope tracing provided direct evidence of photoautotroph-derived carbon from "T. sichuanensis" XZ-Cy5 to Chelatococcus sp. XZ-Ab1. Metagenomic and genomic analyses indicated several mechanisms for metabolic complementarity between the two strains, including As detoxification by the heterotroph and fixed carbon and nitrogen provision by the cyanobacterium, in addition to oxygen production. Our findings reveal a cooperative survival strategy in extreme environments and provide a novel model for engineering synthetic microbial consortia for As bioremediation.},
}

*Arsenic/metabolism/toxicity
*Microbial Consortia/physiology
Biodegradation, Environmental
Photosynthesis
*Cyanobacteria/metabolism
Hot Springs/microbiology
*Symbiosis
Inactivation, Metabolic
Oxidation-Reduction
Coculture Techniques

@article {pmid42780516,
year = {2026},
author = {Jiang, X and Shi, S and Li, M and Zhang, Y and Xing, G and Yan, Q and Li, S and Sun, W and Li, H},
title = {Fecal microbiota transplantation in adolescents with obesity induces limited and donor-dependent remodeling of the gut microbiome.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1927870},
pmid = {42780516},
issn = {1664-2392},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Adolescent ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; *Pediatric Obesity/therapy/microbiology ; Longitudinal Studies ; Metagenome ; },
abstract = {INTRODUCTION: Obesity is a global health challenge, and fecal microbiota transplantation (FMT) is considered a potential intervention; however, its long-term ecological impact remains unclear.

METHODS: In this 182-day longitudinal cohort of adolescents with obesity (378 samples), metagenomic sequencing was used to assess FMT-induced remodeling of the multi-kingdom gut ecosystem through species composition, diversity, microbial networks, and machine learning analyses.

RESULTS: FMT induced only transient shifts in community structure, with limited donor strain engraftment and strong resilience of recipient core taxa. Bacteria were the primary responders, the virome showed short-term perturbation, and network restoration was partial and donor-dependent.

DISCUSSION: FMT exerts limited, donor-dependent ecological effects in obese adolescents. Optimizing donor selection and personalized matching may be essential for improving long-term efficacy.},
}

Humans
*Fecal Microbiota Transplantation/methods
Adolescent
*Gastrointestinal Microbiome/physiology
Female
Male
*Pediatric Obesity/therapy/microbiology
Longitudinal Studies
Metagenome

@article {pmid42781813,
year = {2026},
author = {Astrin, JJ and Labuschagne, K and Avrili, H and Barker, K and Burger, AL and Dhyani, A and Escobari Vargas, B and Johnston, P and Pugh, RS and Grossman, GH and Conradie, EH},
title = {Where Worlds Align: Insights from the Joint GGBN-ISBER Conference on Biodiversity and Biobanking, Cape Town, October 2025.},
journal = {Biopreservation and biobanking},
volume = {},
number = {},
pages = {19475535261488949},
doi = {10.1177/19475535261488949},
pmid = {42781813},
issn = {1947-5543},
abstract = {The 2025 Joint GGBN-ISBER Conference in Cape Town united biodiversity, environmental, and biomedical biobanking communities from 38 countries. The event highlighted biobanks as interdisciplinary and collaborative infrastructures for addressing global challenges-pandemics, biodiversity loss, and food security, among others. Recurring themes throughout the conference were as follows: (1) Harmonization and Quality-adoption of best practices and standards where possible to ensure global interoperability and sample integrity; (2) Equitable Governance-crafting flexible, transparent frameworks for sample and data sharing that uphold sovereignty and benefit local communities; (3) Technological and Data Integration-using artificial intelligence, omics technologies, and standardized metadata to transform physical specimens into scalable digital resources; and (4) Resilient Infrastructure-securing long-term investment in regional biobanking networks and targeted training to build enduring capacity, embedding sustainability by design and safeguarding local knowledge.},
}

@article {pmid42189604,
year = {2026},
author = {Lopes, F and Martinez-Martinez, D and Späth, MR and Hoyer-Allo, KJR and Strubl, S and Cukoski, S and Knieps, L and Brodesser, S and Göbel, H and Schwarz, G and van den Berg, BM and Rabelink, TJ and Schermer, B and Benzing, T and Müller, RU and Beyer, A and Cabreiro, F and Koehler, FC},
title = {The Interplay between Gut Microbiota and Diet-Induced Kidney Protection.},
journal = {Kidney360},
volume = {7},
number = {9},
pages = {1930-1942},
pmid = {42189604},
issn = {2641-7650},
support = {RPG-2022-299//Leverhulme Trust/ ; 102532/Z/12/Z, 102531/Z/13/A/WT_/Wellcome Trust/United Kingdom ; EXC 2030 -390661388//Deutsche Forschungsgemeinschaft/ ; 2020_EKEA.121//Else Kröner-Fresenius-Stiftung/ ; 390661388//Deutsche Forschungsgemeinschaft/ ; RPG-2022-299//Leverhulme Trust/ ; 102532/Z/12/Z, 102531/Z/13/A/WT_/Wellcome Trust/United Kingdom ; EXC 2030 -390661388//Deutsche Forschungsgemeinschaft/ ; 2020_EKEA.121//Else Kröner-Fresenius-Stiftung/ ; 390661388//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Reperfusion Injury/microbiology/prevention & control ; *Gastrointestinal Microbiome/physiology ; Mice ; *Kidney/metabolism/pathology/blood supply ; Male ; *Caloric Restriction ; *Diet ; Mice, Inbred C57BL ; Disease Models, Animal ; *Acute Kidney Injury/prevention & control/microbiology ; },
abstract = {KEY POINTS: Beneficial diets changed the composition of gut microbiota in an ischemia-reperfusion injury‑dependent manner in rodents. Taxonomic and functional profiling revealed a central role of Lachnospiraceae , a main producer of microbially derived short-chain fatty acids. Comparative bulk transcriptomics suggested the metabolic use of these bacterial products as an additional energy source in kidneys of protected mice.

BACKGROUND: On one hand, dietary interventions are known for their pivotal role in regulating diversity, composition, and function of the gut microbiome. On the other hand, specific diets show an immense potential in preventing kidney injury from various damaging stimuli in rodents, and recent findings, in turn, highlight a central role of gut microbiota in kidney health and disease.

METHODS: Three protective dietary regimens-a fasting-mimicking diet, a diet depleted in sulfur-containing amino acids, and caloric restriction-were examined in parallel in a rodent model of ischemia-reperfusion injury (IRI). To delineate the diet-induced effect on gut microbiota in response to ischemic kidney damage, we used comparative shotgun metagenomics for taxonomic and functional profiling. We further examined the renal metabolic response using comparative transcriptomics to unravel the interplay between gut microbiota and kidney protection.

RESULTS: Beneficial dietary preconditioning strategies changed the composition of gut microbiota in an IRI-dependent manner. Using ternary plots to investigate the role of dietary interventions over time before and after ischemic insult, we detected a central role of Lachnospiraceae that commonly expanded in response to renal IRI in dietary preconditioned mice. Further functional profiling of gut microbiota in our model revealed an increase in plasma levels of bacterial-derived short-chain fatty acids in diet-induced kidney protection. Comparative bulk transcriptomics in our model, in turn, pointed toward the metabolic use of these bacterial-derived short-chain fatty acids in kidneys of protected mice.

CONCLUSIONS: Because proximal tubules lack sufficient glycolytic capacity, products of microbial metabolism may serve as an additional energy source to fulfill their high demands when withstanding ischemic damage. Our data shed light on a close interplay between gut microbiota and diet-induced kidney protection calling for further research at the crossroads of microbiology, metabolism, and molecular nephrology.},
}

Animals
*Reperfusion Injury/microbiology/prevention & control
*Gastrointestinal Microbiome/physiology
Mice
*Kidney/metabolism/pathology/blood supply
Male
*Caloric Restriction
*Diet
Mice, Inbred C57BL
Disease Models, Animal
*Acute Kidney Injury/prevention & control/microbiology

@article {pmid42298622,
year = {2026},
author = {Wang, F and Sang, Y and Guo, J and Fu, Y and Yang, M and Shan, F and Chen, Y and Zhang, S and Li, X and Li, J and Zhang, L},
title = {Dietary glycyrrhizic acid improves growth performance and modulates upper respiratory microbiota in weaned piglets.},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {42298622},
issn = {1746-6148},
support = {231111111600//Henan Province Key Research and Development Plan Project/ ; 251111113300//Henan Province Key Research and Development Plan Project/ ; CARS-35//the National Pig Industry Technology System/ ; },
mesh = {Animals ; *Glycyrrhizic Acid/pharmacology/administration & dosage ; Swine/growth & development/microbiology ; Diet/veterinary ; Weaning ; Animal Feed/analysis ; *Microbiota/drug effects ; Dietary Supplements ; Female ; *Respiratory System/microbiology ; },
abstract = {BACKGROUND: Natural products with dual immunomodulatory and antimicrobial functions offer promising strategies to reduce antibiotic use in livestock. Glycyrrhizic acid (GA), the principal bioactive component of licorice, has demonstrated anti-inflammatory and antiviral properties, yet its translational potential in swine health remains underexplored. This study evaluated the efficacy of GA in weaned piglets under commercial nursery conditions as an antibiotic alternative. A total of 225 weaned piglets were assigned to five groups: negative control (CON, basal diet), farm routine (FA, conventional antibiotics), and three GA-supplemented groups (GLL, 0.65 g/kg; GLM, 1.3 g/kg; GLH, 2.6 g/kg).

RESULTS: The result showed that dietary GA supplementation (2.6 g/kg) numerically improved growth performance and reduced cough scores, although not statistically significant. GA significantly decreased the diarrhea index and improved skin scores. GA also significantly increased serum IgG and IgM levels in piglets and showed a trend toward higher IgA levels. Furthermore, GA exhibited a trend toward lowering serum IL‑1β levels while upregulating IFN‑γ and IL‑10 levels. Regarding antioxidant parameters, GA significantly upregulated T‑SOD, GSH‑PX, and CAT activities and downregulated LDH activity. Metagenomic analysis revealed that high‑dose glycyrrhizic acid (GA) significantly increased the abundance of Alloprevotella, while decreasing the abundances of Moraxella pluranimalium and 11 other pathogenic species associated with respiratory diseases and lung injury, including Glaesserella parasuis, Mesomycoplasma hyorhinis, Mesomycoplasma hyopneumoniae, Streptococcus suis, among others, thereby reshaping the upper respiratory tract microbiota of pigs.

CONCLUSIONS: Collectively, these findings support GA as a viable non-antibiotic strategy for improving immune function, antioxidant capacity, and respiratory health in weaned piglets.},
}

Animals
*Glycyrrhizic Acid/pharmacology/administration & dosage
Swine/growth & development/microbiology
Diet/veterinary
Weaning
Animal Feed/analysis
*Microbiota/drug effects
Dietary Supplements
Female
*Respiratory System/microbiology

@article {pmid42439467,
year = {2026},
author = {Luo, Y and Kang, FL and Li, QM and Yang, WC},
title = {Metagenomic Association Uncovers Host Genotype-Structured Rhizobacterial Networks and Novel Taxa That Enhance Soybean Salt Tolerance.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {53},
pages = {e76373},
pmid = {42439467},
issn = {2198-3844},
support = {YSBR-011//CAS project for Young Scientists in Basic Research/ ; 2023YFD1200600//National Key Research and Development Program of China/ ; XDA24010205//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA26030105//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2016QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; },
mesh = {*Glycine max/genetics/microbiology/physiology ; *Salt Tolerance/genetics ; Rhizosphere ; Soil Microbiology ; *Metagenomics/methods ; Genotype ; *Microbiota/genetics ; Plant Roots/microbiology ; },
abstract = {Salinity is an escalating agricultural challenge, yet plant microbiomes offer a promising avenue for improving salt tolerance. Nevertheless, most naturally occurring microbes remain unevaluated for plant growth-promoting function, and systematic approaches to uncover salt-tolerance-enhancing plant growth-promoting rhizobacteria (PGPR) are limited. Here, using soybean as a model, we implement a quantitative framework to characterize rhizosphere microbial networks and nominate novel taxa functionally associated with plant salt tolerance. We introduced a salt tolerance index (STI) to quantify plant salt tolerance and normalize performance across heterogeneous natural soil salinity. Metagenomic sequencing and co-occurrence analysis revealed distinct rhizosphere microbiota structures between tolerant and susceptible soybeans. In tolerant soybeans, Pseudomonas dominated as the hub of a highly interconnected network, whereas susceptible accessions showed a fragmented network dominated by Acinetobacter. Correlation analyses identified bacterial taxa positively associated with STI, including documented salt-tolerant PGPR and novel candidates. Greenhouse experiments showed that one candidate, Thalassospira xiamenensis, enhances soybean salt tolerance and reshapes host ion-transport and oxidative-stress gene expression under salinity, validating our screening strategy. Our culture-independent metagenomic association approach reveals host genotype-structured rhizosphere microbial networks underlying salt tolerance and provides an efficient, labor-saving means for high-throughput identification of salt-tolerant PGPR.},
}

*Glycine max/genetics/microbiology/physiology
*Salt Tolerance/genetics
Rhizosphere
Soil Microbiology
*Metagenomics/methods
Genotype
*Microbiota/genetics
Plant Roots/microbiology

@article {pmid42485926,
year = {2026},
author = {de Bruijn, DGJ and Gusinac, A and Ederveen, THA and Le, ND and Kulkarni, P and Meijer, RI and Janssen, MCH and Zweers, HEE},
title = {Gut microbiota alterations in individuals with mitochondrial disease caused by the m.3243A >G mutation.},
journal = {Molecular genetics and metabolism},
volume = {149},
number = {1-2},
pages = {110208},
doi = {10.1016/j.ymgme.2026.110208},
pmid = {42485926},
issn = {1096-7206},
mesh = {Humans ; *Mitochondrial Diseases/genetics/microbiology ; Female ; Male ; Diabetes Mellitus, Type 1/microbiology/genetics ; Adult ; *Gastrointestinal Microbiome/genetics ; Mutation ; *DNA, Mitochondrial/genetics ; Deafness/genetics/microbiology ; Ruminococcus/isolation & purification/genetics ; Faecalibacterium prausnitzii/isolation & purification/genetics ; Escherichia coli/isolation & purification/genetics ; Feces/microbiology ; Case-Control Studies ; *Dysbiosis/microbiology/genetics ; Middle Aged ; Adolescent ; Young Adult ; Eubacteriales ; },
abstract = {People with mitochondrial disease (MD) associated with the m.3243 A > G mutation often experience gastrointestinal complaints and dysmotility, suggesting dysbiosis of the gut microbiome. A common phenotype of the m.3243 A > G mutation is Maternally Inherited Diabetes and Deafness (MIDD). Previous studies have shown that other forms of diabetes are associated with an altered gut microbiome. Therefore, our study aimed to investigate the gut microbiota of people with MD caused by the m.3243 A > G mutation compared to healthy controls (Lifelines®) and people with type 1 diabetes (T1D). Fecal samples of 30 people with the m.3243 A > G mutation were used for shotgun metagenomic sequencing. The MD group was compared with 60 healthy controls and 60 people with T1D from different datasets, and were matched for age, sex, and BMI. We found that the Bray-Curtis β-diversity of the gut microbiota differed significantly between MD compared to healthy controls and T1D, while there was a non-significant reduction in Shannon α-diversity in the MD group. The gut microbiota of the MD group was characterized by reduced Faecalibacterium prausnitzii, and increased Escherichia coli, Ruminococcus gnavus, and Ruminococcus torques levels compared to healthy controls and T1D. This pattern aligns with microbial signatures reported in inflammatory bowel disease, which is associated with mitochondrial dysfunction in intestinal epithelial cells. Overall, our explorative study suggest that people with the m.3243 A > G mutation exhibit a dysbiotic gut microbiota, which may pave the way for future research aimed at developing new therapies, dietary adjustments and their potentials to improve quality of life.},
}

Humans
*Mitochondrial Diseases/genetics/microbiology
Female
Male
Diabetes Mellitus, Type 1/microbiology/genetics
Adult
*Gastrointestinal Microbiome/genetics
Mutation
*DNA, Mitochondrial/genetics
Deafness/genetics/microbiology
Ruminococcus/isolation & purification/genetics
Faecalibacterium prausnitzii/isolation & purification/genetics
Escherichia coli/isolation & purification/genetics
Feces/microbiology
Case-Control Studies
*Dysbiosis/microbiology/genetics
Middle Aged
Adolescent
Young Adult
Eubacteriales

@article {pmid42677482,
year = {2026},
author = {Wu, Q and Xu, X and Guo, Y and Li, H and Hao, Y and Zhang, Z and Cai, Z and White, JC and Ma, C},
title = {Nano-boron nitride enhances soybean growth and symbiotic nitrogen fixation by modulating the rhizosphere microbiome and biogeochemical cycling.},
journal = {Nanoscale},
volume = {18},
number = {36},
pages = {19815-19829},
doi = {10.1039/d6nr02400a},
pmid = {42677482},
issn = {2040-3372},
mesh = {*Glycine max/growth & development/microbiology/drug effects/metabolism ; *Nitrogen Fixation/drug effects ; *Rhizosphere ; *Microbiota/drug effects ; *Boron Compounds/chemistry/pharmacology ; Symbiosis/drug effects ; Biomass ; },
abstract = {Nanotechnology offers promising strategies for sustainable agriculture, yet the systemic mechanisms by which nanomaterials enhance legume nitrogen fixation remain insufficiently understood. The multi-scale impacts of nano-boron nitride (nano-BN) on soybean growth, biological nitrogen fixation, and rhizosphere microbial communities were investigated. Soil addition of 50 mg kg[-1] nano-BN significantly promoted plant biomass, nodule biomass, and leghemoglobin content by 10.0%, 27.4%, and 39.4%, respectively, compared to the untreated control. Nano-BN also enhanced the NH4[+]-N and NO3[-]-N content by 24.3% and 19.9% in root tissues, while reducing these levels in rhizosphere soil. Additionally, nano-BN enriched rhizosphere-dissolved organic matter, particularly humic-like components. Metagenomic analysis revealed that nano-BN reshaped carbon and nitrogen cycling functional genes, enhancing CO2 fixation and aerobic respiration; the nitrogen fixation functional gene nifH was upregulated by 27.7%. Microbial community analysis demonstrated increased bacterial diversity and abundance of beneficial taxa, particularly Bradyrhizobium, which increased by 24.9%. Co-occurrence network analysis revealed enhanced positive interactions and greater topological complexity upon the addition of nano-BN compared to the untreated control, indicating improved community stability. Collectively, these findings demonstrate that nano-BN promotes soybean growth through integrated regulation of nutrient cycling, symbiotic nitrogen fixation, and rhizosphere microbiome assembly. Nano-BN represents an innovative nano-fertilization strategy for enhancing biological nitrogen fixation, improving nutrient use efficiency, and advancing sustainable agricultural systems.},
}

*Glycine max/growth & development/microbiology/drug effects/metabolism
*Nitrogen Fixation/drug effects
*Rhizosphere
*Microbiota/drug effects
*Boron Compounds/chemistry/pharmacology
Symbiosis/drug effects
Biomass

@article {pmid42684889,
year = {2026},
author = {Mueller, NT and Xiao, S and Liu, T and Debelius, J and Kress, AM and Zhao, N and Moore, B and McKee, KS and Jacobson, LP and Comstock, SS and , },
title = {Mother-infant sharing of gut and vaginal microbes at the species and strain level.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117920},
doi = {10.1016/j.celrep.2026.117920},
pmid = {42684889},
issn = {2211-1247},
mesh = {Female ; Humans ; *Vagina/microbiology ; Infant ; *Gastrointestinal Microbiome/genetics ; Mothers ; Pregnancy ; Microbiota ; Infant, Newborn ; },
abstract = {Mother-to-offspring microbial transmission is a foundational process for seeding the infant gut microbiome, yet the relative contributions of maternal body sites and the influence of birth delivery mode remain incompletely understood. We use shotgun metagenomic sequencing in 68 mother-infant dyads to investigate species- and strain-level sharing of the maternal gut and vaginal microbiomes with the infant gut during the first year of life. At 2-4 months of age, infants share an average of 35% of species with their mother's microbiomes, with markedly greater sharing from the maternal gut than the vagina. Vaginally delivered infants exhibit higher levels of sharing than those born by cesarean section (C-section). Strain-level analyses reveal persistent mother-infant transmission across multiple Bacteroides and Bifidobacterium species genome bins, with strain-sharing frequencies varying by species and birth mode. C-section reduces the extent of mother-infant species- and strain-level sharing.},
}

Female
Humans
*Vagina/microbiology
Infant
*Gastrointestinal Microbiome/genetics
Mothers
Pregnancy
Microbiota
Infant, Newborn

@article {pmid42709542,
year = {2026},
author = {Pinedo-Bardales, M and Erreygers, I and Allonsius, CN and Hiel, M and Eilers, T and Van Rillaer, T and Gehrmann, T and Ahannach, S and Dillen, J and De Boeck, I and Verhoeven, V and Van Puyvelde, S and Segata, N and Wittouck, S and Lebeer, S},
title = {Species and strain sharing in the vaginal microbiome of mothers and their adult daughters.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117942},
pmid = {42709542},
issn = {2211-1247},
mesh = {Female ; *Microbiota/genetics ; *Vagina/microbiology ; Humans ; *Mothers ; Adult ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Nuclear Family ; *Lactobacillus crispatus/genetics/isolation & purification ; Species Specificity ; },
abstract = {The vaginal microbiome is key for women's health. However, its establishment, interindividual variation and dynamics remain poorly understood. Here, we investigate bacterial relatedness at species and strain level in adult mother-daughter pairs from the large-scale citizen-science program Isala. Using metagenomic sequencing with quality control including 16S rRNA profile comparison, along with targeted culturing, we assess intergenerational microbiome sharing. At species level, daughters' vaginal microbiomes are significantly more similar to their mothers' than to those of unrelated mothers, with a strong mother-daughter correlation in Lactobacillus crispatus dominance. Strain-level analyses of metagenomes and isolate genomes reveal intraspecies diversity in L. crispatus, with up to two strains observed within the same host, and support intergenerational vaginal bacteria sharing. SNV counts in shared L. crispatus strains show no correlation with daughters' ages. Together, these findings suggest that maternal transmission, host factors, and (shared) environment collectively shape the vaginal microbiome, providing fundamental ecological insights into vaginal microbiome dynamics and perspectives toward lactobacilli-based applications.},
}

Female
*Microbiota/genetics
*Vagina/microbiology
Humans
*Mothers
Adult
RNA, Ribosomal, 16S/genetics
Metagenome
Nuclear Family
*Lactobacillus crispatus/genetics/isolation & purification
Species Specificity

@article {pmid42772437,
year = {2026},
author = {Kang, D and Ji, Y and Cao, Y and Ou, J and Yang, Q},
title = {Grazing and soil moisture transitions reorganize cross-library co-abundance modules of resistance and virulence genes in alpine wetland soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {410},
number = {},
pages = {129221},
doi = {10.1016/j.envpol.2026.129221},
pmid = {42772437},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs), heavy-metal resistance genes (HMRGs) and virulence factor genes (VFGs) can coexist in soils, yet their joint responses to hydrological and grazing pressures remain unclear. We combined shotgun metagenomics, a unified co-abundance network, fixed-module environmental-stratum deletion, threshold modelling, and contig, metagenome-assembled genome (MAG) and mobile genetic element (MGE) annotations across 32 alpine wetland plots spanning continuous soil water content and two grazing intensities. The unified network identified 14 representative cross-library hubs and four candidate modules whose coordinated states explained peripheral coactivation better than individual hubs, with M01-M03 showing more consistent support across sensitivity analyses than M04. All modules retained all three gene libraries after grazing- or moisture-stratum deletion, but connectivity, occupancy and cross-edge activity changed in module-specific ways. Within this dataset, a candidate soil-water-content transition near 89.4% separated contrasting responses and revealed partial decoupling between sample-level activation and cross-sample topology. Carrier support was heterogeneous, with M03 showing the strongest partial MAG- and MGE-associated support, whereas mobility-related responses varied among modules and environments. Overall, grazing and moisture reorganized rather than uniformly intensified these gene assemblages. Co-abundance and carrier association indicate genomic organization and mobility-related potential, not realized pollution risk or horizontal transfer.},
}

@article {pmid42776951,
year = {2026},
author = {Hu, A and Liu, J and Chen, P and Yang, K and Xu, F and Luo, G and Zhang, J and He, M},
title = {Gut microbiome is associated with stereotypic behavior of the giant panda (Ailuropoda melanoleuca).},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357625},
pmid = {42776951},
issn = {1932-6203},
mesh = {Animals ; *Ursidae/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; *Stereotyped Behavior/physiology ; Feces/microbiology ; *Behavior, Animal ; Male ; },
abstract = {The giant panda (Ailuropoda melanoleuca) is a relict species endemic to China. Captive breeding has boosted its population. However, some captive individuals exhibit stereotypic behavior. Though extensive research showing that host behavior can be influenced by gut microbiota via the gut-brain axis, the gut microbiota related to stereotypic behavior of giant pandas has not been reported. To explore gut microbial composition and functional characteristics of stereotypically behaving (SB) giant pandas, the behavior of 15 captive giant pandas was observed, and their feces were analyzed using 16S ribosomal RNA (rRNA) sequencing (n = 145) and metagenomic sequencing (n = 45). Our study revealed distinct gut microbial diversity, composition, and functions between SB giant pandas and normal controls, indicating gut microbial dysbiosis in SB giant pandas. Serratia sp. Se-RSBMAAmG was significantly enriched in SB giant pandas, five Clostridium species and Lactococcus garvieae exhibited upward trends in SB individuals, whereas the probiotic Enterococcus hirae showed the opposite trend compared with those in normal controls. The Clostridium bacteria may affect propionate metabolism and the gamma-aminobutyric acidergic (GABAergic) synapse pathway, potentially affecting the emergence of stereotypic behavior. These findings suggest a link between gut microbiota and stereotypic behavior of giant pandas, providing novel insights for their conservation.},
}

Animals
*Ursidae/microbiology/physiology
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
*Stereotyped Behavior/physiology
Feces/microbiology
*Behavior, Animal
Male

@article {pmid42778553,
year = {2026},
author = {Meng, JX and Li, WD and Tao, WF and Tu, S and Gao, J and Zhao, X and Li, J and Wu, J and Liu, C and Zhang, Y and Zhu, SJ},
title = {An atlas of colonization factors in the human gut microbiome reveals ecological strategies and inflammatory bowel disease signatures.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42778553},
issn = {2041-1723},
support = {82572567//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Metagenome ; Metagenomics ; Dysbiosis/microbiology ; Phylogeny ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {Long-term residence in the gut enables microbes to interact with the host and influence intestinal health. However, many microbiome studies focus on taxonomic profiles or broad metabolic pathway annotations and provide limited insight into the conserved genes that support microbial residence. Here we show that colonization factors (CFs), defined as gut-enriched genes associated with microbial residence, offer a colonization-centered functional framework for profiling the human gut microbiome. By mapping 79 CF families across 289,231 surveyed microbial genomes, we identify more than seven million CF homologs and reveal their widespread distribution, phylogenetically structured organization and functional stratification into three putative lineage-associated colonization strategies centered on metabolism, stress resistance and microbial communication. Applying this framework to 3,666 metagenomic and metatranscriptomic samples from 10 inflammatory bowel disease (IBD) cohorts, we find that disease-associated dysbiosis is accompanied by recurrent remodeling of CF repertoires. These alterations can be traced to specific colonization-associated functions and microbial carrier species, and are captured by a compact feature panel that discriminates disease status within cohorts. These results establish CF profiling as a mechanism-oriented approach for interpreting the ecological organization of the gut microbiome and prioritizing colonization-associated targets for future disease monitoring and intervention studies.},
}

Humans
*Inflammatory Bowel Diseases/microbiology
*Gastrointestinal Microbiome/genetics/physiology
Metagenome
Metagenomics
Dysbiosis/microbiology
Phylogeny
*Bacteria/genetics/classification/isolation & purification

@article {pmid42778565,
year = {2026},
author = {Lv, Y and Liu, P and Liu, Y and Dong, L and Li, J and Zhang, Y},
title = {Redox-stratified macromolecule degradation supports microbial survival in the oligotrophic Kermadec Trench sediments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42778565},
issn = {2041-1723},
support = {42188102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42122043//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Geologic Sediments/microbiology ; Oxidation-Reduction ; Metagenome ; *Bacteria/genetics/metabolism/classification ; Ecosystem ; Phylogeny ; *Microbiota/genetics ; Pacific Ocean ; },
abstract = {Kermadec Trench is a hadal ecosystem in the South Pacific with the water depth 10,047 m. The trench bottom harbors a highly active and populated microbial community, despite the surface sediment is characterized as extremely pressurized, oligotrophic and with low oxygen concentration. It is intriguing, as well as technically challenging, to investigate the microbial adaptation strategies therein. Here we performed the in situ RNA fixation on sediment samples with the assistant of Fendouzhe manned submersible, to approach natural status of microbial metabolisms on both genomic and transcriptomic levels. We reconstructed 1369 metagenome-assembled genomes (MAGs), revealing dominant heterotrophic lineages encoding carbohydrate-active enzymes targeting complex macromolecules such as peptidoglycan and β-1,4-mannan. These degradation processes were transcriptionally coupled with flexible respiratory pathways utilizing oxygen, nitrate, and nitrite as electron acceptors. Co-expression analyses and microbial co-occurrence networks demonstrated niche partitioning driven by redox stratification, with slope communities favoring oxidative pathways and bottom communities enriched in reductive metabolisms, including denitrification and N2O reduction. Despite compositional divergence, both habitats exhibited conserved functional strategies centered on macromolecule recycling and redox-coupled respiration. Our findings highlight a coordinated system of organic matter remineralization and electron acceptor versatility that underpins microbial survival in Earth's deepest seafloor ecosystems.},
}

*Geologic Sediments/microbiology
Oxidation-Reduction
Metagenome
*Bacteria/genetics/metabolism/classification
Ecosystem
Phylogeny
*Microbiota/genetics
Pacific Ocean

@article {pmid42780152,
year = {2026},
author = {Cui, D and Ren, X and Li, N},
title = {Integrating metagenomics, transcriptomics, and molecular docking to reveal core gene biomarkers and gut microbiota regulatory mechanisms in tuberculous meningitis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1844914},
pmid = {42780152},
issn = {1664-3224},
mesh = {Humans ; *Tuberculosis, Meningeal/microbiology/genetics/metabolism/immunology ; Molecular Docking Simulation ; *Metagenomics/methods ; *Gastrointestinal Microbiome/immunology ; Biomarkers ; Female ; Male ; Gene Expression Profiling ; *Transcriptome ; Dysbiosis/microbiology ; Adult ; Macrophages/immunology/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {PURPOSE: Tuberculous meningitis (TBM) is a severe extrapulmonary tuberculosis with high mortality and neurological sequelae, while the role of gut microbiota and its metabolites in TBM pathogenesis remains poorly understood. This study aimed to characterize gut microbiota alterations in TBM patients and elucidate the "microbiota-metabolite-gene" regulatory axis.

METHODS: Fecal samples from 11 TBM patients and 11 healthy controls were subjected to 16S rRNA sequencing. Core target genes were identified via differential expression screening, machine learning, immune infiltration analysis and gene set enrichment analysis based on the public GSE40586 dataset. The regulatory axis was constructed by database prediction and molecular docking, and the regulatory effect was verified by in vitro functional assays in THP-1-derived macrophages.

RESULTS: TBM patients exhibited significant gut dysbiosis. Two core genes (PIK3CB and JAK2) were identified, which were positively correlated with pro-inflammatory immune cells and enriched in bacterial infection pathways. The constructed regulatory axis showed that upregulated gut bacteria produced bile acid metabolites targeting PIK3CB/JAK2, with strong binding affinity verified by molecular docking. In vitro experiments verified that CDCA dose-dependently upregulated PIK3CB and JAK2 expression and promoted pro-inflammatory activation of macrophages, while silencing of target genes significantly reversed this effect.

CONCLUSION: This study identifies a "gut microbiota-bile acid-PIK3CB/JAK2" regulatory axis in TBM, thus providing novel insights into gut-brain crosstalk and potential diagnostic biomarkers and therapeutic targets.},
}

Humans
*Tuberculosis, Meningeal/microbiology/genetics/metabolism/immunology
Molecular Docking Simulation
*Metagenomics/methods
*Gastrointestinal Microbiome/immunology
Biomarkers
Female
Male
Gene Expression Profiling
*Transcriptome
Dysbiosis/microbiology
Adult
Macrophages/immunology/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid42780395,
year = {2026},
author = {Ma, C and Lei, S and Zhang, G and Hu, X and Qiu, X and Wang, Q and Kang, X},
title = {Multiorgan and gut microbial alterations in ovariectomized mice: a multiomics analysis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1847257},
doi = {10.3389/fimmu.2026.1847257},
pmid = {42780395},
issn = {1664-3224},
mesh = {Animals ; *Ovariectomy ; Female ; Multiomics ; *Gastrointestinal Microbiome ; Mice ; Liver/metabolism ; Metabolomics/methods ; Colon/metabolism/microbiology ; Muscle, Skeletal/metabolism ; Metabolome ; Mice, Inbred C57BL ; Transcriptome ; },
abstract = {INTRODUCTION: Postmenopausal metabolic dysfunction is increasingly recognized as a multisystem disorder associated with estrogen deficiency, yet how gut microbial, metabolic, and tissue-level alterations co-occur across organs remains incompletely characterized.

METHODS: Here, we used an ovariectomy (OVX) mouse model and an integrated multiomics strategy to characterize systemic alterations in gut microbiota, metabolites in colonic contents and circulation, and tissue-level molecular profiles across the colon, liver, skeletal muscle, and bone.

RESULTS: OVX mice showed higher body weights at multiple postoperative time points, lower serum estradiol concentrations, differences in selected inflammatory and bone-turnover markers, representative histological differences across multiple tissues, and OVX-Sham differences in femoral microarchitecture. Shotgun metagenomic profiling showed significant differences in gut microbial composition, with lower evenness-sensitive diversity and differences in dominant taxa. Metabolomic profiling of colonic contents demonstrated global differences in the luminal metabolic profile, including lower relative abundances of major short-chain fatty acids, differences in bile acid composition, and prominent tryptophan-related features. At the host interface, colonic transcriptomic analysis identified annotations related to epithelial membrane polarity, vesicle trafficking, endoplasmic reticulum protein processing, and bile acid- and energy-sensing pathways. Among the 19 differential circulating bile acids and short-chain fatty acids, most were lower in OVX mice. Feature-level analyses identified multiple hepatic metabolite and bile acid differences, whereas the hepatic transcriptome did not show significant global separation; differential-expression and gene-set enrichment analyses nonetheless identified selected differences related to lipid metabolism, energy metabolism, and molecular transport. Distal tissues also displayed molecular differences, including a significant global transcriptomic difference in skeletal muscle and a significant global metabolomic difference in bone; differential bone metabolites were annotated to energy-, amino-acid-, lipid-, and cyclic guanosine monophosphate-protein kinase G (cGMP-PKG)-related pathways.

DISCUSSION: Collectively, these findings define a gut-associated, multiorgan pattern of OVX-related remodeling characterized by concurrent microbial, metabolite, and tissue-level differences. This descriptive, associative, and hypothesis-generating dataset provides a reference for future studies testing the relevance of these OVX-associated patterns to menopause-associated metabolic dysfunction.},
}

Animals
*Ovariectomy
Female
Multiomics
*Gastrointestinal Microbiome
Mice
Liver/metabolism
Metabolomics/methods
Colon/metabolism/microbiology
Muscle, Skeletal/metabolism
Metabolome
Mice, Inbred C57BL
Transcriptome

@article {pmid42271018,
year = {2026},
author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG},
title = {Disruption of the spinal cord-gut axis alters microbial dynamics and carbohydrate cross-feeding in the gut.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42271018},
issn = {2399-3642},
support = {890085//Craig H. Neilsen Foundation (Neilsen Foundation)/ ; ABI#2149505//National Science Foundation (NSF)/ ; DBI#2022070//National Science Foundation (NSF)/ ; },
mesh = {Animals ; Female ; Mice, Inbred C57BL ; Mice ; Male ; *Gastrointestinal Microbiome ; *Spinal Cord/physiology ; *Spinal Cord Injuries/microbiology/metabolism ; Metagenome ; *Carbohydrate Metabolism ; Metagenomics ; },
abstract = {Spinal cord-gut communication regulates gut bacteria, yet the underlying mechanisms remain poorly understood. Previous studies relied primarily on gene markers with limited functional analysis or genome-resolved snapshots from small cohorts. Here, we assessed microbiome dynamics via genome-resolved metagenomics on 333 samples from male and female C57BL/6 mice collected before and up to six months after surgical disruption of the spinal cord-gut axis. This resulted in 6,635 microbial draft genomes as a foundation for a new "Mouse B6 Gut Catalog" that significantly expands species and strain representation for this widely used laboratory mouse strain. Sampling revealed that disrupted spinal cord-gut signaling causes persistent, lesion-severity-, sex-, and time-specific shifts in microbial community composition, with consistent depletion of Lactobacillus johnsonii. Feeding purified L. johnsonii to spinal cord-injured mice prevented metabolic defects and systemic inflammation caused by disruption of the spinal cord-gut axis. Analyses using genome-resolved and community-based metabolic profiling indicated altered carbohydrate sharing and utilization of gut microbes, potentially depleting L. johnsonii, providing a genome-inferred mechanism for future hypothesis testing. This study improves murine microbiome catalogs, illustrates how metagenome-informed microbial interventions can provide a mechanistic understanding to improve host health, and underscores the vital role of a healthy spinal cord in regulating gut ecosystem function.},
}

Animals
Female
Mice, Inbred C57BL
Mice
Male
*Gastrointestinal Microbiome
*Spinal Cord/physiology
*Spinal Cord Injuries/microbiology/metabolism
Metagenome
*Carbohydrate Metabolism
Metagenomics

@article {pmid42560056,
year = {2026},
author = {Bernate, E and Shi, Y and Franck, E and Crofts, TS},
title = {A functionally selected Acinetobacter sp. phosphoethanolamine transferase gene from the goose fecal microbiome confers colistin resistance in E. coli.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {9},
pages = {e0246825},
pmid = {42560056},
issn = {1098-5336},
support = {7004080//National Institute of Food and Agriculture/ ; },
mesh = {*Colistin/pharmacology ; Animals ; *Escherichia coli/drug effects/genetics ; *Acinetobacter/genetics/enzymology ; *Anti-Bacterial Agents/pharmacology ; *Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; *Ethanolaminephosphotransferase/genetics/metabolism ; *Microbiota ; *Bacterial Proteins/genetics/metabolism ; },
abstract = {Polymyxins are last-resort antibiotics for infections caused by multidrug-resistant gram-negative bacteria such as Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii. This makes the rise of bacteria exhibiting polymyxin E (colistin) resistance, largely through modification of lipid A moieties, concerning and suggests that it is important to document the potential sources of the corresponding resistance genes. This study searched for potential emerging colistin resistance genes from the environment by investigating a previously performed functional metagenomic selection for colistin resistance of a goose fecal microbiome. We found that the selection captured Acinetobacter sp. DNA fragments that all contained eptA genes. We confirmed their ability to confer significant colistin resistance in Escherichia coli via modification of lipid A in the outer membrane. Furthermore, we found evidence for mobilization of closely related eptA genes in Acinetobacter genomes, marking them as potential mcr genes or their precursors. This study highlights the potential for functional metagenomic selections for colistin resistance to capture genes from unexpected environmental sources such as the goose fecal microbiome.IMPORTANCEColistin is an important antibiotic of last resort, and increasing resistance to this drug via mobile phosphoethanolamine transferase genes, such as mcr-1, threatens its clinical utility. Given the discovery of mcr-1 in pigs, the ability of animals to act as vectors in the spread of colistin resistance is alarming. We show here that functionally selected Acinetobacter phosphoethanolamine transferase genes from the goose microbiome have the ability to confer clinical levels of colistin resistance when transferred into E. coli. While the genes are annotated as eptA homologs, closer study of these genes suggests that they may be mobilized within the Acinetobacter genus, suggesting that they may be mcr genes of concern instead.},
}

*Colistin/pharmacology
Animals
*Escherichia coli/drug effects/genetics
*Acinetobacter/genetics/enzymology
*Anti-Bacterial Agents/pharmacology
*Feces/microbiology
*Drug Resistance, Bacterial/genetics
*Ethanolaminephosphotransferase/genetics/metabolism
*Microbiota
*Bacterial Proteins/genetics/metabolism

@article {pmid42772323,
year = {2026},
author = {Li, SS and Niu, YH and Yu, HJ},
title = {A retrospective metagenomic analysis of fecal microbiota transplantation donors from five countries: Safety considerations for donor screening and core microbiome profiles of qualified donors.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {9},
pages = {e2604010},
doi = {10.71150/jm.2604010},
pmid = {42772323},
issn = {1976-3794},
support = {//Shanghai Engineering Research Center of Innovative Probiotic Drugs/ ; },
mesh = {Humans ; Retrospective Studies ; *Fecal Microbiota Transplantation/adverse effects ; *Metagenomics ; *Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Canada ; New Zealand ; Netherlands ; China ; United States ; *Tissue Donors ; *Donor Selection ; Virulence Factors/genetics ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; },
abstract = {Fecal microbiota transplantation (FMT) has been successfully applied on clinical aspects, but its clinical outcomes remain unpredictable due to inconsistent donor screening protocols across hospitals, institutions, and countries. Hence, a retrospective analysis of metagenomic data from published studies on FMT donors via a unified bioinformatics workflow might contribute to the understanding of the safety considerations for donor screening and the fecal microbial profiles of qualified donors. In this study, we reanalyzed metagenomic data of 475 screened donor fecal samples from 24 studies spanning China, the USA, Canada, New Zealand, and the Netherlands. The genomic safety risks were evaluated by profiling antibiotic resistance genes (ARGs) and virulence factors (VFs), the results of which showed that no major toxin-associated virulence genes, such as Shiga toxin, Shiga-like toxin, or botulinum neurotoxin (BoNTs) genes harbored in the detected Escherichia coli, Clostridium butyricum, and Streptococcus pneumoniae, but several high-risk ARGs remained insufficiently addressed. The distribution of ARG-harboring bacteria in eligible FMT donors was country-specific. The alpha-diversity and microbial community structure were comparable between donor fecal samples from China and the USA. Interestingly, the core microbiome in fecal samples from Canada, the Netherlands, and New Zealand formed a single guild, while that from China and the USA formed two guilds, with predominantly positive intra-guild and negative inter-guild correlations, indicating that the co-abundance patterns of the core microbiome were conserved among certain countries. Furthermore, an exploratory retrospective classifier was developed based on core microbiome profiles to distinguish eligible FMT donors from general healthy individuals. These results provide evidence for integrating metagenomic sequencing into future FMT donor screening strategies.},
}

Humans
Retrospective Studies
*Fecal Microbiota Transplantation/adverse effects
*Metagenomics
*Feces/microbiology
*Bacteria/genetics/classification/isolation & purification
Canada
New Zealand
Netherlands
China
United States
*Tissue Donors
*Donor Selection
Virulence Factors/genetics
*Metagenome
*Gastrointestinal Microbiome/genetics
*Microbiota/genetics

@article {pmid42566872,
year = {2026},
author = {Pei, Y and Xu, Z and Xie, L and Wang, H},
title = {Enrichment of bile salt hydrolase-producing bacteria mediated by tetracycline resistance genes is associated with intestinal barrier damage in Rana chensinensis tadpoles.},
journal = {Ecotoxicology and environmental safety},
volume = {323},
number = {},
pages = {120624},
doi = {10.1016/j.ecoenv.2026.120624},
pmid = {42566872},
issn = {1090-2414},
mesh = {Animals ; Larva/drug effects/microbiology ; Intestinal Barrier Function/drug effects ; *Amidohydrolases/metabolism/genetics ; Bile Acids and Salts/metabolism ; *Tetracycline Resistance/genetics ; *Ranidae/microbiology ; *Intestines/drug effects/pathology ; *Tetracycline/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Bacteria/genetics/drug effects/enzymology ; *Water Pollutants, Chemical/toxicity ; *Anti-Bacterial Agents/toxicity ; },
abstract = {Tetracycline (TET) is a pervasive contaminant in aquatic environments, yet how it reshapes gut microbiota composition and function to influence bile acid (BA) profiles and intestinal health remains poorly understood. In this study, Rana chensinensis tadpoles at Gosner stage 26 (Gs26) were exposed to environmentally relevant concentrations of tetracycline hydrochloride (10 and 100 μg/L) until metamorphic climax Gs38 and examined using a multi-pronged approach integrating histological analysis, intestinal targeted BA metabolomics, and fecal metagenomic sequencing. Our results showed that TET exposure disrupted intestinal barrier integrity in a dose-dependent manner, as evidenced by reduced enterocyte height, widened intercellular spaces, and irregular nuclear morphology. Metagenomic profiling revealed that TET treatment significantly enriched tetracycline resistance genes (e.g., tet(Q), tet(T), tetA(46), tetA(60)), which was accompanied by an increased abundance of bile salt hydrolase (BSH)-producing bacteria, including Bacteroides, Parabacteroides, and Vibrio. This microbial shift was accompanied by enhanced BA deconjugation, as reflected by a significantly increased ratio of unconjugated to conjugated BAs (p < 0.01). Notably, the enhanced deconjugation activity was paralleled by a marked accumulation of the hydrophobic and cytotoxic BA, chenodeoxycholic acid (CDCA) (p < 0.001), which was accompanied by a 73.9% reduction in total BA levels - a pattern that may reflect Farnesoid X Receptor (FXR)-mediated negative feedback regulation of hepatic BA synthesis, although this pathway was not directly examined. Furthermore, elevated CDCA levels were associated with intestinal histopathological damage. Collectively, these findings suggest a potential mechanistic cascade in which TET-induced enrichment of antibiotic resistance genes is associated with the expansion of BSH-active microbiota, together with disrupted BA homeostasis and compromised intestinal barrier function in amphibians. Causal relationships within this cascade await functional validation. Our study highlights the hidden ecological risks of antibiotic contamination in aquatic ecosystems and underscores the need for further molecular investigations into the signaling pathways involved.},
}

Animals
Larva/drug effects/microbiology
Intestinal Barrier Function/drug effects
*Amidohydrolases/metabolism/genetics
Bile Acids and Salts/metabolism
*Tetracycline Resistance/genetics
*Ranidae/microbiology
*Intestines/drug effects/pathology
*Tetracycline/toxicity
*Gastrointestinal Microbiome/drug effects
*Bacteria/genetics/drug effects/enzymology
*Water Pollutants, Chemical/toxicity
*Anti-Bacterial Agents/toxicity

@article {pmid42615618,
year = {2026},
author = {Hutchinson, NT and Maino-Vieytes, CA and Valls, C and Allen, J and Rund, LA and Johnson, RW and Woods, JA},
title = {Fermentation capacity of the gut microbiota influences exercise motivation and neuroendocrine integration.},
journal = {mSystems},
volume = {11},
number = {9},
pages = {e0087626},
pmid = {42615618},
issn = {2379-5077},
mesh = {Animals ; *Motivation/physiology ; Mice ; Mice, Inbred C57BL ; *Fermentation ; *Gastrointestinal Microbiome/physiology/drug effects ; Male ; *Physical Conditioning, Animal/physiology ; *Neurosecretory Systems/physiology/metabolism ; Prebiotics ; Corticosterone/blood ; Fatty Acids, Volatile/metabolism ; },
abstract = {UNLABELLED: Physical inactivity contributes substantially to global disease burden, yet the physiological mechanisms underlying exercise motivation remain poorly understood. The gut-brain axis presents a potentially modifiable target for behavioral intervention. Emerging evidence demonstrates that the gut microbiota influences motivated behaviors, but the specific metabolic functions and physiological mechanisms mediating these effects remain poorly defined. Here, we demonstrate that the predicted fermentation capacity of the gut microbiota influences voluntary wheel running (VWR) acquisition and neuroendocrine integration during exercise in C57BL/6J mice. Antibiotic-induced microbiome depletion reduced VWR acquisition, while shifting predicted function toward aerobic respiration and away from anaerobic fermentation. Supplementation with short-chain fatty acids, the primary fermentative products, restored normal VWR activity in microbiome-depleted mice. Conversely, 4-week dietary pretreatment with 2.5% prebiotic fiber (inulin) increased predicted fermentative capacity of the microbiota and VWR activity above baseline levels. Microbiome manipulation produced bidirectional dysregulation of corticosterone responses to exercise: acute antibiotic depletion increased post-exercise concentrations, while germ-free development decreased them, despite elevated striatal catecholamines. This exercise-specific uncoupling reveals microbiome-dependent integration of metabolic demand signals in the coordination of sympathetic and hypothalamic-pituitary-adrenal axis responses. Furthermore, the inulin-induced enhancement in VWR activity was associated with increased striatal histamine concentrations following exercise, suggesting additional mechanisms of neuromodulation. These findings demonstrate that the fermentative capacity of the gut microbiota influences exercise motivation and neuroendocrine regulation, providing novel insights into dietary interventions targeting physical activity.

IMPORTANCE: Physical inactivity is a leading cause of global morbidity and mortality, and our lack of understanding of the biological forces driving motivation to exercise limits our ability to develop interventions that enhance engagement. Using a rodent model of voluntary exercise along with microbiota depletion and metabolite replacement, we uncovered that the gut microbiota and its capacity to ferment dietary components into short-chain fatty acids drive exercise habit acquisition and help facilitate coordination between neurochemical signals and systemic stress hormones during exercise. Additionally, microbiome depletion "uncoupled" these systems, resulting in dysregulated stress responses during forced exercise. Finally, we showed that enhancement of microbiota fermentation capacity via dietary addition of prebiotic fiber was able to increase exercise engagement while also enhancing concentrations of histamine, a neuromodulator that potentiates locomotor activity, in the striatum. These findings suggest that the gut microbiome is a modifiable target for behavior change that facilitates integration of metabolic demand in neuroendocrine activity. Collectively, this work provides a mechanistic foundation to support the use of dietary interventions in sedentary populations to start exercise habits.},
}

Animals
*Motivation/physiology
Mice
Mice, Inbred C57BL
*Fermentation
*Gastrointestinal Microbiome/physiology/drug effects
Male
*Physical Conditioning, Animal/physiology
*Neurosecretory Systems/physiology/metabolism
Prebiotics
Corticosterone/blood
Fatty Acids, Volatile/metabolism

@article {pmid42635434,
year = {2026},
author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ},
title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.},
journal = {mSystems},
volume = {11},
number = {9},
pages = {e0030326},
pmid = {42635434},
issn = {2379-5077},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; //McGill University Health Centre/ ; /NH/NIH HHS/United States ; },
mesh = {Humans ; *Prophages/drug effects/genetics ; *Ciprofloxacin/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Metagenome/drug effects ; *Virus Activation/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/virology/genetics ; Species Specificity ; Metagenomics ; },
abstract = {Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction, and whether it is associated with antibiotic exposure. In two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in certain bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.IMPORTANCEBacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host cell to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death, which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro, whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations.},
}

Humans
*Prophages/drug effects/genetics
*Ciprofloxacin/pharmacology
*Gastrointestinal Microbiome/drug effects/genetics
*Metagenome/drug effects
*Virus Activation/drug effects
*Anti-Bacterial Agents/pharmacology
*Bacteria/drug effects/virology/genetics
Species Specificity
Metagenomics

@article {pmid42671180,
year = {2026},
author = {Li, T and Lu, X and Alomeir, N and Gaca, A and Sohn, M and Gill, S and Smith, B and Munger, J and Xiao, J},
title = {Longitudinal development of infant oral ecosystem: salivary metabolomic, bacteriome, and virome dynamics in early infancy.},
journal = {mSystems},
volume = {11},
number = {9},
pages = {e0094626},
pmid = {42671180},
issn = {2379-5077},
support = {R01 DE031025/DE/NIDCR NIH HHS/United States ; R01DE031025/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Saliva/microbiology/virology/metabolism ; Infant ; *Virome ; Female ; *Metabolome ; Longitudinal Studies ; Metabolomics/methods ; *Mouth/microbiology ; Male ; Child, Preschool ; Microbiota ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Prospective Studies ; Dental Plaque/microbiology/virology ; Multiomics ; },
abstract = {This prospective cohort study investigated the longitudinal development of the salivary bacteriome, virome, and metabolome during early infancy. We assessed the associations between oral bacteria, viruses, and metabolites from 10 mother-infant dyads, with oral samples collected at 1 and 2 years of age. Forty saliva and plaque samples underwent untargeted metabolomic analysis, and infant saliva samples underwent metagenomic sequencing. Maternal salivary and plaque metabolomic profiles remained largely stable, whereas infant profiles were clearly separated from maternal profiles and changed with age. Notably, infant dental plaque metabolism underwent more substantial changes from year 1 to year 2 than saliva, with age-dependent metabolite shifts mainly involving energy, amino acid, nucleotide, and lipid metabolic pathways. Our findings also revealed significant developmental shifts in salivary bacteriome, virome, and functional pathway profiles during early childhood. The most abundant oral bacteria in early life, comprising over 75% of total abundance, included Veillonella, Streptococcus, Rothia, Prevotella, Neisseria, and Actinomyces species. While human viruses like Roseolovirus were detected, bacteriophages constituted the majority of the virome. Comparing infants at year 1 and year 2, we identified differentially abundant bacteria, viruses, metabolic functional pathways, and specific metabolites. We observed associations between bacteria and viruses, noting that these cross-kingdom relationships attenuated as infants grew. The study results underscore the complex and dynamic development of the oral microbiome, virome, and metabolome during early childhood.IMPORTANCEThe human oral cavity undergoes substantial microbial and metabolic development during early childhood, yet the temporal changes in the infant oral ecosystem remain incompletely understood. In this study, we longitudinally profiled the salivary metabolome, bacteriome, and virome of infants at 1 and 2 years of age. We demonstrated that the infant oral metabolome undergoes substantial developmental shifts, particularly in pathways related to energy, amino acid, and lipid metabolism; whereas maternal metabolic profiles remained stable over the same period. Furthermore, our results revealed the dynamic assembly of infant salivary virome and bacteriome and their associations with the functional pathways and metabolites. These findings provide new insights into the complex and dynamic development of the oral microbiome, virome, and metabolome in early infancy.},
}

Humans
*Saliva/microbiology/virology/metabolism
Infant
*Virome
Female
*Metabolome
Longitudinal Studies
Metabolomics/methods
*Mouth/microbiology
Male
Child, Preschool
Microbiota
*Bacteria/genetics/classification/metabolism/isolation & purification
Prospective Studies
Dental Plaque/microbiology/virology
Multiomics

@article {pmid42678156,
year = {2026},
author = {Wu, Q-Q and Li, C-Y and Chen, S-S and Xu, J and Yan, W-H and Lu, L-N and Feng, H-X and Zhou, J-A and Wang, L and Liu, N-N and Jiang, L and Wang, Y},
title = {Multi-kingdom gut microbiota analyses identify biomarkers of different types of pediatric short bowel syndrome.},
journal = {mSystems},
volume = {11},
number = {9},
pages = {e0031626},
pmid = {42678156},
issn = {2379-5077},
support = {82370525//National Natural Science Foundation of China/ ; 2023YFC2706505//National Key R&D Program of China/ ; //Shanghai JiaoTong University School of Medicine "Double Hundred Talents" Program/ ; 82470602//National Natural Science Foundation of China/ ; 82570601//National Natural Science Foundation of China/ ; 23ZR1452600//Natural Science Foundation of Shanghai Municipality/ ; 22ZR1441100//Natural Science Foundation of Shanghai Municipality/ ; 2023005//Shanghai medical New Star Outstanding Young Medical Talents Project/ ; 20234Z0004//Shanghai Municipal Health Commission/ ; 2022YFA1305600//National Key R&D Program of China/ ; },
mesh = {Humans ; *Short Bowel Syndrome/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Child, Preschool ; Male ; Biomarkers ; Feces/microbiology ; Infant ; Bacteria/genetics/classification/isolation & purification ; Child ; Archaea/genetics/isolation & purification/classification ; },
abstract = {Despite recent advances in bacterial profiling across the three anatomical types of pediatric short bowel syndrome (SBS), the gut multi-kingdom remains unexplored. We characterized the four-kingdom gut microbiota using modified DNA extraction and deep shotgun metagenomic sequencing of fecal samples from 26 healthy controls and 34 pediatric SBS patients comprising three types (8 SBS I, 15 SBS II, and 11 SBS III). Overall, children with SBS exhibited a significant reduction in α-diversity compared with controls, with no difference observed among SBS types. Compared with controls, the proportion of archaea was significantly decreased in all SBS types, while bacteria, fungi, and viruses remained similar across types. Different types of SBS exhibited distinct microbial signatures: SBS I was enriched with pathogens (such as species from the Streptococcus and Klebsiella genera); SBS II was marked by a depletion of beneficial short-chain fatty acid-producing species (such as Faecalibacterium prausnitzii); and SBS III displayed loss of bile acid-metabolizing species, alongside a significant expansion of Lactobacillus species. Ecological networks were rewired in SBS, with disruption pronounced in SBS I. Functional analysis revealed that core metabolic pathways were markedly suppressed in SBS I compared with controls. Integrated correlation analyses revealed ileocecal valve loss as the primary determinant of SBS I microbial profiles, linking it to impaired secretory functions and hepatic injury. Our findings deciphered type-specific alterations in the multi-kingdom microbiota and their functional profiles, providing the basis for designing precision microbial therapies aimed at improving long-term outcomes for children with SBS.IMPORTANCEPediatric short bowel syndrome (SBS) is a primary cause of intestinal failure, yet prior research characterizing the gut microbiota has focused almost exclusively on bacteria. In this study, we characterized the multi-kingdom microbiome (including bacteria, fungi, archaea, and viruses) across the three anatomical types of pediatric SBS. We found that different SBS subtypes showed distinct microbial patterns: SBS I was enriched in pathogens, SBS II exhibited a depletion of beneficial short-chain fatty acid-producing species, and SBS III was characterized by a loss of bile acid-metabolizing microbes with an expansion of Lactobacillus. Functional analysis showed that SBS I had markedly suppressed core metabolic pathways, and integrated analyses identified the ileocecal valve as a key determinant of microbial gene profiles, with its loss linked to impaired secretion and liver injury. These findings provide a comprehensive multi-kingdom view of the pediatric SBS microbiome and highlight anatomical determinants shaping host-microbiome dysfunction.},
}

Humans
*Short Bowel Syndrome/microbiology
Female
*Gastrointestinal Microbiome/genetics
Child, Preschool
Male
Biomarkers
Feces/microbiology
Infant
Bacteria/genetics/classification/isolation & purification
Child
Archaea/genetics/isolation & purification/classification

@article {pmid42679417,
year = {2026},
author = {Li, H and Gao, H and Fu, J and Yang, S and Chen, L and Zhou, J},
title = {Comparative analysis of microbial communities, assembly processes, and life-history strategies in a mariculture-impacted eutrophic bay and adjacent coastal sediments.},
journal = {Ecotoxicology and environmental safety},
volume = {323},
number = {},
pages = {120750},
doi = {10.1016/j.ecoenv.2026.120750},
pmid = {42679417},
issn = {1090-2414},
mesh = {*Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bays/microbiology ; Eutrophication ; *Microbiota/drug effects ; China ; *Bacteria/genetics/classification/drug effects ; Metagenomics ; Seawater/microbiology ; Life History Traits ; },
abstract = {Coastal embayments are increasingly subjected to intensive mariculture, which delivers sustained nutrient, organic matter, and antibiotics to sediments, yet microbiome responses remain poorly understood. Here we compared sediment microbiomes of the eutrophic Xiangshan Bay (XSB) and oligotrophic East China Sea (ECS), integrating cell counts, 16S rRNA amplicon, metagenomics, and cultivation-based resistance assays. Cell counts and amplicon data showed that XSB harbored higher microbial abundance (1.28 ×10[8]-1.34 ×10[9] vs. 2.07 ×10[7]-4.43 ×10[8] cells g[-1]), Chao1 richness (10,374-16,674 vs. 8311-12,281), and Shannon diversity (6.31-7.43 vs. 5.95-6.68). Amplicon-based null and neutral models indicated that community assembly in XSB was less stochastic and more deterministically selected than in the ECS. Life-history traits inferred directly from metagenomic data were consistently elevated in XSB relative to ECS, including 16S rRNA gene copy number (3.35 vs. 2.37), codon usage bias (0.0219 vs. 0.0188), maximum growth potential (0.1208 vs. 0.0844 h[-1]), genome size (5.63 vs. 5.38 Mb), GC content (56.26% vs. 54.48%), and transposase abundance (3.91% vs. 2.55%), collectively indicating a transition from K- to r-selected life-history strategies. Moreover, metagenomic annotation revealed a similarly expanded resistome in XSB, with 4.5-fold higher antibiotic resistance gene abundance (17.40-45.37 vs. 7.96-25.96 RPM) dominated by efflux-pump mechanisms, while plate assays showed roughly two-fold higher phenotypic resistance to macrolides, tetracyclines, and sulfonamides. These findings demonstrate that microbial community, life-history strategies, and antibiotic resistance respond as a coupled system to mariculture-driven eutrophication, providing a trait-based framework for predicting microbiome trajectories under anthropogenic nutrient enrichment.},
}

*Geologic Sediments/microbiology
RNA, Ribosomal, 16S/genetics
*Bays/microbiology
Eutrophication
*Microbiota/drug effects
China
*Bacteria/genetics/classification/drug effects
Metagenomics
Seawater/microbiology
Life History Traits

@article {pmid42754330,
year = {2026},
author = {Na, SI and Kim, J and Kim, SY and Park, J and Cho, YJ},
title = {SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {9},
pages = {e2606011},
doi = {10.71150/jm.2606011},
pmid = {42754330},
issn = {1976-3794},
support = {//National Research Foundation of Korea/ ; RS-2023-00301850//Ministry of Education/ ; RS-2026-25491179//Ministry of Science and ICT/ ; 2024ER210600//Korea National Institute of Health research project/ ; },
mesh = {*Microbiota ; Internet ; *Software ; Bacteria/classification/genetics ; *Computational Biology/methods ; Workflow ; Metagenomics/methods ; },
abstract = {Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.},
}

*Microbiota
Internet
*Software
Bacteria/classification/genetics
*Computational Biology/methods
Workflow
Metagenomics/methods

@article {pmid42765765,
year = {2026},
author = {Benot, AO and Waldschmidt, G and Gilvarg, SC and Legge, EOL and Okyere, IJ and Tiyapun, C and Lucas, SK and Vander Yacht, AL and Goff, JL},
title = {Prescribed burns drive lasting changes in soil nitrogen cycling and microbial function.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0085226},
doi = {10.1128/msystems.00852-26},
pmid = {42765765},
issn = {2379-5077},
abstract = {Fire is a major pulse disturbance to soil microbial communities, with broad implications for nutrient cycling; however, regular burning is also a natural and often-essential process maintaining biodiversity in unique and imperiled fire-dependent ecosystems. Prescribed fire is widely used to promote this biodiversity and simultaneously reduce wildfire risk. Although such repeated burning is known to alter surface biodiversity, belowground soil geochemistry, and soil microbial community structure, the functional consequences (i.e., the metabolic capabilities that underlie the ecosystem services soil microorganisms provide) remain underexplored. Here, we examined the effects of 30 years of repeated prescribed fire at the Albany Pine Bush-a fire-dependent, inland pitch pine barren ecosystem of the northeastern United States. Compared with the control stands, we observed that this long-term fire management has led to substantial depletion of inorganic soil nitrogen, specifically nitrate. We found no meaningful differences in the higher-level taxonomic composition of soil prokaryotic or fungal communities; however, analysis of metagenome-assembled genomes assembled from these soils revealed several differentially abundant populations. Furthermore, our metagenomic analysis revealed significant changes in the nitrogen-cycling functional potential, specifically decreased dissimilatory nitrate reduction and denitrification potential in repeatedly burned soils. These functional shifts have important implications for both nutrient cycling and emissions of trace nitrogen gases from these soils. Our results suggest that functionally meaningful changes in the soil microbiome can persist between burn events, even when higher-order community membership appears stable. This may imply that repeated fire can deplete reactive nitrogen emissions from soils by lowering the functional capacity of nitrogen-reducing microbes.IMPORTANCEPrescribed fire is widely used by land managers to reduce wildfire risk and promote biodiversity. While the effects of fire on aboveground processes are well understood, much less is known about how repeated burning influences soil biological properties-including the functional role that soil microorganisms play in nutrient cycling and greenhouse gas production. We addressed this gap by studying soils from the Albany Pine Bush, a rare and endangered ecosystem that has experienced regular prescribed fires for 30 years. Long-term fire management significantly altered soil chemistry, specifically lowering the amount of nitrogen in the soil. In addition, we found that fire management decreased the genetic potential of the soil microbial community to produce nitrogen oxides-potent contributors to climate change. Thus, prescribed fire's contribution to greenhouse gas emissions may involve a complex relationship between direct fire-driven emissions, increased fire resilience of promoted vegetation, and-as suggested by our results-the reduced ability of soil microbes to produce greenhouse gases.},
}

@article {pmid42767975,
year = {2026},
author = {Burge, K and Velsko, IM and Salazar-García, DC and Uriarte, MH and Lomba Maurandi, J and Warinner, C},
title = {Comparing the Performance of Double-Stranded and Single-Stranded DNA Libraries for Ancient Oral Microbiome Reconstruction.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70201},
pmid = {42767975},
issn = {1755-0998},
support = {//Werner Siemens-Stiftung/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; //National Science Foundation/ ; },
mesh = {Animals ; *Microbiota ; *Mouth/microbiology ; *Gene Library ; Humans ; *DNA, Ancient ; Sequence Analysis, DNA ; DNA, Single-Stranded/genetics ; Neanderthals ; *Metagenomics/methods ; },
abstract = {DNA library construction methods can affect the recovery of ancient DNA, thus influencing downstream analyses. While single-stranded library preparation (ssLib) has been shown to outperform double-stranded (dsLib) for highly degraded vertebrate host DNA, especially for samples older than 40,000 years, few studies have examined how library protocols shape ancient microbial community reconstruction. Here, we compare the sequencing output of paired ssLib and dsLib dental calculus libraries generated from 12 Neanderthals and two Chalcolithic humans, prepared using implementations of the Gansauge et al. and Meyer and Kircher protocols, respectively, and sequenced with identical Illumina chemistry. We compared read length and GC%, read duplication and taxonomic profiles across normalization strategies to assess protocol-specific biases. Double-stranded libraries retained a significantly higher proportion of sequenced reads throughout data processing (dsLib 72.1%, ssLib 37.9%), a higher proportion of oral reads (dsLib 9.78%, ssLib 6.75%), significantly longer median oral DNA read lengths (dsLib 57.5 bp, ssLib 50.5 bp) and more GC-rich fragments (dsLib 60.5% GC, ssLib 52.5% GC). In contrast, ssLibs exhibited slightly higher Shannon diversity and a greater proportion of unique reads. Despite these differences, species richness and overall community composition was not significantly different between protocols, with individual and preservation status explaining the most variance. Stratifying reads by length (< 50 bp vs. ≥ 50 bp) resulted in different classification rates but only had minor effects on diversity estimates. Together, these results demonstrate that dsLib and ssLib protocols impose distinct trade-offs and library choice should be guided by study-specific goals.},
}

Animals
*Microbiota
*Mouth/microbiology
*Gene Library
Humans
*DNA, Ancient
Sequence Analysis, DNA
DNA, Single-Stranded/genetics
Neanderthals
*Metagenomics/methods

@article {pmid42768305,
year = {2026},
author = {Avershina, E and Birkeland, EE and Bucher-Johannessen, C and Rounge, TB},
title = {CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734649},
pmid = {42768305},
issn = {1949-0984},
mesh = {Humans ; *Interspersed Repetitive Sequences ; *Bacteria/genetics/classification/immunology/isolation & purification/virology ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems ; Plasmids/genetics ; Feces/microbiology ; Middle Aged ; Metagenome ; Norway ; Female ; Diet ; Bacteriophages/genetics ; Gastrointestinal Tract/microbiology ; },
abstract = {Bacteria in the human gut influence host physiology and disease risk, but their ecology is strongly shaped by mobile genetic elements (MGEs) such as phages and plasmids. Past interactions between bacteria and MGEs can be inferred from CRISPR-Cas cassettes, which contain short DNA fragments derived from invading elements. To lay the groundwork for research on the impact of such interactions on the human host, we constructed an extended microbiome resource comprising 1.7 K prokaryotic mOTUs, 19.5 K viral vOTUs, and 24.2 K plasmid PTUs, using fecal shotgun metagenomes from 1034 adults over 55 y of age residing in South-East Norway. We also recovered 74.2 K unique CRISPR-Cas cassettes to map past bacteria-MGE interactions and assessed their associations with the human diet and lifestyle factors. CRISPR-Cas spacers, and which viruses and plasmids they targeted, varied substantially within bacterial species, but were predominantly directed towards cohort-specific MGEs. Moreover, bacteria were more likely to target MGEs present in the same sample, consistent with local exposure. Plasmid MGEs were more often targeted by Type II CRISPR-Cas cassettes, whereas viruses were more likely to be targeted by Type I CRISPR-Cas cassettes. Bacteria also shared more targets within taxonomic families than across families, where mobilizable plasmids were more frequent among the targets. CRISPR-Cas cassettes mirrored microbiome associations to human demographic and lifestyle factors and enabled the recovery of dairy-associated B. animalis. Together, this research provides a large-scale resource and a structured analysis of bacteria-MGE interactions in the gut microbiome and their contribution to microbial ecosystem dynamics.},
}

Humans
*Interspersed Repetitive Sequences
*Bacteria/genetics/classification/immunology/isolation & purification/virology
*Gastrointestinal Microbiome/genetics
*CRISPR-Cas Systems
Plasmids/genetics
Feces/microbiology
Middle Aged
Metagenome
Norway
Female
Diet
Bacteriophages/genetics
Gastrointestinal Tract/microbiology

@article {pmid42771532,
year = {2026},
author = {Igwe, AN and Afkhami, ME},
title = {Redundancy maintains microbial ecosystem functional potential despite taxonomic shifts between serpentine and nonserpentine soils.},
journal = {Microbial genomics},
volume = {12},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001835},
pmid = {42771532},
issn = {2057-5858},
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Bacteria/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; California ; *Microbiota/genetics ; *Fungi/classification/genetics/isolation & purification ; Metagenomics/methods ; Ecosystem ; Metagenome ; },
abstract = {Environmental filtering and buffering are complementary processes responsible for stabilizing ecosystem services across landscapes. The extent to which either of these processes structures microbial composition and functions in extreme soil systems can be highly context-dependent, requiring site-specific examination to elucidate general principles of community function under stress. Serpentine soils have high amounts of heavy metals and magnesium and low levels of plant nutrients and exist in close proximity to nutrient-rich and plant-productive nonserpentine soils, making them an ideal system for evaluating selection and redundancy under stress. Combining biogeographical field surveys and shotgun metagenomic sequencing of microbiomes from 23 pairs of serpentine and nonserpentine soils across California, we investigated selection and functional redundancy between disparate soil types. We hypothesized that the strong selective pressure present in serpentine soils would result in distinct bacterial and functional profiles. Bacterial and fungal community taxonomic compositions were indeed distinct between serpentine and nonserpentine soils, while archaeal communities were similar between soil types. In contrast, functional repertoires of all microbial community groups were largely similar between soil types, with many of the same taxa carrying out functions across soil types. Still specialized functions in serpentine soils represented adaptations to stress in contrast to the carbon-rich environment of nonserpentine soils. For example, specialized functions - such as siderophore biosynthesis proteins, which are involved in the biosynthesis of iron-chelating compounds - were distinctive features of serpentine soils and specialized functions notably had similar functional redundancy but distinct taxa carrying out the functions across soil types. These results highlight taxa that perform the functions that have been selected for survival in an extreme soil ecosystem and the functions that are most at risk in the face of environmental disturbances.},
}

*Soil Microbiology
*Soil/chemistry
*Bacteria/classification/genetics/isolation & purification
Archaea/classification/genetics/isolation & purification
California
*Microbiota/genetics
*Fungi/classification/genetics/isolation & purification
Metagenomics/methods
Ecosystem
Metagenome

@article {pmid42555106,
year = {2026},
author = {Luo, Z and Liu, Y and Wu, H and Xiao, Y and Li, Y and Liu, M and Li, C and Zhu, D and Jin, LN and Dong, T and Yan, W},
title = {Zoo gut plastispheres enable pathogen escape and adaptation.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag207},
pmid = {42555106},
issn = {1751-7370},
support = {22425041//National Natural Science Foundation of China/ ; 22188102//National Natural Science Foundation of China/ ; 2023JJ30986//National Natural Science Foundation of China/ ; 2024JJ1016//National Natural Science Foundation of China/ ; 2022RC1118//Science and Technology Innovation Program of Hunan Province/ ; GZC20242059//Postdoctoral Science Foundation/ ; XLKJ202303//Scientific Research Project of Hunan Provincial Department of Education/ ; P0040336//Scientific Research Project of Hunan Provincial Department of Education/ ; },
mesh = {Animals ; Feces/microbiology/chemistry ; *Animals, Zoo/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microplastics/analysis ; *Gastrointestinal Microbiome ; Humans ; Biofilms ; Metagenomics ; Adaptation, Physiological ; },
abstract = {In zoos, intensive human contact and artificial feeding may create pathways for microplastic (MP) ingestion and gut colonization. We hypothesized that ingested MPs form intestinal plastispheres with elevated pathogenic potential and enhanced environmental persistence. To test this, we surveyed feces from 15 zoo-dwelling species and coupled particle characterization, feces-derived intestinal simulations, metagenomic sequencing, and a subsequent water-exposure experiment. Zoo feces contained more abundant MPs than reported for wild counterparts, with fragments predominating and polyethylene terephthalate (PET)/polystyrene (PS) dominating polymer profiles. MP burdens tracked human-animal interaction patterns, with human-fed species (e.g. Tiger, Elephant) carrying the highest loads (88-212 items/g). MPs supported dense biofilms whose composition diverged from bulk gut communities, exhibiting greater compositional variability and substrate-specific assembly. Metagenomic analyses revealed coordinated enrichment of potentially pathogenic taxa, virulence factor genes (VFGs), and antibiotic resistance genes (ARGs), with ARG profiles dominated by efflux- and inactivation-related mechanisms and tightly associated with mobile genetic elements. Elevated Type II/III/IV/VI secretion systems and effector delivery-related VFGs occurred within extracellular polymeric substance-rich biofilms, suggesting enhanced potential for ARG retention and horizontal gene transfer. During the 35-day aquatic exposure, MP-associated communities persisted longer than non-plastic particle-associated communities and free gut microbiota, suggesting that plastic-specific properties promote microbial persistence. PET/PS plastispheres showed the slowest declines in bacterial activity and favored the persistence of Enterococcus, Enterobacter, and Clostridium. Overall, intestinal MPs in zoo animals may select, enrich, and export high-risk microbiomes, highlighting the need for MP mitigation and evidence-based management of zoos and adjacent ecosystems.},
}

Animals
Feces/microbiology/chemistry
*Animals, Zoo/microbiology
*Bacteria/genetics/classification/isolation & purification
*Microplastics/analysis
*Gastrointestinal Microbiome
Humans
Biofilms
Metagenomics
Adaptation, Physiological

@article {pmid42657522,
year = {2026},
author = {Zheng, Y and Zhuang, H and Dan, L and Zhou, Y and Yan, B and Zhang, Y and Zou, D and Wang, X and Sun, J},
title = {Resistant starch alleviates intestinal fibrosis involving an acetate-mediated HDAC2-H3K27ac axis in fibroblasts.},
journal = {Food & function},
volume = {17},
number = {18},
pages = {8215-8230},
doi = {10.1039/d6fo01179a},
pmid = {42657522},
issn = {2042-650X},
mesh = {Animals ; Mice ; *Starch/pharmacology/metabolism ; *Fibroblasts/metabolism/drug effects ; Humans ; *Histones/metabolism ; Male ; Fibrosis ; Mice, Inbred C57BL ; *Histone Deacetylase 2/metabolism/genetics ; *Acetates/metabolism ; Colitis/chemically induced/metabolism ; *Intestines/pathology ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Dextran Sulfate ; },
abstract = {Dietary fibre-based interventions are of growing interest for the prevention and treatment of digestive diseases. In this study, we investigated the effect of resistant starch (RS) on intestinal fibrosis, a stricturing condition driven by excessive extracellular matrix (ECM) accumulation. RS was found to alleviate intestinal fibrosis in a dextran sulfate sodium (DSS)-induced chronic colitis mouse model, as evidenced by restored colon length, reduced ECM deposition (fibronectin and collagen I), and decreased levels of α-smooth muscle actin. Given that RS is fermented by the gut microbiota in the colon, metagenomic sequencing revealed that RS reshaped the composition of the gut microbiota and increased the abundance of beneficial gut bacteria, including Bacteroides acidifaciens, Faecalibaculum rodentium, and Bifidobacterium pseudolongum, which are known to enhance the production of short-chain fatty acids. Targeted metabolomic analysis further showed a marked increase in acetate levels, which was associated with reduced intestinal fibrosis. However, direct in vivo evidence that acetate is required for the anti-fibrotic effect of RS remains lacking. Using human (CCD-18Co) and primary mouse intestinal fibroblasts, the major ECM-producing cells that drive fibrosis progression, we demonstrated that acetate inhibited TGF-β-induced fibroblast activation by inhibiting histone deacetylase 2, thereby enhancing the acetylation level of histone H3 at lysine 27. Collectively, these results suggest a potential microbial-metabolic-epigenetic axis linking RS and acetate to fibrosis attenuation, which awaits causal validation in vivo. This axis holds promise as a therapeutic target for fibrotic diseases.},
}

Animals
Mice
*Starch/pharmacology/metabolism
*Fibroblasts/metabolism/drug effects
Humans
*Histones/metabolism
Male
Fibrosis
Mice, Inbred C57BL
*Histone Deacetylase 2/metabolism/genetics
*Acetates/metabolism
Colitis/chemically induced/metabolism
*Intestines/pathology
Gastrointestinal Microbiome/drug effects
Disease Models, Animal
Dextran Sulfate

@article {pmid42762131,
year = {2026},
author = {Xiang, Q and Li, Y and Yang, J},
title = {Translational efficiency guides microbial community remodeling.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2736907},
doi = {10.1080/19490976.2026.2736907},
pmid = {42762131},
issn = {1949-0984},
mesh = {*Microbiota ; Metagenomics ; *Microbial Interactions ; *Bacteria/genetics/metabolism ; *Protein Biosynthesis ; },
abstract = {While metagenomics provides compositional insights, its correlative nature limits causal community remodeling. Overcoming this, in a recent Cell study, Moyne et al. introduced the Microbial Interaction and Niche Determination (MIND) framework. By leveraging translational efficiency to map resource competition and niche partitioning, MIND establishes a mechanistic blueprint for rational engineering.},
}

*Microbiota
Metagenomics
*Microbial Interactions
*Bacteria/genetics/metabolism
*Protein Biosynthesis

@article {pmid42764218,
year = {2026},
author = {Huang, QY and Xiang, HR and Tu, HK},
title = {[Current research status of the intratumoral microbiome and evolution of detection technologies].},
journal = {Zhonghua zhong liu za zhi [Chinese journal of oncology]},
volume = {48},
number = {9},
pages = {1124-1138},
doi = {10.3760/cma.j.cn112152-20260303-00105},
pmid = {42764218},
issn = {0253-3766},
support = {82574197//National Natural Science Foundation of China/ ; K20230085//Healthy Zhejiang One Million People Cohort/ ; },
mesh = {Humans ; *Microbiota ; *Tumor Microenvironment ; *Neoplasms/microbiology/pathology ; Metagenomics ; Bacteria/isolation & purification ; },
abstract = {As a core functional component of the tumor microenvironment, the regulatory role of intratumoral microbiome in tumorigenesis and progression has become as a frontier research direction in oncology. Microorganisms such as bacteria, fungi, and viruses participate in the regulation of tumor biological mechanisms through multiple pathways, including metabolite secretion, induction of genomic instability, and remodeling of the immune microenvironment; their species composition and abundance characteristics exhibit distinct cancer-type specificity, and their impact on patient prognosis is highly context-dependent. Current detection systems for the intratumoral microbiome mainly encompass in situ detection technologies, metagenomic sequencing, and computational pathology-driven intelligent detection, each with its own advantages and limitations, among which intelligent detection centered on deep learning is gradually overcoming the technical bottlenecks of identifying low-abundance microbial signals, achieving accurate quantification, and resolving spatial distribution. In the future, with the deep integration of three-dimensional pathological imaging, spatial omics, and multi-modal foundation models, intratumoral microbiome research will advance toward the in-depth development of multi-dimensional data integration, providing innovative ideas and technical pathways for elucidating the regulatory mechanisms between microorganisms and the host and for developing precision diagnostic and treatment strategies based on individual microecological characteristics.},
}

Humans
*Microbiota
*Tumor Microenvironment
*Neoplasms/microbiology/pathology
Metagenomics
Bacteria/isolation & purification

@article {pmid42765266,
year = {2026},
author = {Wang, DD and Xie, YQ and Huang, YF and Jia, HC},
title = {[Seasonal Response Features of Microbial Community Structure for Nitrogen Transformation in Inland Lakes on the Qinghai-Xizang Plateau].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {9},
pages = {6558-6568},
doi = {10.13227/j.hjkx.202507365},
pmid = {42765266},
issn = {0250-3301},
mesh = {*Lakes/microbiology/chemistry ; *Nitrogen/metabolism/isolation & purification ; Seasons ; China ; *Bacteria/metabolism/classification ; *Water Microbiology ; Ecosystem ; *Microbiota ; },
abstract = {Studying the nitrogen transformation characteristics of microbial communities in the inland lakes of the Qinghai-Xizang Plateau （QXP） is of great significance for a deeper understanding of the nitrogen budget balance and biogeochemical cycling in the regional lake ecosystems. Based on metagenomic sequencing technology， this study constructed a non-redundant gene library of nitrogen-transforming microorganisms and conducted multivariate statistical analysis to explore the characteristics and assembly mechanisms of nitrogen-transforming microbial communities in inland lakes on the QXP. The results indicate： ① Bacteria were the main group of nitrogen transformation microbes in the plateau inland lakes. The dominant bacterial phylum involved in nitrogen conversion both in summer and winter was Pseudomonadota， with an average proportion of 39.35% and 35.09% at different sampling sites in different seasons， respectively. The dominant bacterial genera in summer and winter were Candida_planktophila （the average proportion of different sampling sites was 4.04%） and unclassified_c_Actinomycetes （the average proportion of different sampling sites was 7.91%）. ② Salinity and dissolved oxygen were the most significant environmental factors affecting the microbial community structure of nitrogen transformation in different seasons. There were differences in the process of nitrogen transformation microbial community assembly in different seasons and different sampling lakes. ③ There were differences in the abundance of functional genes of nitrogen transformation microbes in different seasons， and denitrification was the most widely involved process of microbial communities in the plateau inland lakes in different seasons. The environmental factors driving the abundance of nitrogen transformation genes in different seasons were altitude， water temperature， total dissolved solids， and salinity. Overall， there was significant spatiotemporal heterogeneity in the assembly process of nitrogen transformation microbial communities in the plateau inland lakes. The results of this study can provide data support for the understanding of nitrogen-transforming microbes in the plateau inland lake ecosystem and provide a theoretical basis for lake water ecological management and regional greenhouse gas emissions.},
}

*Lakes/microbiology/chemistry
*Nitrogen/metabolism/isolation & purification
Seasons
China
*Bacteria/metabolism/classification
*Water Microbiology
Ecosystem
*Microbiota

@article {pmid42761166,
year = {2026},
author = {Li, M and Zhao, X and Zhang, B and Cao, R and Wang, Z and Huang, Z and Cheng, C and Lu, S and Jiang, X},
title = {Gut microbiome-metabolome signatures of osteosarcopenia in fracture patients in China.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1863988},
pmid = {42761166},
issn = {1664-2392},
mesh = {Humans ; Female ; Male ; Middle Aged ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Prospective Studies ; *Fractures, Bone/metabolism/microbiology/complications/epidemiology ; Aged ; China/epidemiology ; *Metabolome ; *Sarcopenia/microbiology/metabolism/epidemiology ; Multiomics ; Metabolomics ; Metagenomics ; },
abstract = {BACKGROUND: Osteosarcopenia, defined as the coexistence of low bone mass and sarcopenia, is a disabling musculoskeletal condition, yet its gut microbial and metabolic characteristics in clinical populations remain incompletely understood. Integrative multi-omics approaches may help clarify species-metabolite networks associated with this condition, particularly in fracture patients.

METHODS: In this single-center, prospective cross-sectional study, 69 fracture patients aged ≥50 years were classified into four phenotypes: Normal (n = 18), isolated low bone mass (Bone, n = 18), isolated sarcopenia (Muscle, n = 19), and osteosarcopenia (Both, n = 14). Fecal samples were analyzed using shotgun metagenomics and untargeted metabolomics, yielding paired multi-omics data for 52 participants.

RESULTS: The Bone group had the highest mean age (66.6 ± 9.46 years), whereas the mean ages of the other groups ranged from 60.6 to 61.8 years (overall p = 0.029), while sex, BMI, lifestyle factors, and comorbidities did not differ significantly. Neither α-diversity nor overall β-diversity showed marked differences across phenotypes, suggesting that broad community replacement was not observed. A multi-stage, multi-method strategy yielded a 17-species consensus feature set associated with differences among musculoskeletal phenotypes. Taxonomic patterns were consistent with a candidate fiber/short-chain fatty acid (SCFA)-associated module, whereas exploratory microbe-metabolite correlations suggested a candidate lipid/sterol-associated module. The latter included correlations linking Firmicutes bacterium CAG:24053_14 with putatively annotated cholesterol and N-acylethanolamines.

CONCLUSIONS: Osteosarcopenia in fracture patients was associated with unadjusted differences in selected gut microbial taxa and fecal metabolites within a broadly shared microbial community. These findings are hypothesis-generating and require validation in larger independent cohorts before clinical or biomarker application.},
}

Humans
Female
Male
Middle Aged
Cross-Sectional Studies
*Gastrointestinal Microbiome
Prospective Studies
*Fractures, Bone/metabolism/microbiology/complications/epidemiology
Aged
China/epidemiology
*Metabolome
*Sarcopenia/microbiology/metabolism/epidemiology
Multiomics
Metabolomics
Metagenomics

@article {pmid42669226,
year = {2026},
author = {Gongpan, P and Yang, J and Fu, H and Wu, S and Zhu, X and Chen, R and Liu, L and Geng, CA},
title = {Preparation and chemical characterization of polyphenol-rich extract from Tsaoko Fructus: alleviation of ulcerative colitis in mice by modulating gut microbiota and suppressing the JNK1-cJun signaling.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {161},
number = {},
pages = {158752},
doi = {10.1016/j.phymed.2026.158752},
pmid = {42669226},
issn = {1618-095X},
mesh = {Animals ; *Colitis, Ulcerative/drug therapy/microbiology/chemically induced ; *Polyphenols/pharmacology/chemistry ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/pharmacology/chemistry ; Male ; *Anti-Inflammatory Agents/pharmacology ; Disease Models, Animal ; Dextran Sulfate ; Signal Transduction/drug effects ; *Mitogen-Activated Protein Kinase 8/metabolism ; Mice, Inbred C57BL ; Colon/drug effects ; Molecular Docking Simulation ; },
abstract = {BACKGROUND: Tsaoko Fructus, a traditional Chinese medicinal herb, has long been used to alleviate gastritis and enteritis. Nevertheless, the active constituents and underlying anti-inflammatory mechanisms remain insufficiently characterized.

PURPOSE: This study aims to optimize a polyphenol-rich fraction (3CB) from Tsaoko Fructus, evaluate its effects against ulcerative colitis (UC), and reveal the underlying mechanisms of action.

METHODS: The preparation of 3CB was optimized using response surface methodology (RSM), and its major constituents were identified by LC-PDA-MS analysis. A murine UC model was established by administering dextran sulfate sodium (DSS). To evaluate the effects of 3CB on UC mice, metagenomic sequencing of the intestinal microbiome and RNA sequencing of colon tissues were conducted. The anti-inflammatory activity of 3CB and its principal constituents was further verified by quantitative real-time PCR (qPCR), Enzyme linked immunosorbent assay (ELISA), Western blotting, immunohistochemical staining, and histopathological analysis. Network pharmacology, molecular docking, and surface plasmon resonance (SPR) assays were employed to elucidate the molecular mechanisms underlying the anti-inflammatory effects of 3CB.

RESULTS: 3CB significantly alleviated UC symptoms in DSS-induced mice, reshaped the gut microbiota with reducing pathogenic Pseudomonadota and Deferribacterota while enriching beneficial Bacteroidota, and restored microbial amino sugar and nucleotide sugar metabolism pathways of intestinal flora. Additionally, 3CB preserved colonic oxidative phosphorylation, protected the mucus barrier, and suppressed inflammatory cell infiltration and the expression of cytokines. Seven major polyphenols were identified in 3CB, with epicatechin (3) and epiafzelechin (6) being the most abundant. Mechanistic investigation revealed that the anti-inflammatory effect of 3CB was partially dependent on the JNK1-modulated MAPK signaling pathway. JNK1 was identified as a direct target of 3CB, with epiafzelechin (6) exhibiting a high binding affinity (Kd = 10.4 μM).

CONCLUSION: 3CB ameliorates UC potentially through modulation of gut microbiota, protection of the mucus barrier, and JNK1-targeted anti-inflammatory effects, highlighting its potential as a protective intervention for inflammatory bowel disease (IBD).},
}

Animals
*Colitis, Ulcerative/drug therapy/microbiology/chemically induced
*Polyphenols/pharmacology/chemistry
*Gastrointestinal Microbiome/drug effects
Mice
*Drugs, Chinese Herbal/pharmacology/chemistry
Male
*Anti-Inflammatory Agents/pharmacology
Disease Models, Animal
Dextran Sulfate
Signal Transduction/drug effects
*Mitogen-Activated Protein Kinase 8/metabolism
Mice, Inbred C57BL
Colon/drug effects
Molecular Docking Simulation

@article {pmid42697040,
year = {2026},
author = {Frangieh, MR and Saad, M and Fattouh, N and Sawan, S},
title = {Antibiotics and nanoparticles in Parkinson's disease: From gut microbiota dysbiosis to neuroprotection and targeted nanotherapies.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {203},
number = {},
pages = {119903},
doi = {10.1016/j.biopha.2026.119903},
pmid = {42697040},
issn = {1950-6007},
mesh = {Humans ; Animals ; *Anti-Bacterial Agents/adverse effects/administration & dosage/therapeutic use/pharmacology ; *Parkinson Disease/drug therapy/microbiology ; *Dysbiosis/drug therapy ; *Neuroprotective Agents/administration & dosage/therapeutic use/adverse effects ; *Nanoparticles ; *Gastrointestinal Microbiome/drug effects/physiology ; *Neuroprotection/drug effects ; Nanoparticle Drug Delivery System ; Nanomedicine/methods ; },
abstract = {Parkinson's disease (PD) is increasingly linked to gut-brain axis dysfunction. While broad-spectrum antibiotics may contribute to gut dysbiosis, which has been associated with an increased abundance of curli-producing Enterobacteriaceae and processes implicated in α-synuclein aggregation, certain antibiotic classes, particularly tetracyclines and β-lactams, have demonstrated neuroprotective properties in pre-clinical models of PD. This creates a therapeutic paradox: antibiotics may exert either beneficial or detrimental effects depending on many factors including host microbiome composition. Importantly, much of the current evidence remains observational or pre-clinical, and a direct causal relationship between antibiotic exposure and PD has not yet been established. This review synthesizes current epidemiological, mechanistic, and pre-clinical evidence regarding this paradox and explores the emerging role of nanotechnology in resolving it. Preclinical studies suggest that nanoparticle-based drug delivery systems may enhance BBB penetration and enable more targeted drug release. Such approaches have been proposed as a means to reduce systemic exposure and potentially limit microbiota disruption, although these benefits have not yet been demonstrated in clinical PD populations. We further discuss the translational hurdles, including nanotoxicity and regulatory requirements, and propose a roadmap for future research that integrates metagenomics with precision nanomedicine. Collectively, these findings provide a framework for future investigation of targeted therapeutic strategies for PD. However, substantial mechanistic, clinical, and translational validation is required before their therapeutic potential can be established.},
}

Humans
Animals
*Anti-Bacterial Agents/adverse effects/administration & dosage/therapeutic use/pharmacology
*Parkinson Disease/drug therapy/microbiology
*Dysbiosis/drug therapy
*Neuroprotective Agents/administration & dosage/therapeutic use/adverse effects
*Nanoparticles
*Gastrointestinal Microbiome/drug effects/physiology
*Neuroprotection/drug effects
Nanoparticle Drug Delivery System
Nanomedicine/methods

@article {pmid42758711,
year = {2026},
author = {Emfietzoglou, M and Bantounou, MA and Osmani, S and Narimatsu, T and Baroutis, KG and Varsamidaki, A and Skondra, D and Papaconstantinou, D and Theodossiadis, P and Chatziralli, I and Miller, JW and Vavvas, DG},
title = {Shotgun metagenomic profiling of the fecal microbiome in Lamp2 knockout mice reveals limited genotype-associated differences under standard housing.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357009},
doi = {10.1371/journal.pone.0357009},
pmid = {42758711},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology ; Mice ; Male ; Mice, Knockout ; *Metagenomics/methods ; *Lysosomal-Associated Membrane Protein 2/genetics ; Genotype ; *Gastrointestinal Microbiome/genetics ; Shotgun Sequencing ; Metagenome ; },
abstract = {BACKGROUND: Lysosomal pathways influence host-microbe interactions, but the microbiome consequences of lysosomal dysfunction remain incompletely defined. LAMP2 is required for autophagosome-lysosome fusion, and pathogenic variants in LAMP2 cause Danon disease. Whether Lamp2 loss alters the gut microbiome in vivo has not been systematically evaluated using methods that profile both taxonomic composition and microbial functional potential, such as shotgun metagenomics.

METHODS: We performed shotgun metagenomic sequencing on 50 fecal samples from male Lamp2 knockout (Lamp2KO) mice and wild-type (WT) littermates sampled at 3, 6, 9, and 12 months under single-genotype cages or mixed-genotype cohousing. Two low-depth libraries (<3 × 105 classified genus-level reads) were excluded from primary inference (primary set: n = 48). We analyzed genus-level alpha diversity, beta diversity, and differential abundance using compositional, cage-aware mixed-effects models and cage-blocked permutation testing. We analyzed functional pathway profiles using copies-per-million abundances with centered-log-ratio transformation and mixed-effects modeling. We controlled multiple testing using the Benjamini-Hochberg false discovery rate.

RESULTS: In the primary set (48 samples from 27 cages), Lamp2KO and WT mice showed similar genus-level alpha diversity and overall community composition (PERMANOVA using Aitchison and Bray-Curtis distances). Primary mixed-effects models detected no genera with differential abundance after false discovery rate correction. Taxonomic profiles were broadly similar between genotypes and were dominated by Bacteroidota and Bacillota. Exploratory within-cage (paired) analyses identified consistent directional differences in a small set of genera, but these signals were not supported by the primary mixed-effects models. Functional pathway profiles were similar between genotypes; one pathway (dTDP-β-L-rhamnose biosynthesis) showed an exploratory association (FDR q < 0.10) within the 50 most abundant pathways.

CONCLUSIONS: In this controlled mouse cohort, we did not detect robust, cage-independent shifts in fecal microbiome composition or inferred functional pathway profiles associated with Lamp2 deficiency under standard SPF husbandry and chow; given the sample size, smaller or compartment-specific effects cannot be excluded.},
}

Animals
*Feces/microbiology
Mice
Male
Mice, Knockout
*Metagenomics/methods
*Lysosomal-Associated Membrane Protein 2/genetics
Genotype
*Gastrointestinal Microbiome/genetics
Shotgun Sequencing
Metagenome

@article {pmid42760068,
year = {2026},
author = {Toufiq, R and Shahid, A and Zahra, R and Lankapalli, AK and Oduwo, J and Owinoh, EO and Aftab, S and Hassan, B and Thomson, K and Walsh, TR and Sands, K},
title = {Cohort profile: Infant Gut Bacterial Study in Pakistan (INBUGS-P) longitudinal birth cohort.},
journal = {BMJ open},
volume = {16},
number = {9},
pages = {e120775},
doi = {10.1136/bmjopen-2026-120775},
pmid = {42760068},
issn = {2044-6055},
mesh = {Humans ; Pakistan ; Female ; Infant ; Longitudinal Studies ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Breast Feeding/statistics & numerical data ; Anti-Bacterial Agents/therapeutic use ; Birth Cohort ; Adult ; Milk, Human/microbiology ; },
abstract = {PURPOSE: The Infant Gut Bacterial Study in Pakistan (INBUGS-P) was established to characterise the longitudinal development of the infant gut microbiome and resistome during the first year of life in a low- and middle-income country setting. The influence of early-life exposures, including mode of delivery, antibiotic use and infant feeding practices on gut bacterial diversity and antimicrobial resistance gene (ARG) profiles is being evaluated.

PARTICIPANTS: A total of 107 mother-infant pairs were recruited at the Pakistan Institute of Medical Sciences between December 2023 and June 2024. Follow-up was conducted at 10 predefined timepoints from birth to 12 months, during which 921 infant stool samples, 158 maternal rectal swabs, 246 breast milk samples and 2171 environmental swabs were collected. Sociodemographic, clinical, cultural and biological data were collected at enrolment and at each follow-up visit using Research Electronic Data Capture.

FINDINGS TO DATE: Baseline characteristics of 98/107 mother-infant dyads are included in the analysis. The cohort reflects an urban low-income population: median household income was PKR 30,000 per month (approximately US$170 per capita per month). Caesarean section accounted for 55% (54/98) of deliveries; 13.0% of infants were late preterm, and 10.0% had low birth weight (<2500 g). Breastfeeding was the predominant feeding mode though only 24 infants were exclusively breastfed from birth to 6 months. Antibiotics were prescribed to almost all mothers following delivery, and 19 infants received antibiotics during follow-up, most commonly amikacin combined with ceftazidime.

FUTURE PLAN: Shotgun metagenomic sequencing of infant stool samples is underway to enable species-level and plasmid-level profiling of microbial communities and ARGs. Subject to funding, hybrid long- and short-read sequencing and extended follow-up to 24 months are planned.},
}

Humans
Pakistan
Female
Infant
Longitudinal Studies
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Breast Feeding/statistics & numerical data
Anti-Bacterial Agents/therapeutic use
Birth Cohort
Adult
Milk, Human/microbiology

@article {pmid42761040,
year = {2026},
author = {Ribeiro, GO and Guimarães, LO and Foro Ramos, EDS and Couto, RDS and Telles-de-Deus, J and Helfstein, VC and Morais, VDS and Reginato, SL and Mucci, LF and Bergo, ES and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Leal, É and Kirchgatter, K},
title = {RNA virome comparison between sylvatic and urban-interface mosquitoes from Southeastern Brazil.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1894867},
pmid = {42761040},
issn = {2235-2988},
mesh = {Animals ; Brazil ; *Virome/genetics ; *Culicidae/virology/classification ; *RNA, Viral/genetics ; *Mosquito Vectors/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Forests ; },
abstract = {INTRODUCTION: Mosquitoes (Diptera: Culicidae) are primary vectors of public health pathogens, yet their core viromes remain poorly characterized, particularly in Neotropical sylvatic lineages. This study investigated the RNA virome of multiple mosquito species across urban-to-forest gradients in São Paulo State, Brazil, including neglected sylvatic taxa such as Sabethes, Psorophora, Shannoniana, and Wyeomyia.

METHODS: The RNA virome of multiple mosquito species was investigated across urban-to-forest gradients in São Paulo State, Brazil. Ecological analyses were performed to assess the effects of host taxonomy and environment on virome composition. Network analysis was conducted to investigate virus-host associations and viral sharing across ecological interfaces.

RESULTS: Our analysis identified 919 viral contigs across 217 viral species and 37 distinct families, revealing a substantial fraction of "viral dark matter" with low amino acid identity (median < 40%) in predominantly sylvatic mosquito species. Although viral families containing known arboviruses, such as Flaviviridae, Phenuiviridae, and Peribunyaviridae, were detected, no high-consequence human pathogens were identified within the sensitivity limits of our sampling and sequencing depth. Ecological analyses demonstrated that virome composition was strongly structured by host taxonomy and environment (R[2]=0.570, p=0.001), with host species explaining 32.9% of the unique variance (PERMANOVA, R[2]=0.329, p=0.001), whereas ecotope played a secondary role (R[2]=0.029, p=0.001). Network analysis revealed a highly modular virus-host structure dominated by host-restricted specialists, with a limited number of bridge species facilitating viral sharing across ecological interfaces.

DISCUSSION: These findings indicate that intrinsic mosquito biology is the main driver of viral community structure, while environmental gradients play a secondary role, and highlight the importance of host-associated processes in shaping viral diversity at the Neotropical forest-urban interface.},
}

Animals
Brazil
*Virome/genetics
*Culicidae/virology/classification
*RNA, Viral/genetics
*Mosquito Vectors/virology
*RNA Viruses/genetics/classification/isolation & purification
Forests

@article {pmid41667306,
year = {2026},
author = {Tong, Y and Chen, Y and Dong, Y and Chen, K and Yang, J and Dong, X and Wan, X and Luo, Z and Fang, J and Liu, Y and Li, W and Wang, Z and Gu, X},
title = {Characterization of the oral microbiota of Kawasaki disease patients by metagenomic analysis: A pilot study.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {59},
number = {5},
pages = {556-564},
doi = {10.1016/j.jmii.2026.01.007},
pmid = {41667306},
issn = {1995-9133},
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/drug therapy ; Female ; Male ; *Metagenomics/methods ; Pilot Projects ; Child, Preschool ; *Microbiota/genetics ; *Mouth/microbiology ; Immunoglobulins, Intravenous/therapeutic use ; Infant ; Bacteria/classification/genetics/isolation & purification ; Child ; Metagenome ; },
abstract = {BACKGROUND: Kawasaki disease (KD) is an acute febrile systemic vasculitis characterized by vascular inflammation. Its pathogenesis has been linked to the infiltration of IgA[+] plasma cells within the respiratory tract, suggesting the upper airway may act as a potential portal of entry. However, evidence connecting respiratory infections to KD remains limited. This study aimed to explore the relationship between oral microbiota and KD development.

METHODS: Oral swab samples were collected from 25 KD patients before and after intravenous immunoglobulin (IVIG) treatment, as well as from 25 healthy controls. Metagenomic sequencing was performed to characterize overall microbial composition and identify potential microbial markers associated with KD.

RESULTS: Significant alterations in oral microbiota composition were observed between KD patients and healthy controls. The diversity of oral microbiota in KD patients was markedly lower than that in healthy controls, and exhibited an upward trend following IVIG treatment. Elevated levels of Streptococcus, Prevotella, and Veillonella, along with reduced levels of Haemophilus, Neisseria, and Rothia, were closely associated with KD development. Putative novel pathogen Abiotrophia defectiva was significantly enriched in patients with KD. Correlation analysis revealed that the relative abundances of several Haemophilus species were positively correlated with albumin levels in KD patients before IVIG treatment. Additionally, the anti-inflammatory bacterium Rothia mucilaginosa may play a protective role against the development of coronary artery lesions in KD.

CONCLUSION: These findings provide new evidence that distinct alterations in the oral microbiome are associated with KD development. Oral microbiota-based biomarkers may represent a potential strategy for KD therapy.},
}

Humans
*Mucocutaneous Lymph Node Syndrome/microbiology/drug therapy
Female
Male
*Metagenomics/methods
Pilot Projects
Child, Preschool
*Microbiota/genetics
*Mouth/microbiology
Immunoglobulins, Intravenous/therapeutic use
Infant
Bacteria/classification/genetics/isolation & purification
Child
Metagenome

@article {pmid42259841,
year = {2026},
author = {Deng, F and Fan, Y and Yan, J and Zhang, X and Guo, Y and Li, M and Peng, Y and Zhao, L and Liu, F and Zheng, Y and Deng, B and Deng, J and Chen, S and Jiang, H and Chai, J and Zhao, J and Li, Y},
title = {Genome-resolved and culture-based atlas of the feline gut microbiome enables host-adapted probiotic development.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42259841},
issn = {2055-5008},
mesh = {Animals ; Cats/microbiology ; *Probiotics ; Feces/microbiology ; Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; Genome, Bacterial ; Escherichia coli ; },
abstract = {Domestic cats (Felis catus) depend on their gut microbiome for metabolism, immunity, and pathogen defense, yet its genomic characterization remains limited. We combined large-scale metagenomics and culturomics to define the feline gut microbiome and identify indigenous probiotic candidates. Analysis of 412 feline fecal metagenomes produced 2852 strain-resolved metagenome-assembled genomes (MAGs) grouped into 514 species-level genome bins, including 106 putative novel taxa. This catalog revealed 24 core species and two enterotypes: ET-P, deaminated by Prevotella, and ET-CB, enriched for Collinsella, Blautia, Bifidobacterium, Ligilactobacillus, MAG-based screening prioritized 113 candidate probiotic species. Culturomics recovered 2904 isolates representing 110 species-level taxa, including 75 putative novel species and a candidate novel genus. Six feline-derived isolates were selected for downstream testing, and five exhibited favorable probiotic traits in vitro, including acid and bile tolerance, anti-Escherichia coli activity, and favorable cytokine responses. In a pathogenic Escherichia coli-induced dirrhea model in cats, a five-strain indigenous consortium improved fecal scores and reduced IL-2, IL-1β, and IL-6, with TNF-α suppression superior to antibiotics or a commercial probiotic. These results establish FelMGDB as a resource for feline microbiome research and highlights indigenous probiotics as promising interventions for feline gut health.},
}

Animals
Cats/microbiology
*Probiotics
Feces/microbiology
Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Metagenome
*Bacteria/classification/genetics/isolation & purification
Phylogeny
Genome, Bacterial
Escherichia coli

@article {pmid42321634,
year = {2026},
author = {Pandey, S and Parmar, B and Gupta, A and Singh, A and Chauhan, A and Huang, KW and Karan, R},
title = {Eco-technological potential of salinity-driven functional specialization in Indian solar salterns revealed by integrated culturomics and whole-metagenome profiling.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42321634},
issn = {1471-2180},
support = {RFS #5974//King Abdullah University of Science and Technology/ ; IoE/2024-25/12/FRP and IoE/2025-26/12/FRP//University of Delhi/ ; },
mesh = {*Salinity ; India ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Metagenomics/methods ; Phylogeny ; *Metagenome ; Microbiota/genetics ; Ecosystem ; *Seawater/microbiology/chemistry ; },
abstract = {Solar salterns are environmentally stable yet biologically extreme ecosystems that serve as vital models for understanding and managing hypersaline environments, including industrial saline effluents. Despite their ecological and biotechnological significance, Indian solar salterns remain functionally underexplored. In this study, we integrated culture-dependent isolation with whole-metagenome sequencing to investigate microbial community assembly, functional specialization, and eco-technological potential across four geographically distinct Indian salterns.Physicochemical analyses revealed pronounced spatial variation in salinity, pH, and electrical conductivity, which together strongly structured microbial communities. Metagenomic sequencing generated between 4.84 and 8.68 Gb of raw data across individual site, yielding between 429,420 and 669,991 predicted genes in high-salinity locations. Taxonomic reconstruction demonstrated archaeal dominance at extreme salinity, particularly among Euryarchaeota, whereas comparatively moderate salinity sites supported more balanced bacterial-archaeal assemblages. Alpha diversity patterns indicated higher richness in Tamil Nadu and Rajasthan, while Gujarat exhibited reduced evenness consistent with environmental filtering.Culture-dependent approaches recovered 42 halophilic and polyextremophilic isolates, primarily affiliated with Halobacteriaceae and Bacillaceae, complementing the broad taxonomic detection of these lineages inferred from metagenomic data. Functional annotation revealed extensive enrichment of genes involved in ion transport, energy production, osmoprotectant biosynthesis, and DNA repair, reflecting an adaptive mechanism critical for survival in high-salinity industrial processes. Amino acid metabolism genes exceeded 25,000 hits in selected sites, and replication and repair genes reached 32,554 in Gujarat, indicating heightened stress-response activity. Secondary metabolite biosynthetic gene clusters, including pathways for novel antimicrobial peptides, terpene, ribosomally synthesized and post-translationally modified peptide-like, and type III polyketide synthase pathways, were widely distributed, offering new biological control mechanisms for environments impaired by stress. Antimicrobial resistance signatures were limited and unevenly distributed across sites.These findings demonstrate that salinity acts as a dominant ecological filter driving both taxonomic composition and functional specialization in Indian solar salterns. By linking environmental gradients to adaptive genomic traits, this study establishes a functional baseline for hypersaline ecosystems.},
}

*Salinity
India
*Bacteria/classification/genetics/isolation & purification
*Archaea/genetics/classification/isolation & purification
Metagenomics/methods
Phylogeny
*Metagenome
Microbiota/genetics
Ecosystem
*Seawater/microbiology/chemistry

@article {pmid42330763,
year = {2026},
author = {Goel, A and Ncho, CM and Jeong, CM and Gupta, V and Jung, JY and Ha, SY and Yang, JK and Choi, YH},
title = {Dietary polyphenols from shredded, steam-exploded pine particles mitigate the adverse effects of heat stress in broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107298},
pmid = {42330763},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/genetics ; Diet/veterinary ; *Polyphenols/administration & dosage/metabolism ; Animal Feed/analysis ; *Hot Temperature/adverse effects ; Dietary Supplements/analysis ; *Pinus/chemistry ; Random Allocation ; *Heat-Shock Response/drug effects ; Male ; *Gastrointestinal Microbiome/drug effects ; *Gene Expression/drug effects ; },
abstract = {The current study investigated the impact of supplementing polyphenols extracted from shredded, steam-exploded pine particles (PSPP) on the performance, gene expression, and gut metagenome of broilers exposed to cyclic heat stress (CHS). A total of 216 chickens were distributed into a 2 (temperature) by 3 (diets) design, with each treatment consisting of six replicates of six chickens. Specifically, chickens were fed diets containing 0% PSPP, 0.5% PSPP, and 1% PSPP and exposed to two temperature conditions: CHS (31°C) and Thermoneutral (NT, 21°C). The CHS was conducted for 6 hours every day for 7 consecutive days. Final body weight, average daily gain, and average daily feed intake (ADFI) were decreased, while feed conversion ratio and rectal temperature were increased in heat-exposed chickens. Dietary PSPP supplementation enhanced ADFI. The weight of the liver, bursa, and length of the jejunum and ileum were decreased in heat-exposed chickens. Plasma cholesterol was increased, and triglycerides were decreased in heat-exposed chickens. After heat exposure, gene expression of ZO1, ZO2, GLP2, NOX1, SOD, GPX, HSP70, HSP90, NRF2, TLR2, and TLR4 increased in the jejunum. GLP2 gene expression was similar in 1%PSPP exposed to HS in comparison to the entire NT-exposed chickens. Concerning microbiota analysis, alpha diversity indices, such as Shannon and Gini-Simpson, were increased following CHS exposure. Beta diversity, measured through unweighted and weighted UniFrac distances, showed temperature, dose, and interaction effects. The relative abundance of the phylum Candidatus Melainabacteria was increased, while Tenericutes populations were decreased in heat-exposed chickens. Furthermore, a total of thirty genera were identified as microbial biomarkers of CHS. Interestingly, the relative abundance of five pathogenic bacterial genera was found to be decreased in the 0.5%PSPP treatment. Overall, CHS negatively influences growth performance, modulates the expression of the gut antioxidant-related genes, and favors the colonization of pathogenic bacteria. However, 0.5% PSPP may mitigate CHS by reducing pathogen colonization in the gut of broilers.},
}

Animals
*Chickens/physiology/genetics
Diet/veterinary
*Polyphenols/administration & dosage/metabolism
Animal Feed/analysis
*Hot Temperature/adverse effects
Dietary Supplements/analysis
*Pinus/chemistry
Random Allocation
*Heat-Shock Response/drug effects
Male
*Gastrointestinal Microbiome/drug effects
*Gene Expression/drug effects

@article {pmid42335767,
year = {2026},
author = {Li, T and Guo, T and Cui, M and Cao, Y and Zhi, Z and Wang, P and Li, Q and Zhang, J},
title = {Rearing systems shape the successional dynamics of the gut microbiota, resistome, and mobilome in Lueyang Black-boned chickens.},
journal = {Poultry science},
volume = {105},
number = {10},
pages = {107322},
pmid = {42335767},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology ; *Animal Husbandry/methods ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial ; *Bacteria/drug effects/genetics ; },
abstract = {Understanding the ecological factors shaping antimicrobial resistance (AMR) dissemination in agricultural environments is critical for global "One Health". Here, we performed metagenomic sequencing to investigate the impact of intensive cage-reared (CR) and free-range (FR) systems on the gut microbiota, resistome, and mobilome dynamics of Lueyang Black-boned chickens across different production stages. Our analyses revealed that distinct rearing systems drove resistome alterations by reshaping microbial community assembly and horizontal gene transfer (HGT) pathways. Specifically, the CR system imposed strong deterministic stress, thereby enriching opportunistic taxa (such as Desulfovibrio) and promoting a highly connected but topologically fragile microbial network. Conversely, the FR system exhibited a higher total abundance of commensal resistance genes, a process mainly driven by diverse transposon-mediated integrations including tnpA and ISBf10. In contrast, the CR system was associated with high-risk, clinically relevant resistance determinants. These included extended-spectrum beta-lactamases and multidrug resistance cassettes. Targeted network tracking unmasked highly divergent potential host-vector-ARG associations. Resistance expansion under confined CR conditions showed strong vector-dependency, being fundamentally linked to the broad-host-range plasmid IncQ1 alongside clinically relevant mobilization elements, including Class 1 integrons. Longitudinally, the FR resistome achieved ecological stabilization. In contrast, the CR microbiota exhibited continued genetic flux, continuously acquiring transient resistance elements during the observed production period. These findings demonstrate that welfare-friendly rearing management serves as a critical ecological intervention to limit the proliferation of mobile, high-risk resistance traits. Ultimately, future agricultural surveillance must transition beyond quantifying total resistance gene abundance to prioritize functional risk assessments and mobilization potential.},
}

Animals
*Chickens/microbiology
*Animal Husbandry/methods
*Gastrointestinal Microbiome
Gene Transfer, Horizontal
*Drug Resistance, Bacterial
*Bacteria/drug effects/genetics

@article {pmid42351266,
year = {2026},
author = {Chen, T and Xiao, J and Li, S and Peng, R and Xu, Y and Zhuang, Y and Zhao, X and Sha, M and Wang, J and Ma, J and Wang, W and Gao, J and Ma, M and Li, S and Cao, Z and Liu, S},
title = {Differential rumen and hindgut microbiome and metabolome in Holstein female calves with divergent feed efficiency.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42351266},
issn = {2049-2618},
mesh = {Animals ; Female ; Cattle/microbiology ; *Rumen/microbiology ; *Metabolome ; Feces/microbiology ; Animal Feed/analysis ; Multiomics ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fermentation ; Metagenomics ; Metabolomics ; },
abstract = {BACKGROUND: Significant environmental problems have challenged animal agriculture, improving feed efficiency in animals has become a vital research direction for sustainable agriculture. Bacteria play a critical role in the feed efficiency of animals. However, our current understanding of bacteria communities in the gastrointestinal tract of high-feed efficiency animals and their metabolic mechanisms remains unclear.

RESULTS: Twenty Holstein female calves were used in this multi-omics study that integrated metagenomic and metabolomic analyses of 20 Holstein female calves to investigate feed efficiency, as measured by residual feed intake (RFI). From an initial cohort of 84 calves, the 10 with the highest RFI (HRFI, low efficiency) and the 10 with the lowest RFI (LRFI, high efficiency) were selected at 84 days of age. Rumen fluid, feces, and serum samples from these calves were collected for subsequent analyses. We found that LRFI calves harbored rumen and fecal microbiomes with significantly different community structures and co-occurrence networks compared to HRFI calves. Multi-omics integration identified robust microbial and metabolite biomarkers discriminating RFI groups. These microbiomes were functionally linked to differential nutrient utilization, LRFI calves were characterized by enhanced starch and protein digestibility coupled with propionate-oriented fermentation, associated with key species like Erysipelotrichaceae_bacterium and Hungatella_sp. Conversely, HRFI calves showed higher fat digestibility and acetate production. Notably, serum glutamate was enriched in LRFI calves despite lower intake, correlating with potential microbial metabolites (ribitol, taurine). Subsequent validation confirmed that glutamate supplementation in mice improved nitrogen metabolism and gut barrier function.

CONCLUSIONS: In summary, this multi-omics study reveals that high feed efficiency in calves is associated with distinct microbial ecosystems characterized by functions such as starch degradation and propionate production, where glutamate metabolism serves as a central node. Video Abstract.},
}

Animals
Female
Cattle/microbiology
*Rumen/microbiology
*Metabolome
Feces/microbiology
Animal Feed/analysis
Multiomics
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Fermentation
Metagenomics
Metabolomics

@article {pmid42750901,
year = {2026},
author = {Musleh, L and Montilli, M and Ammendolia, MG and Sciarra, A and Riccioli, A and Maurizi, L and Longhi, C},
title = {More than an infection: the ecological puzzle of recurrent urinary tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1927507},
pmid = {42750901},
issn = {2235-2988},
mesh = {Humans ; *Urinary Tract Infections/microbiology/diagnosis/drug therapy/immunology ; Recurrence ; Microbiota ; Reinfection/microbiology ; Host Microbial Interactions ; Dysbiosis ; Urinary Tract/microbiology ; },
abstract = {Recurrent urinary tract infections (rUTIs) represent one of the most common infectious conditions worldwide, yet their pathophysiology extends far beyond repeated episodes of acute bacterial cystitis. Increasing evidence indicates that recurrence may arise through overlapping mechanisms including reinfection from intestinal or periurethral reservoirs, intracellular bacterial persistence, microbial dysbiosis, impaired mucosal immunity and chronic inflammatory remodelling of the bladder microenvironment. Current diagnostic frameworks remain largely based on symptom-based definitions and standard urine culture, approaches that incompletely capture the biological complexity of recurrent disease. This limitation is evident even at the definitional level, where clinically pragmatic categories often fail to reflect the heterogeneous mechanisms underlying recurrence. Advances in expanded urine culture techniques, metagenomics and metabolomics have reshaped the understanding of the urinary tract as a dynamic ecological system interconnected with vaginal, intestinal and prostatic microbial compartments. These approaches have identified diverse microbial communities, virulence-associated functional profiles and host-microbe interactions linked to recurrence-prone phenotypes. Significant challenges continue to persist in elucidating the biological mechanisms driving recurrence. Addressing these gaps is essential to improve disease characterization and support the development of more effective diagnostic and therapeutic approaches.},
}

Humans
*Urinary Tract Infections/microbiology/diagnosis/drug therapy/immunology
Recurrence
Microbiota
Reinfection/microbiology
Host Microbial Interactions
Dysbiosis
Urinary Tract/microbiology

@article {pmid42753610,
year = {2026},
author = {Feng, Y and Xu, G and Wu, D and Sun, D and Shao, Q and Xu, H},
title = {Community-level eDNA decay patterns in marine zooplankton: Implications for optimizing eDNA-based marine environmental monitoring.},
journal = {Marine pollution bulletin},
volume = {233},
number = {Pt 3},
pages = {120341},
doi = {10.1016/j.marpolbul.2026.120341},
pmid = {42753610},
issn = {1879-3363},
abstract = {Environmental DNA (eDNA) has the potential to greatly transform marine ecological monitoring, yet its capacity for accurate biodiversity estimates is constrained by its decay process. Previous research has largely focused on laboratory-cultured single species, and thus the dynamics of mixed-species eDNA from natural communities remain poorly understood. Here, we conducted a 10-day time-series experiment to track the community-level eDNA decay process following the complete removal of zooplankton, employing an integrated approach of morphological analysis, quantitative PCR (qPCR), metabarcoding, and metagenomics. Our results reveal that the decay of marine zooplankton eDNA is a complex, heterogeneous process. Total community eDNA declined rapidly during the first two days (0-2 d), followed by a slower decline (4-10 d), as quantified by qPCR. Crucially, the taxonomic composition of the detectable eDNA pool changed substantially over time: the relative read abundance of copepods declined sharply after only two days, whereas that of medusae persisted high throughout the experiment. Furthermore, methodological comparison revealed significant discrepancies in temporal trajectories between metabarcoding and metagenomics regarding the detected community composition. To optimize eDNA-based marine environmental monitoring, we propose matching target taxa and molecular methods to the temporal scale of interest. Short-lived signals of copepods might support timely, near-snapshot assessments of recent environmental change by eDNA metabarcoding, whereas long-lived medusa eDNA appears to integrate occurrence over time. Taxon-specific signal persistence and method-dependent detectability should therefore be considered when interpreting eDNA monitoring data. This framework can strengthen the reliability of eDNA-based biodiversity assessments and support more effective marine ecosystem monitoring.},
}

@article {pmid42754770,
year = {2026},
author = {Petri, RM and Ricci, S and Jelinski, M and Hund, A},
title = {Observational study of the microbiome of perforated abomasal ulcers in unweaned beef calves in Canada.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42754770},
issn = {1573-7446},
mesh = {Animals ; Cattle ; *Abomasum/microbiology/pathology ; *Cattle Diseases/microbiology ; RNA, Ribosomal, 16S/analysis/genetics ; *Stomach Ulcer/veterinary/microbiology ; Canada ; Bacteria/classification/genetics/isolation & purification ; Male ; *Microbiota ; },
abstract = {In western Canada, perforating abomasal ulcers (AU) are generally diagnosed postmortem in beef calves up to 2 months of age. Certain microbes have been associated with AU, but the evidence is circumstantial. Thus, analyzing the abomasal microbiome in calves with and without AU may provide insight into the etiology of the disease. Using 16S rRNA gene sequencing, abomasal tissues from Western Canadian beef calves, with (n = 27) and without AU (n = 17), were analyzed for microbial diversity. No significant differences were seen between microbiomes of AU and CON calves despite numerical differences in abundance. Therefore, a subsample of 18 tissues (12 AU, 6 CON) were analyzed using untargeted metagenomic sequencing for determination of phylogeny, and the presence of antimicrobial resistance genes (ARGs). Staphylococcaceae (1.5%), Campylobacteraceae (1.4%) and Enterobacteriaceae (1.4%) were seen across all samples. Differential abundance analysis revealed Streptomyces spp. REN17 to be less abundant in AU calves, suggesting a potential association between Streptomyces spp. and calf gut health. An ARG associated with polymyxin resistance was found to be differentially abundant in calves with a history of antimicrobial therapy. Although differences were observed in the predicted metabolic functions among groups, none reached statistical significance. In our study, no consistent microbial signature associated with AU was identified, despite the differential abundance of individual taxon, nor did prior antimicrobial therapy associate to the growth of specific microbiota. To better understand the potential role of the abomasal microbiota in AU etiology and the impact of early life interventions in beef calves, a larger sample size is needed.},
}

Animals
Cattle
*Abomasum/microbiology/pathology
*Cattle Diseases/microbiology
RNA, Ribosomal, 16S/analysis/genetics
*Stomach Ulcer/veterinary/microbiology
Canada
Bacteria/classification/genetics/isolation & purification
Male
*Microbiota

@article {pmid42755618,
year = {2026},
author = {Li, L and Luo, Y and Liu, S and Liang, C and Ruan, H and Peng, P and Huang, Z},
title = {Genome-resolved gut metagenomics identifies an Escherichia coli-Collinsella signature associated with Wagner 4 gangrenous diabetic foot ulcers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1893357},
pmid = {42755618},
issn = {1664-3224},
mesh = {Humans ; *Escherichia coli/genetics ; *Diabetic Foot/microbiology ; *Metagenomics/methods ; *Diabetes Mellitus, Type 2/complications/microbiology ; *Gastrointestinal Microbiome/genetics ; *Actinobacteria/genetics ; Metagenome ; Male ; Female ; Feces/microbiology ; },
abstract = {Diabetic foot ulcers (DFU) are a major complication of type 2 diabetes mellitus, but whether the gut microbiome captures systemic microbial features associated with advanced ulcer severity remains unclear. We performed shotgun metagenomic sequencing of stool samples from 43 patients with type 2 diabetes mellitus and active DFU, comparing Wagner grades 1-3 (n = 30) with Wagner 4 gangrenous disease (n = 13). De novo assembly and binning recovered 440 dereplicated metagenome-assembled genomes (MAGs) meeting medium-quality or high-completeness/low-contamination thresholds. Community-level diversity and dominant-taxon composition did not separate Wagner 4 from Wagner 1-3, indicating that advanced disease was not reflected by broad ecological restructuring. Feature-level analysis instead identified a genome-resolved MAG profile. To prioritize robust candidates, we combined two complementary approaches: random forest (RF) stability selection, which identified 24 MAGs with reproducibly high classification importance across resampled folds, and covariate-adjusted MaAsLin2 differential-abundance testing. Intersecting the results of both approaches prioritized three MAGs supported by each method: one Escherichia coli MAG enriched in Wagner 4 and two Collinsella MAGs depleted in Wagner 4. This three-MAG signature (out-of-bag AUC = 0.703) retained much of the discriminatory information captured by the broader 24-MAG RF classifier, with concordant, opposing abundance directions across classifier interpretation, differential-abundance testing, and per-MAG abundance distributions. Functional annotation further separated the Wagner 4-enriched Escherichia coli from the Collinsella MAGs. The Escherichia coli MAG carried antibiotic-resistance and virulence-factor signals and encoded respiratory metabolic capacity, whereas the two Collinsella MAGs lacked detectable resistance and virulence hits and showed metabolically compact profiles. Exploratory clinical association analysis linked the E. coli-Collinsella abundance score to longer DFU duration, consistent with a gut microbial correlate of chronic or advanced disease burden. These findings support longitudinal gut metagenomic validation to determine whether this signal tracks DFU progression, treatment response, or recovery.},
}

Humans
*Escherichia coli/genetics
*Diabetic Foot/microbiology
*Metagenomics/methods
*Diabetes Mellitus, Type 2/complications/microbiology
*Gastrointestinal Microbiome/genetics
*Actinobacteria/genetics
Metagenome
Male
Female
Feces/microbiology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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