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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

CLINICALTRIALS: gov registration: NCT06633705.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid42784241,
year = {2026},
author = {Gulliver, D and Ross, DE and Flett, S},
title = {Uncovering potential autotrophs in coal seams: characterization, enrichment, and genome-resolved metabolisms of a subsurface coal seam microbiome.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {10},
pages = {e0062426},
pmid = {42784241},
issn = {1098-5336},
support = {//U.S. Department of Energy/ ; },
mesh = {*Coal/microbiology ; *Microbiota ; *Autotrophic Processes ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Genome, Bacterial ; Carbon Dioxide/metabolism ; },
abstract = {UNLABELLED: Biological transformation of inorganic carbon into organic compounds is an extremely important biosynthetic process, and many organisms catalyze this reaction autotrophically, using CO2 as the sole carbon source. Natural autotrophic pathways are diverse, as are the organisms that employ them, driven in part by the varied ecological niches they inhabit. One understudied ecological niche, coal seams, contains autotrophic acetogens that catalyze an intermediate step in the conversion of coal to methane. Here, we characterize the geochemistry and microbiology of coal seam produced water (CSPW) from the Appalachian Basin and, through continued anaerobic enrichment on H2:CO2, show enhanced growth and acetate production. Specifically, the enriched CSPW microbiome was comprised of Proteiniphilum, Proteiniclasticum, Gudongella, Acetobacterium, Propionicimonas, and Mesobacillus. Genome-resolved metabolisms revealed six potential autotrophic pathways, including four natural pathways (the reductive pentose phosphate pathway, the reversed oxidative tricarboxylic acid cycle, the reductive acetyl-CoA pathway, and the reductive glycine pathway) and two proposed synthetic pathways (the serine-threonine cycle and the pyruvate formate-lyase threonine cycle), with many metagenome-assembled genomes encoding multiple pathways. Overall, these findings suggest a nuanced and adaptable carbon conversion strategy, shedding light on carbon reactions in coal seams, and the potential applications for biological production of valuable chemicals/fuels using mixed microbial communities.

IMPORTANCE: Coal seams harbor taxonomically diverse microorganisms, specifically acetogens and methanogens, suggesting an untapped potential for autotrophic carbon conversion. Here, we show that an enriched coal seam-produced water microbiome utilized CO2 and/or NaHCO3 for growth and produced acetate. Genome-resolved metabolisms revealed that most microorganisms encode multiple autotrophic pathways, with the reductive glycine pathway being the most prevalent. This work provides insight into potential microbial strategies for obtaining and transforming carbon in coal seams, and importantly, with proper engineering of operational parameters and reactor design, the enriched microbiome has the potential to be used as a biocatalyst for alternative carbon conversion technologies.},
}

*Coal/microbiology
*Microbiota
*Autotrophic Processes
*Bacteria/metabolism/genetics/classification/isolation & purification
Genome, Bacterial
Carbon Dioxide/metabolism

@article {pmid42803581,
year = {2026},
author = {Lim, S and Murali, R and Speth, DR and Szabo, RE and Cordero, OX and Orphan, VJ},
title = {Activity and diversity of sulfate- and methane-based pathways of anaerobic chitin and N-acetylglucosamine degradation in marine sediments.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {10},
pages = {e0128026},
pmid = {42803581},
issn = {1098-5336},
support = {543495//Simons Foundation/ ; },
mesh = {*Geologic Sediments/microbiology ; *Chitin/metabolism ; *Acetylglucosamine/metabolism ; *Methane/metabolism ; *Sulfates/metabolism ; Anaerobiosis ; *Bacteria/metabolism/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Archaea/metabolism ; },
abstract = {UNLABELLED: Sulfate reduction is estimated to account for half of the organic carbon respiration in anoxic, organic-rich ocean sediments. Sulfate-reducing microorganisms (SRMs) typically oxidize simple carbon compounds, such as primary alcohols, or small fatty acids. However, much of the organic input to the seafloor is complex, driving interactions between terminal respirers, such as SRMs and methanogens, and primary degraders that initiate the breakdown of complex organic carbon. To explore how these interactions shape sediment microbiomes, we conducted multi-month microcosm experiments using serially diluted sediments in deep 96-well plates. Sediments from a former deep-sea whalefall site were amended with either the insoluble polymer chitin or its soluble monomer N-acetylglucosamine. The high replication in these experiments allowed us to evaluate the effects of complex versus labile carbon on degradation activity, microbial diversity, community structure, and functional redundancy over time. Geochemical analysis, combined with 16S rRNA gene sequencing and metagenomics, revealed that chitin addition preserved higher microbial diversity and increased predicted interactions among microorganisms. Despite anaerobic chitin degradation producing N-acetylglucosamine, microbial communities enriched by these substrates showed low nestedness over the 7-month experiment. Complex carbon inputs fostered unique microbial assemblages and functional interactions, including the emergence of diverse methanogenic lineages at medium to high dilutions-less apparent in monomer treatments. In microoxic sediments, methanogens and other rare biosphere members co-exist with SRM and dynamically respond to complex carbon inputs. Our results highlight the contribution of carbon complexity and recalcitrance in stimulating metabolically diverse community members in sediments, driving the assembly of functional microbial networks.

IMPORTANCE: Deep-sea sediments cover over 60% of the planet's surface and harbor diverse microbial communities that are important contributors to the carbon and nitrogen budget of the ocean. Despite their importance, the mechanisms by which these communities maintain diversity are poorly understood. In this work, we discuss the contribution of complex carbon to the community structure of marine sediment microbial consortia through the establishment of highly replicated anaerobic incubations provided with either the complex cosmopolitan carbon source chitin or its monomer N-acetylglucosamine.},
}

*Geologic Sediments/microbiology
*Chitin/metabolism
*Acetylglucosamine/metabolism
*Methane/metabolism
*Sulfates/metabolism
Anaerobiosis
*Bacteria/metabolism/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Microbiota
Archaea/metabolism

@article {pmid42820741,
year = {2026},
author = {Napier, BA and Merrill, BD and Krieger, M and Gevers, D and Reid, G},
title = {Formulations containing co-biotic compounds mediate microbiome function and composition without increased gas production in an ex vivo gastrointestinal model.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {10},
pages = {e0131126},
pmid = {42820741},
issn = {1098-5336},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Fatty Acids, Volatile/metabolism ; *Dietary Supplements/analysis ; Fermentation ; *Gastrointestinal Tract/microbiology ; *Gases/metabolism ; Adult ; Bacteria/classification/metabolism/genetics/isolation & purification ; Male ; *Vitamins ; Female ; Hydrogen-Ion Concentration ; },
abstract = {UNLABELLED: Dietary supplement formulations that contain co-biotics or compounds that modulate biological processes in both the host and microbiome to confer a health benefit are an emerging strategy to fine-tune both host physiology and gut microbiome function. Here, we evaluated three novel formulations containing co-biotic compounds (DM-02, a multivitamin; AM-02, formulated for energy and focus; and PM-02, formulated to promote sleep) for their effects on human gut microbiome composition and function. The three formulations and untreated control (Unt-Ctrl) were subjected to upper gastrointestinal digestion, after which the digesta were exposed to 24-h simulated colonic fermentation in the validated ex vivo systemic intestinal fermentation research (SIFR) technology (n = 6 healthy adults). Outcomes included pH, short-chain fatty acid (SCFA) and gas production, ultra-deep metagenomic profiling, and untargeted metabolomics of post-colonic supernatants, each compared to Unt-Ctrl. All three formulations significantly reduced pH (3%-4%) and increased total SCFAs (9%-11%) and acetate (9%-12%), with AM-02 and PM-02 also increasing butyrate by 20% and propionate by 7%-8%, without increasing gas production. Each formulation significantly enriched specific SCFA- and B-vitamin-producing taxa. AM-02 significantly increased the abundance of two pyruvate fermentation to acetate/lactate pathways. PM-02 significantly increased the abundance of two tryptophan biosynthesis pathways, accompanied by an increase in available tryptophan and the abundance of tryptophan-producing microbes. All three formulations increased the availability of microbiome-derived metabolites, indicating microbiome functional modulation by the treatments. These findings support clinical evaluation of these novel formulations as a strategy to enhance microbiome composition and function.

IMPORTANCE: The gut microbiome produces metabolites, including short-chain fatty acids, B vitamins, and tryptophan derivatives, that are critical regulators of host physiology, from energy metabolism and gut barrier integrity to sleep and immune function. While probiotics introduce live microorganisms, and prebiotics selectively feed existing microbes, co-biotics represent a distinct category of compounds that simultaneously modulate host cell biology and microbiome activity. Despite growing interest in co-biotic supplementation, the impact of complete co-biotic-containing formulations on gut microbiome composition and functional output has not been evaluated. Using a validated ex vivo gastrointestinal model inoculated with fecal microbiota from six healthy adults, we demonstrate that three supplement formulations containing co-biotic compounds consistently increased production of health-associated metabolites, selectively enriched beneficial microbial taxa, and modulated functional metabolic pathways, all without increasing gas production. These findings establish a mechanistic foundation for the clinical investigation of co-biotic formulations as targeted, tolerable interventions for optimizing gut microbiome function across diverse human populations.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Fatty Acids, Volatile/metabolism
*Dietary Supplements/analysis
Fermentation
*Gastrointestinal Tract/microbiology
*Gases/metabolism
Adult
Bacteria/classification/metabolism/genetics/isolation & purification
Male
*Vitamins
Female
Hydrogen-Ion Concentration

@article {pmid42833252,
year = {2026},
author = {Vorstenbosch, RV and Esenkova, EE and Jonkers, DMAE and Vilalta, ME and Graaf, M and Keszthelyi, D and Pachen, D and Schooten, FV and Mujagic, Z and Smolinska, A},
title = {Investigating the presence of microbiota-based phenotypes in irritable bowel syndrome.},
journal = {Journal of breath research},
volume = {20},
number = {4},
pages = {},
doi = {10.1088/1752-7163/aeb043},
pmid = {42833252},
issn = {1752-7163},
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/physiopathology ; Phenotype ; Female ; Feces/chemistry/microbiology ; Male ; Adult ; *Gastrointestinal Microbiome/physiology ; Volatile Organic Compounds/analysis ; Middle Aged ; Gas Chromatography-Mass Spectrometry ; },
abstract = {Irritable bowel syndrome (IBS) is heterogenous disorder of gut-brain interaction, with a key role for the dysregulated host-gut microbiota interplay. IBS subtyping is based only on symptoms of bowel habits, reflecting limited insight into underlying biological mechanisms. This study aimed to define microbiota-based IBS phenotypes and to compare these to traditional stool-based subtyping. The study utilized data from the Maastricht IBS cohort. Gut microbiota composition was analysed using shotgun metagenomic sequencing. Faecal volatile organic compounds (VOCs) were measured by gas chromatography mass spectrometry. Dietary intake and gastrointestinal and mental health symptoms were assessed using a food frequency questionnaire, the Dutch Healthy Diet-15 index, the gastrointestinal symptom rating scale, and hospital anxiety and depression scores, respectively. Machine-learning approaches were applied to identify microbiota-based phenotypical clusters, which were compared with established Rome III subtypes, and associated with faecal VOCs, gastrointestinal symptom severity, diet and mental health. 178 IBS patients and 134 healthy controls were included. Gut microbiota composition distinguished IBS patients from healthy controls with an AUCROC 0 · 8. This discriminatory profile was not associated with Rome III subtypes, while statistically significant associations were found with faecal VOCs profiles (i.e.R= 0 · 67,p= 4 · 46e-4) and symptom severity scores of abdominal pain (p= 0 · 05), reflux (p= 0 · 03), diarrhoea (p= 0 · 01) and depression (p< 0 · 001). Dietary associations varied across clusters. These results suggest that gut microbiota profiling might provide a basis to define relevant IBS endotypes. Further exploration and validation efforts into this direction are needed using longitudinal studies to refine IBS patient stratification ultimately.},
}

Humans
*Irritable Bowel Syndrome/microbiology/physiopathology
Phenotype
Female
Feces/chemistry/microbiology
Male
Adult
*Gastrointestinal Microbiome/physiology
Volatile Organic Compounds/analysis
Middle Aged
Gas Chromatography-Mass Spectrometry

@article {pmid42901678,
year = {2027},
author = {Niu, J and Li, W and Chen, X and Zhu, H and Sun, W and Li, X and Sun, B},
title = {Microbial succession and genome-resolved metabolic functions shape flavor evolution during sauce-flavor Baijiu fermentation.},
journal = {Food microbiology},
volume = {142},
number = {},
pages = {105326},
doi = {10.1016/j.fm.2026.105326},
pmid = {42901678},
issn = {1095-9998},
mesh = {Fermentation ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Flavoring Agents/metabolism ; Taste ; *Fermented Foods/microbiology/analysis ; *Microbiota ; Food Microbiology ; Metagenome ; },
abstract = {Sauce-flavor Baijiu (SFB) fermentation is characterized by a unique multi-round solid-state process, during which complex microbial succession drives flavor formation. However, the functional differentiation and metabolic mechanisms of microbial communities across successive fermentation rounds remain poorly understood. In this study, the physicochemical properties, microbial assembly, and metabolic profiles of fermented grains (FG) were investigated across seven production rounds (R1-R7). The results revealed that as fermentation rounds progressed, the FG environment evolved toward elevated acidity and reduced pH, driving a directional shift in the microbial community from an initially diverse assemblage to a structure dominated by acid-tolerant Acetilactobacillus, which established pronounced ecological dominance in later rounds. Metabolomic analysis further indicated that this dynamic adjustment of microbial structure drove the evolution of the flavor profile, specifically manifesting as differential accumulation of compounds such as esters, alcohols, and pyrazines across the various rounds. Co-occurrence network analysis demonstrated that positive microbial interactions significantly predominated within the fermentation system, and that community function exhibited a convergent trend as the rounds increased. Furthermore, 158 metagenome-assembled genomes (MAGs) were recovered, and metabolic reconstruction elucidated the potential contributions of genera such as Pediococcus, Bacillus, and Oceanobacillus to key metabolic pathways, including glycolysis, phenylalanine metabolism, and pyrazine biosynthesis. This work provides important insights into microbial regulation and quality improvement in SFB fermentation.},
}

Fermentation
*Bacteria/metabolism/genetics/classification/isolation & purification
*Flavoring Agents/metabolism
Taste
*Fermented Foods/microbiology/analysis
*Microbiota
Food Microbiology
Metagenome

@article {pmid42902375,
year = {2026},
author = {Yahia, S and Murugesan, S and Al Khodor, S},
title = {Decoding the human milk virome: a comparative analysis of composition, colonization, and health impacts.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42902375},
issn = {1479-5876},
mesh = {Humans ; *Milk, Human/virology ; *Virome ; Female ; *Health ; },
abstract = {BACKGROUND: Breast milk (BM) is a complex biological system that not only delivers essential nutrition to the baby, but is also a rich collection of microorganisms, including bacteria, viruses and fungi. Dominated by bacteriophages and eukaryotic viruses, the BM virome plays a role in shaping the infant gut microbiome composition, influencing immune development and long-term health outcomes. Emerging research confirms the vertical transmission of bacteriophages from the mother to her infant via breastfeeding, and the shared viral taxa suggest functional roles in modulating bacterial populations and maintaining gut homeostasis. Disruptions in this early life virome, driven by factors such as maternal health, mode of delivery, and geographic location, have been linked to dysbiosis and disease susceptibility for conditions ranging from inflammatory bowel disease to metabolic disorders.

METHODS: A systematic literature search was conducted in NCBI/PUBMED and the European Nucleotide Archive (ENA) using the keywords "Milk virome," "Milk phage," "Milk phageome," and "Milk metagenome". After applying our inclusion and exclusion criteria, two studies remained. This comparative analysis explores the composition and diversity of the BM virome across two geographically distinct cohorts-Turkey and the United States-revealing significant differences in viral diversity and composition.

RESULTS: The Turkish cohort exhibited a significantly higher viral richness and unique taxonomic distributions compared to the USA group. Notably, bacteriophage families like Myoviridae, Siphoviridae, and Podoviridae were shown to be abundant in both populations. The Turkish BM virome featured a higher prevalence of plant- and insect-derived viruses (e.g. Partitiviridae, Tospoviridae), likely tied to dietary or regional agricultural practices.

CONCLUSIONS: Despite limitations related to sample size and methodological variability, this study emphasizes how dietary habits, environmental exposures, and geographic location may shape the breast milk virome. Further research integrating longitudinal data from a multi-ethnic population, cohorts is essential to fully harness the diagnostic and therapeutic potential of the human milk virome.},
}

Humans
*Milk, Human/virology
*Virome
Female
*Health

@article {pmid42904046,
year = {2025},
author = {Zheng, K and Liang, Y and Zhang, Y and Páez-Espino, D and Shao, H and Sung, YY and Mok, WJ and Wong, LL and Wang, S and McMinn, A and Wang, M},
title = {Diversity of reverse-transcriptase-containing viruses through global metagenomics.},
journal = {hLife},
volume = {3},
number = {1},
pages = {52-56},
pmid = {42904046},
issn = {2949-9283},
}

@article {pmid42905275,
year = {2026},
author = {Chen, K and Li, J and Chen, J and Zheng, K and Zhou, L and Su, Y and Sun, S and Chen, X and Wang, W and Liang, Y and Shao, H and Liu, Y and Zou, X},
title = {Jestvirus, a Novel Genus in the Family Autotranscriptaviridae Infecting Aeromonas.},
journal = {Current microbiology},
volume = {83},
number = {12},
pages = {},
pmid = {42905275},
issn = {1432-0991},
support = {42120104006 and 42176111//the Natural Science Foundation of China/ ; 2025M770867//the China Postdoctoral Science Foundation/ ; },
mesh = {Phylogeny ; Genome, Viral ; *Bacteriophages/classification/genetics/isolation & purification/ultrastructure ; Viral Proteins/genetics ; DNA, Viral/genetics ; *DNA Viruses/classification/genetics/isolation & purification ; *Aeromonas/virology ; Sequence Analysis, DNA ; },
abstract = {Aeromonas species are ubiquitous, aquatic, opportunistic pathogens; however, their viral predators remain underexplored. Here, we isolated and characterized Aeromonas phage vB_AsaP_JS1, a dsDNA phage with a short non-contractile tail that infects Aeromonas salmonicida. Comparative analyses indicate that vB_AsaP_JS1 diverges from representative T7-like phages, with gene content similarity below 50% and a maximum amino acid identity of 70% or less. It forms a supported monophyletic clade in both phylogenomic and protein-based trees. Gene-sharing network analysis further shows that vB_AsaP_JS1 and its closest relatives form a distinct, isolated cluster, clearly separated from all currently recognized genera within the family Autotranscriptaviridae and related lineages of Caudoviricetes. Collectively, these features satisfy ICTV criteria for genus demarcation and support the establishment of a novel phage genus, tentatively designated Jestvirus. Functional annotation highlights a compact transcriptional module containing a single-subunit T7-like RNA polymerase and a streamlined replication packaging operon. Several putative host-interaction-related genes, including a deoxycytidine kinase homolog, a PelC-like protein, and a putative glycosidase, are encoded in the genome; their possible roles in nucleotide scavenging or host interaction during infection represent hypotheses that require experimental validation. Metagenomic read mapping reveals sequence-level signals related to vB_AsaP_JS1 in wastewater datasets from multiple geographic regions, suggesting a potentially wider environmental distribution for this phage lineage than previously recognized, though confirmation of phage identity and prevalence will require further investigation. Together, our results expand the known genomic diversity of T7-like phages and provide taxonomic, functional, and ecological evidence for a new phage lineage within Caudoviricetes.},
}

Phylogeny
Genome, Viral
*Bacteriophages/classification/genetics/isolation & purification/ultrastructure
Viral Proteins/genetics
DNA, Viral/genetics
*DNA Viruses/classification/genetics/isolation & purification
*Aeromonas/virology
Sequence Analysis, DNA

@article {pmid42906136,
year = {2026},
author = {Cheng, J and Hui, M and Yu, M and Wang, M and Sha, Z},
title = {Early holobiont-level divergence and adaptation across seafloor geochemical contrasts in the deep-sea squat lobster Shinkaia crosnieri.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag262},
pmid = {42906136},
issn = {1537-1719},
abstract = {Deep-sea hydrothermal vents and methane seeps host unique animal communities sustained by chemosynthetic symbioses, yet how biological diversification proceeds across these geochemically distinct and geographically fragmented habitats remains poorly understood. Previous studies have largely focused on either host genomic adaptation or symbiont diversity as drivers of isolation, leaving unresolved how environmental geochemistry and host-microbe associations jointly shape evolutionary trajectories in chemosynthetic ecosystems. Here, we addressed this gap by combining chromosome-level host genomics, population resequencing, and episymbiont metagenomics in the deep-sea chemosynthetic lobster Shinkaia crosnieri, a dominant species inhabiting both hydrothermal vents and methane seeps. Genomic innovations-including sensory trade-offs (vision loss versus chemosensory expansion), metabolic compensation for pigment loss, and positive selection on respiratory protein-underpin deep-sea colonization of S. crosnieri. Populations from the Okinawa Trough vent and the South China Sea seep exhibit pronounced genetic divergence, potentially driven by Pleistocene vicariance and reinforced by divergent selection across sulfur-enriched (vent) versus sulfur-depleted, methane-dominated (seep) environments. This selection target host genes involved in chemoreception and immunity, with coordinated signatures in both sequence evolution and structural variation. Crucially, holobiont-level adaptation is amplified by habitat-specific recruitment of episymbionts: sulfur-oxidizing Campylobacterales/Thiotrichales dominate vent-associated lobsters, while methanotrophic Methylococcales prevail at seep counterparts. These symbionts partition energy niches metabolically, with seep-associated communities enhancing biosynthesis of key cofactors (e.g., coenzyme Q, tetrahydrofolate). Host transporters for these nutrients are concurrently upregulated, demonstrating functional synergy. Our findings establish that diversification in extreme environments operates holobiont-wide, where geochemical gradients synergistically shape host genomic plasticity and symbiont metabolic specialization to drive early-stage divergence.},
}

@article {pmid42380482,
year = {2026},
author = {Kang, X and He, P and Zhang, H and Lü, F},
title = {Virus-mediated prokaryotic community adaptation dynamics under thermal stress in municipal organic solid waste microbiomes.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42380482},
issn = {2399-3642},
mesh = {*Microbiota ; *Adaptation, Physiological ; *Heat-Shock Response ; Refuse Disposal ; Metagenomics ; *Bacteriophages/genetics/physiology ; Stress, Physiological ; },
abstract = {Temperature influences microbial metabolic activity, which is crucial for biotechnological processes and bioproducts stabilization. However, temperature-driven responses of complex viruses and prokaryotic communities, and the modulatory role of viruses in prokaryotic community within environmental biotechnology systems, remain poorly understood. We developed a continuous thermal stress system with temperature gradients and high-resolution temporal sampling of metagenomics and metatranscriptomics, using municipal organic solid waste as a biological model. An optimized meta-omics pipeline integrating genomic potential and activity was applied to investigate the adaptive dynamics of complex prokaryotic and viral communities. Continuous thermal stress triggered stress responses in paired virus-hosts within the system. Thermal stress exerted distinct effects on temperate and virulent viruses. Viruses formed quasi-symbiotic alliances with their hosts to withstand thermal stress by integrating protein folding genes, stress response, and metabolic function genes, shaping host adaptability under thermal pressure. Equipped with multiple defense and counter-defense systems, viruses accelerated the accumulation of beneficial mutations under thermal stress, enabling them to escape host immunity and intensify competition with prokaryotic communities. This study demonstrates how viruses accelerated both the restructuring and adaptive responses of prokaryotic communities under thermal stress, advancing our understanding of phage-based therapeutic strategies in temperature-variable engineering applications.},
}

*Microbiota
*Adaptation, Physiological
*Heat-Shock Response
Refuse Disposal
Metagenomics
*Bacteriophages/genetics/physiology
Stress, Physiological

@article {pmid42901654,
year = {2027},
author = {Guo, Z and Zeng, Z and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Ni, B and Zhang, W and Sun, R},
title = {Serum metaviromic profiling of yaks and Tibetan sheep provides a pre-harvest viral baseline for food-producing ruminants.},
journal = {Food microbiology},
volume = {142},
number = {},
pages = {105301},
doi = {10.1016/j.fm.2026.105301},
pmid = {42901654},
issn = {1095-9998},
mesh = {Animals ; Cattle/virology/blood ; Sheep/virology/blood ; Tibet ; Phylogeny ; *Virome ; *Viruses/genetics/classification/isolation & purification ; Metagenomics ; },
abstract = {Pre-harvest viral profiles of food-producing ruminants in high-altitude pastoral systems remain poorly defined, limiting the selection of viral targets for monitoring along animal-derived food chains. In this study, we performed viral metagenomic profiling of 142 pooled serum libraries generated from 712 individual blood samples collected from yaks and Tibetan sheep across the Qinghai-Tibet Plateau. A total of 2.87 billion raw reads were obtained, of which 26.34 million were assigned to viral taxa. The serum viromes were dominated by single-stranded DNA and single-stranded RNA viruses, with Parvoviridae being the most abundant family. Yaks harboured significantly greater viral richness and diversity than Tibetan sheep, and community-level analysis showed distinct host-associated virome structures. Phylogenetic reconstruction recovered parvovirus-, astrovirus-, hepacivirus-, and genomovirus-related sequences, including a divergent erythroparvovirus-related lineage; the nepovirus-related sequence was categorized separately as a likely dietary or environmentally derived viral nucleic acid signal. These findings provide a serum-based viral reference for high-altitude pastoral production systems and identify viral lineages that may be considered for exploratory screening in downstream matrices, pending validation of their presence and infectivity. While viral nucleic acids detected in serum do not directly indicate contamination of animal-derived foods or foodborne transmission, they provide baseline data on serum-associated viral diversity that can guide subsequent assessment of potential spillover and food-chain relevance.},
}

Animals
Cattle/virology/blood
Sheep/virology/blood
Tibet
Phylogeny
*Virome
*Viruses/genetics/classification/isolation & purification
Metagenomics

@article {pmid41368505,
year = {2025},
author = {Di Leo, D and Nilsson, E and Krinos, A and Pinhassi, J and Lundin, D},
title = {The Nextflow nf-core/metatdenovo pipeline for reproducible annotation of metatranscriptomes, and more.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20328},
pmid = {41368505},
issn = {2167-8359},
support = {//Linnaeus University/ ; 2019-00242 AND 2023-00184//Swedish Research Council VR Swedish Biodiversity Data Infrastructure (SBDI)/ ; DE-SC0020347//U.S. Department of Energy/ ; },
mesh = {*Software ; Reproducibility of Results ; Workflow ; *Transcriptome ; *Computational Biology/methods ; *Molecular Sequence Annotation/methods ; *Metagenomics/methods ; },
abstract = {Metatranscriptomics-the sequencing of community RNA-has become a popular tool in microbial ecology, proving useful for both in situ surveys and experiments. However, annotating raw sequence data remains challenging for many research groups with limited computational experience. Standardized and reproducible analyses are important to enhance transparency, comparability across studies, and long-term reproducibility. To simplify metatranscriptome processing for biologists, and to promote reproducible analyses, we introduce nf-core/metatdenovo, a Nextflow-based workflow. Nextflow pipelines run on different computing platforms, from standalone systems to high-performance computing clusters and cloud platforms (e.g., AWS, Google Cloud, Azure) and use container technology such as Docker or Singularity to reproducibly provision software. Biologists can access the pipeline using either the command line or the Seqera platform, which provides a web browser-based interface to Nextflow pipelines. Collaborating with nf-core ensures high-quality, documented, reproducible workflows. Our nf-core/metatdenovo pipeline adheres to these established standards, enabling FAIR metatranscriptome de novo assembly, quantification, and annotation.},
}

*Software
Reproducibility of Results
Workflow
*Transcriptome
*Computational Biology/methods
*Molecular Sequence Annotation/methods
*Metagenomics/methods

@article {pmid42374042,
year = {2026},
author = {Chen, X and Chen, C and Zhang, P and OuYang, X and Ma, H and Chen, W and Li, T and Han, J and Wang, Y and Wang, H and Zhou, Q and Cheng, G and Zhou, W and Yu, Z and Zhou, W and Wang, M and Zeng, S},
title = {Bifidobacterium animalis reshapes the bile acid pool and prevents neonatal jaundice: a clinical microbiome study from correlation to causation.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42374042},
issn = {2055-5008},
support = {2024YFC2707700//National Key R&D Program of China, Key Special Project for "Reproductive Health and Maternal and Child Health Security"/ ; 82571963//the National Natural Science Foundation of China/ ; 2025A1515012162//Natural Science Foundation of Guangdong Province, China/ ; JCYJ20250604145739052//Shenzhen Science and Technology Innovation Bureau/ ; Y2024001//the Research Initiation Fund of Longgang District Maternity & Child Healthcare Hospital of Shenzhen City/ ; },
mesh = {Humans ; Animals ; *Bile Acids and Salts/metabolism ; *Jaundice, Neonatal/prevention & control/microbiology ; Infant, Newborn ; *Bifidobacterium animalis/physiology ; Mice ; Feces/microbiology ; *Gastrointestinal Microbiome ; Disease Models, Animal ; *Probiotics/administration & dosage ; Dysbiosis/microbiology ; Female ; Metagenomics/methods ; Male ; Multiomics ; Bacteriophages ; Bacteria/classification/genetics ; },
abstract = {Neonatal jaundice (NJ) affects 60-80% of neonates, yet the underlying microbial mechanisms remain elucidated, despite known links between gut dysbiosis and bilirubin and bile acid (BA) metabolism. Through two-stage shotgun metagenomic-metabolomic analysis of 150 fecal samples from 120 neonates, we identified key taxa linked to bile acid (BA) metabolism in moderate-to-severe NJ. Furthermore, multi-omics integration revealed significant interkingdom correlations among gut phages, bacteria, and BAs. Dysbiosis featured enriched Streptococcus and Escherichia, depleted Bifidobacterium animalis, and group-specific phage signatures. In the independent clinical validation cohort, jaundice intervention normalized the dysbiotic profile, demonstrating significant suppression of pathogenic taxa concomitant with restoration of B. animalis abundance. In vitro, B. animalis subsp. lactis Y103-OTU5 remodeled BA via deconjugation. In a phenylhydrazine hydrochloride (PHZ)-induced murine model of hemolytic jaundice, oral administration of isolated B. animalis subsp. lactis Y103-OTU5 significantly attenuated hyperbilirubinemia and hepatic inflammation, likely via Cyp7a1/Cyp7b1-dependent modulation of BA synthesis and detoxification pathways. Structural equation modeling revealed a tripartite regulatory network: phages indirectly modulated BA through bacterial remodeling, while B. animalis directly regulated BA pathways, positioning it as a potential therapeutic candidate for hemolysis-associated neonatal jaundice. Collectively, these findings reveal a gut phage-bacteria-BA network in NJ, highlighting B. animalis as a therapeutic candidate with dual modulation of BA metabolism and phage-bacteria interactions.},
}

Humans
Animals
*Bile Acids and Salts/metabolism
*Jaundice, Neonatal/prevention & control/microbiology
Infant, Newborn
*Bifidobacterium animalis/physiology
Mice
Feces/microbiology
*Gastrointestinal Microbiome
Disease Models, Animal
*Probiotics/administration & dosage
Dysbiosis/microbiology
Female
Metagenomics/methods
Male
Multiomics
Bacteriophages
Bacteria/classification/genetics

@article {pmid42734327,
year = {2026},
author = {Sahu, K and Aich, P},
title = {A robustness-first cross-disease framework supports a candidate shared microbial redox axis and disease-specific metabolic divergence in colorectal cancer, Crohn's disease, and liver cirrhosis.},
journal = {mSystems},
volume = {11},
number = {10},
pages = {e0083626},
doi = {10.1128/msystems.00836-26},
pmid = {42734327},
issn = {2379-5077},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism ; *Crohn Disease/microbiology/metabolism ; *Liver Cirrhosis/microbiology/metabolism ; Oxidation-Reduction ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology/metabolism ; Cross-Sectional Studies ; Metabolomics/methods ; Metagenomics ; },
abstract = {UNLABELLED: Gut microbiome dysbiosis is associated with colorectal cancer (CRC), Crohn's disease (CD), and liver cirrhosis (LC), yet whether these diseases share conserved microbial vulnerabilities remains unresolved. Analytical pipeline choices alone can shift apparent performance from near-zero to near-perfect on identical data, rendering cross-disease comparison unreliable. Here, in a secondary cross-sectional analysis of public data sets, maximin optimization is introduced as a proposed pipeline-selection criterion guaranteeing worst-case performance across all tasks simultaneously. Benchmarking 1,152 preprocessing-model configurations across six tasks using gut metagenomics and serum metabolomics from CRC, CD, and LC reveals a candidate 19-species microbiome signature in which Firmicutes bacterium CAG:41 is the sole threshold-stable cross-disease taxon, depleted in all three diseases. Microbiome pathway enrichment converges on sulfur-selenium redox metabolism and B-vitamin biosynthesis, while host metabolomic responses are predominantly disease-specific. CD and LC are dominated by single discriminative taxa; CRC requires community-level integration. Exploratory external evaluation was adequately powered only for CRC (AUC = 0.769, 95% bootstrap CI 0.678-0.849); CD and LC assessments were exploratory only.

IMPORTANCE: Cross-disease microbiome comparison has lacked a principled analytical foundation: arbitrary preprocessing choices can shift apparent classification performance from near-random to near-perfect on identical data, making biological conclusions unreliable when pooled across diseases. Maximin optimization addresses this by providing a decision-theoretic guarantee that every classification task contributes valid signal, enabling the first analytically controlled cross-disease comparison of gut metagenomics and serum metabolomics across three major gut-associated diseases. The identification of Firmicutes bacterium CAG:41 as the sole threshold-stable cross-disease taxon, harboring predicted functions in sulfur-selenium metabolism, offers a concrete target for experimental characterization and prospective screening validation. The two-layer dysbiosis architecture-universal microbial vulnerability with disease-specific host metabolic responses-provides a conceptual template for cross-disease microbiome study design in other gut-associated conditions, pending prospective confirmation.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism
*Crohn Disease/microbiology/metabolism
*Liver Cirrhosis/microbiology/metabolism
Oxidation-Reduction
*Gastrointestinal Microbiome
Dysbiosis/microbiology/metabolism
Cross-Sectional Studies
Metabolomics/methods
Metagenomics

@article {pmid42765688,
year = {2026},
author = {Xu, P and Arévalo-Martínez, DL and Middelboe, M and Pohlmann, M and Bange, HW and Löscher, CR},
title = {Microbial diversity and nitrogen cycling across oxygen gradients in the eastern tropical Pacific during two La Niña years.},
journal = {mSystems},
volume = {11},
number = {10},
pages = {e0089326},
doi = {10.1128/msystems.00893-26},
pmid = {42765688},
issn = {2379-5077},
support = {29411//Villum Fonden/ ; 2310112//Danmarks Frie Forskningsfond/ ; },
mesh = {*Oxygen/metabolism/analysis ; *Nitrogen Cycle ; Pacific Ocean ; Biodiversity ; Nitrogen/metabolism ; Seawater/microbiology/chemistry ; *Microbiota ; *El Nino-Southern Oscillation ; Bacteria/metabolism/genetics/classification ; Metagenomics ; Tropical Climate ; },
abstract = {The rapid expansion of ocean oxygen minimum zones (OMZs) may significantly affect the microbial processes that regulate marine nitrogen cycling. The eastern tropical Pacific (ETP) bears one of the largest perennial OMZs, which is strongly influenced by the recurring El Niño Southern Oscillation (ENSO). However, how microbial diversity and nitrogen cycling respond to oxygen variability under comparable ENSO conditions remains unclear. Here, we applied metagenomics to analyze changes in microbial communities across a dissolved oxygen (DO) gradient from oxic to suboxic conditions in the ETP during the 2022 La Niña event and compared our findings to the Tara Oceans data set from the same region during the 2011 La Niña. In 2022, we observed a decline in microbial alpha diversity and abundance, coupled with an increase in nitrogen metabolism genes as DO decreases. The relative abundance of many dominant microbes shifted at a DO threshold of 80 μmol kg[-1], while dominant nitrogen cycle genes varied under different DO thresholds (120, 20, 5 μmol kg[-1]). Despite the 11-year interval between sampling efforts, microbial alpha diversity was similar between 2011 and 2022. We observed a significant reduction of SAR11 and an increase of Poseidoniia in 2022 compared with 2011. While certain nitrogen cycling genes differed in relative abundance in a depth-dependent manner, overall functional group composition was largely consistent, with spatial variation exceeding interannual differences. Overall, our study presents a comprehensive examination of possible shifts of microbial diversity, community, and their potential for nitrogen cycling under deoxygenation during two La Niña years.IMPORTANCEThe eastern tropical Pacific oxygen minimum zones (OMZs), largely impacted by the natural climate cycle-El Niño-Southern Oscillation, are predicted to continually expand while their core may shrink. While deoxygenation is known to profoundly influence microbial ecosystems, how microbial diversity, composition, and nitrogen cycling would shift across oxic/hypoxic/suboxic gradients, and its association with ENSO dynamics remains poorly understood. We surveyed microbial communities under two La Niña years with an 11-year gap and found that vertical variability is more critical than temporal variations for both microbial diversity and microbe-mediated nitrogen pathways, as only slight differences in microbial diversity and nitrogen cycles were detected between the two studied years despite ENSO dynamics, which might have disrupted the system among the 11 years. Moreover, we identified oxygen thresholds causing dominant microbes and potential nitrogen pathways to shift, thus helping to improve prediction on how various microbes and nitrogen pathways might respond to further deoxygenation.},
}

*Oxygen/metabolism/analysis
*Nitrogen Cycle
Pacific Ocean
Biodiversity
Nitrogen/metabolism
Seawater/microbiology/chemistry
*Microbiota
*El Nino-Southern Oscillation
Bacteria/metabolism/genetics/classification
Metagenomics
Tropical Climate

@article {pmid42788735,
year = {2026},
author = {Shi, H and Chen, Y and Liu, X and Yang, J and Yan, D and Zhang, H and Chen, J and Wu, Z and Yuan, D and Lu, H and Li, L},
title = {Clinical severity score-guided metagenomic analysis identifying gut microbial taxonomic and functional markers for severe hepatitis E progression.},
journal = {mSystems},
volume = {11},
number = {10},
pages = {e0095626},
doi = {10.1128/msystems.00956-26},
pmid = {42788735},
issn = {2379-5077},
support = {2024YFC2309904//National Key Research and Development Program of China/ ; 2022YFC3602000//National Key Research and Development Program of China/ ; 81874038//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; *Metagenomics/methods ; Biomarkers ; Severity of Illness Index ; *Hepatitis E/microbiology/pathology ; Disease Progression ; Feces/microbiology ; Adult ; *Bacteria/classification/genetics ; Middle Aged ; Metagenome ; },
abstract = {Although gut microbiome alterations have been reported in hepatitis E (HE), the taxonomic and functional determinants of disease severity remain poorly defined. Here, we performed shotgun metagenomic sequencing of fecal samples from 125 individuals spanning acute non-icteric hepatitis (ANIH), acute icteric hepatitis (AIH), acute liver failure (ALF), and healthy controls. We constructed a surrogate clinical severity index from routine blood parameters and developed an integrative analytical framework that combined XGBoost-based taxonomic modeling with LASSO-driven functional feature selection to explore microbiome-severity associations. The taxonomic model discriminated patients from controls (area under the curve [AUC] = 0.944) and identified nine bacterial species significantly associated with severity, independent of age, sex, and body mass index (BMI) (permutation test, P < 0.05), with Veillonella atypica emerging as the most robust candidate biomarker. The signature featured enrichment of lactate-utilizing Veillonella spp. and Ligilactobacillus salivarius, alongside depletion of beneficial commensals (Dorea longicatena, Ruminococcus timonensis, Eubacterium ramulus), collectively suggesting a pathogenic "lactate axis." The HE-enriched lactate utilizers were positively associated with 13 core severity-increasing KOs involved in oxidative stress adaptation (npr, hemQ, NUDT1, nfr1) and secretion/biofilm formation (gspD, fhaC, vpr, sinR) and negatively with three severity-decreasing KOs, including the butyrate fermentation gene (K14534). Strikingly, the stringent 16-KO core (intersection of four methods) explained more variance in disease severity than the broader set identified by at least three methods (R[2] = 0.61 vs. 0.47). Collectively, these findings reveal a strong link between microbiome-derived lactate metabolism and HE severity, highlighting its potential as a basis for microbiome-based severity stratification and motivating further mechanistic exploration.IMPORTANCEHepatitis E virus (HEV) infection ranges from ANIH to ALF, yet the role of the gut microbiome remains poorly understood across the severity spectrum. By performing shotgun metagenomic sequencing on fecal samples from 125 individuals and applying an integrative framework combining XGBoost-based taxonomic modeling with LASSO-driven functional selection, we identified robust microbiome-severity associations as quantified by a surrogate clinical severity index derived from routine blood parameters. These associations were characterized by enrichment of lactate-utilizing Veillonella species (notably Veillonella atypica), depletion of beneficial butyrate-producing commensals, and severity-linked shifts in microbial functional gene profiles. Such patterns are consistent with a perturbed microbial "lactate axis" in gut-liver crosstalk, although all associations remain correlational. Our findings nominate candidate microbial markers for severity stratification in hepatitis E and provide a hypothesis-generating framework to guide future mechanistic studies and microbiome-based therapeutic strategies.},
}

Humans
Male
*Gastrointestinal Microbiome/genetics
Female
*Metagenomics/methods
Biomarkers
Severity of Illness Index
*Hepatitis E/microbiology/pathology
Disease Progression
Feces/microbiology
Adult
*Bacteria/classification/genetics
Middle Aged
Metagenome

@article {pmid42813801,
year = {2026},
author = {Xu, J and Fan, Y and Qu, G and Li, J and Peng, Y and Wang, M and Zhang, J and Feng, Y and Liu, X and Hu, Y and Kan, B and Li, Z and Zeng, M and Lu, X},
title = {Comparative gut microbiome in diarrheal and non-diarrheal children: an individually matched case-control study.},
journal = {mSystems},
volume = {11},
number = {10},
pages = {e0019826},
doi = {10.1128/msystems.00198-26},
pmid = {42813801},
issn = {2379-5077},
support = {2025ZD01901101//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Mayor Project/ ; 2024YFC3406305//National Key Research and Development Program of China/ ; 22193064//Major Projects of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; Case-Control Studies ; *Diarrhea/microbiology ; Female ; Child, Preschool ; Infant ; Male ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Virulence Factors/genetics ; *Bacteria/genetics/classification/isolation & purification ; Child ; Metagenomics ; Drug Resistance, Microbial/genetics ; },
abstract = {Diarrhea, a leading cause of under-five mortality in developing countries, drives therapeutic challenges amid global antibiotic resistance. This study aimed to compare gut microbiota, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) in diarrheal and non-diarrheal children, explore reasons for asymptomatic pathogen carriage, and develop a microbiome-based model to predict the potential etiology of diarrhea. This individually matched case-control study analyzed 42 paired fecal samples (selected from 716 diarrhea/non-diarrhea cases) to compare gut microbiome profiles, ARGs, MGEs, and VFs using metagenomic sequencing and pathogen-specific PCR. Diarrheal children showed reduced alpha diversity, increased Proteobacteria, and elevated VFs and MGEs. Surprisingly, ARGs were more abundant in non-diarrheal children, suggesting ARG colonization in healthy hosts. Actinomyces was enriched in non-diarrheal pathogen carriers and may be associated with asymptomatic bacterial pathogen carriage. A random forest (RF) model incorporating non-pathogenic bacteria achieved high accuracy in predicting diarrheal status and pathogen carriage. This study reveals distinct microbial ecologies between diarrheal and healthy children. The enrichment of specific bacterial taxa in asymptomatic carriers may be associated with pathogen tolerance. The unexpected ARG abundance in healthy children highlights a hidden antimicrobial resistance reservoir. These findings inform microbiome-based diagnostics and antibiotic stewardship in pediatric diarrhea.IMPORTANCEThis study is significant because it provides robust, individually matched case-control evidence linking childhood diarrhea to gut microbiome dysbiosis and the distribution of pathogenic and resistance-related genetic elements. By integrating metagenomic sequencing with pathogen-specific polymerase chain reaction (PCR), it offers a comprehensive comparison of microbial composition, virulence factors (VFs), mobile genetic elements (MHEs), and antibiotic resistance genes (ARGs) between diarrheal and non-diarrheal children. The findings demonstrate reduced microbial diversity and enrichment of Proteobacteria, virulence factors, and mobile genetic elements in diarrheal cases, highlighting microbiome instability during infection. Importantly, the unexpectedly higher abundance of antibiotic resistance genes in non-diarrheal children underscores the underestimated role of healthy populations as reservoirs of resistance. Furthermore, the establishment of predictive models for diarrhea status and pathogen carriage enhances the translational value of the study. Overall, this work advances the understanding of pediatric diarrheal disease and informs prevention, surveillance, and treatment strategies in the context of global antimicrobial resistance.},
}

Humans
Case-Control Studies
*Diarrhea/microbiology
Female
Child, Preschool
Infant
Male
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Virulence Factors/genetics
*Bacteria/genetics/classification/isolation & purification
Child
Metagenomics
Drug Resistance, Microbial/genetics

@article {pmid42813975,
year = {2026},
author = {Aitolo, GL and Rambo, IM and Weisend, RE and Mullis, MM and Tringe, S and Kosmopoulos, JC and Anantharaman, K and Kiel Reese, B and Baker, BJ and De Anda, V},
title = {Shifts in vegetation impact estuary microbiomes.},
journal = {mSystems},
volume = {11},
number = {10},
pages = {e0107126},
doi = {10.1128/msystems.01071-26},
pmid = {42813975},
issn = {2379-5077},
support = {LI-SIAME-00002001//Simons Foundation/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; },
mesh = {*Microbiota/genetics ; Bacteria/genetics/classification/metabolism ; *Estuaries ; Geologic Sediments/microbiology/virology ; Archaea/genetics/classification ; Metagenome ; Phylogeny ; Wetlands ; Viruses/genetics/classification ; Avicennia/microbiology ; Carbon/metabolism ; },
abstract = {Coastal wetlands, including mangrove-cordgrass mosaics, are among Earth's most effective carbon stores sequestering >1 Pg C/year. Rapid sea level rise, warming, and storm intensification are now reshaping these habitats. Vegetation type influences root exudates, sediment redox profiles, and organic matter quality. However, the impacts of vegetation on microbe-virus networks that mediate carbon burial and nutrient cycling remain unclear. Here, we sampled coastal sediment profiles in patches of cordgrass (dominated by Sporobolus alterniflorus), black mangrove (Avicennia germinans), and seagrass on the Texas Gulf Coast. We obtained 491 bacterial and archaeal metagenome assembled genomes (MAGs) and 1,097 viral MAGs (vMAGs) from 55 surface sediment samples spanning day and night during summer and fall. Phylogenetic and comparative analyses revealed dominant lineages across the distinct vegetation types, organized into metabolic guilds based on similar protein compositions, revealing contrasting and complementary sulfur, iron, and nitrogen cycling pathways that regulate greenhouse gas emissions and encode genes important for carbon metabolism. Inference from virus-host linkages revealed that dominant lineages were infected, and viral communities have genes for organic carbon degradation, potentially shaping the microbial community dynamics in this ecosystem. This spatio-temporal characterization of estuary ecotone microbiomes provides a framework to better understand the diversity and metabolism of these productive coastal ecosystems.IMPORTANCECoastal wetlands are among the most effective environments for storing carbon and regulating climate. As sea level rise and changing weather patterns drive shifts in coastal vegetation, these vulnerable ecosystems are undergoing rapid transformation. Yet, little is known about the microbes that regulate carbon storage and nutrient cycling. Here, we characterized microbial and viral communities associated with coastal wetland sediments along the Texas Gulf Coast. We identified key microbial groups responsible for key carbon, sulfur, nitrogen, and iron cycling and showed that vegetation type influences their distribution and ecological roles. We also found that viruses interact with dominant microbial groups and carry genes linked to carbon processing, suggesting an important role in shaping ecosystem function. These findings provide insights into the mechanisms that sustain coastal wetlands and help predict how shifts in vegetation may affect nutrient cycling and ecosystem resilience in the future.},
}

*Microbiota/genetics
Bacteria/genetics/classification/metabolism
*Estuaries
Geologic Sediments/microbiology/virology
Archaea/genetics/classification
Metagenome
Phylogeny
Wetlands
Viruses/genetics/classification
Avicennia/microbiology
Carbon/metabolism

@article {pmid42843345,
year = {2026},
author = {Zhao, S and Haryono, MAS and Lai, CWM and Seah, F and Tang, YL and Lim, M and Febriana, E and Lee, MH and Tan, KS and Fu, JH and Yip, JK and Preshaw, PM and Williams, RBH and Toh, SA and Lee, JWJ and Goh, CE},
title = {Oral microbial nitrate metabolism is associated with lower prevalence of prediabetes.},
journal = {Cell reports. Medicine},
volume = {7},
number = {10},
pages = {103092},
doi = {10.1016/j.xcrm.2026.103092},
pmid = {42843345},
issn = {2666-3791},
mesh = {*Nitrates/metabolism ; Humans ; *Prediabetic State/microbiology/epidemiology/metabolism ; *Microbiota ; Nitrites/metabolism ; Prevalence ; *Mouth/microbiology ; Tongue/microbiology ; Saliva/metabolism/microbiology ; },
abstract = {The oral microbiome is a key microbial interface for dietary or oral nitrate metabolism, yet its role in early glycemic dysregulation remains poorly defined. In a population-based cohort (n = 472), we perform metagenomic profiling of tongue dorsum microbiomes and identify 11 taxa and nine microbial pathways associated with prediabetes. Among these, Rothia mucilaginosa and microbial nitrate reduction emerge as the only taxon and the strongest pathway associated with lower prediabetes prevalence. Individuals without prediabetes show higher salivary nitrate and nitrite concentrations, supporting enhanced oral nitrate bioavailability. Functional characterization of an isolated Rothia mucilaginosa strain demonstrates its capacity to mediate both nitrate-nitrite-NO and nitrate-nitrite-NH4[+] pathways under oxygen-limited conditions. Incorporating nitrate metabolism-associated microbial features into clinical risk factors improves risk stratification for progression to prediabetes. These findings support oral nitrate metabolism as a microbial pathway linking oral ecology to systemic metabolic health and suggest that tongue cleaning may modulate microbial functions involved in this pathway.},
}

*Nitrates/metabolism
Humans
*Prediabetic State/microbiology/epidemiology/metabolism
*Microbiota
Nitrites/metabolism
Prevalence
*Mouth/microbiology
Tongue/microbiology
Saliva/metabolism/microbiology

@article {pmid42854696,
year = {2026},
author = {Cabello-Yeves, E and Samarra, A and Summers, K and Comas, I and Wellington, E and Millard, A and Collado, MC and Marina, A},
title = {Breastfeeding and maternal microbial reservoirs are associated with infant gut phageome development during the first year of life.},
journal = {Cell reports. Medicine},
volume = {7},
number = {10},
pages = {103107},
doi = {10.1016/j.xcrm.2026.103107},
pmid = {42854696},
issn = {2666-3791},
mesh = {Humans ; Infant ; Female ; *Bacteriophages/genetics/physiology ; *Breast Feeding ; *Gastrointestinal Microbiome ; Metagenomics ; *Virome ; Infant, Newborn ; Mothers ; Feces/microbiology/virology ; },
abstract = {The early-life assembly of the gut microbiome is a critical determinant of long-term health, yet the role of bacteriophages in this process remains poorly understood. Here we longitudinally profile the gut phageome of 34 mother-infant dyads during the first year of life with metagenomics and a phage-centered computational workflow. Phage diversity increases with age, paralleling bacterial diversification but following distinct ecological trajectories. Shared viral populations across maternal and infant samples are consistent with potential maternal contribution, although not indicative of direct transmission. Feeding-related variables are consistently associated with phageome composition at specific developmental stages. No single factor fully explains phageome variation, supporting a multifactorial model involving maternal, environmental, and dietary inputs. Together, these findings provide a framework for understanding early-life phage ecology, positioning phages as active participants in early microbiome assembly and supporting the inclusion of viral components in microbiome-based strategies aimed at promoting healthy ecosystem development in infancy.},
}

Humans
Infant
Female
*Bacteriophages/genetics/physiology
*Breast Feeding
*Gastrointestinal Microbiome
Metagenomics
*Virome
Infant, Newborn
Mothers
Feces/microbiology/virology

@article {pmid42896018,
year = {2026},
author = {Ciappina, G and Maltese, T and Mauro, GD and Fiorentino, V and Ieni, A and Ottaiano, A and Simone, C and Consolo, P and Pollicino, T and Berretta, M},
title = {Gut Microbiota and Immunotherapy: Baseline 16S rRNA Profiling as a Pragmatic Tool for Clinical Stratification.},
journal = {Cancer control : journal of the Moffitt Cancer Center},
volume = {33},
number = {},
pages = {10732748261500279},
doi = {10.1177/10732748261500279},
pmid = {42896018},
issn = {1526-2359},
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/genetics/immunology/drug effects ; *Neoplasms/microbiology/therapy/immunology/drug therapy ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; },
abstract = {The gut microbiota is a complex and dynamic ecosystem involved in the modulation of host immune responses. Accumulating evidence links gut microbial composition to the efficacy and toxicity of immune checkpoint inhibitors (ICIs), although most evidence supporting microbiota-based biomarkers remains observational. Higher baseline alpha-diversity has been associated with favorable outcomes in several cohorts, but these associations are not uniform, and individual taxonomic signatures show substantial inter-study variability. In this perspective, we discuss baseline microbiota profiling as a promising investigational approach to patient stratification in immuno-oncology. Despite its methodological limitations, 16S rRNA sequencing remains a scalable, reproducible, and clinically feasible approach compared with more complex techniques such as shotgun metagenomics. Standardization of sampling procedures, sequencing methodologies, and bioinformatic pipelines is essential for the reliable implementation of microbiota-based biomarkers in routine clinical care. Integrating gut microbiota assessment into pre-treatment evaluation may improve patient selection and support a more biologically informed approach to immunotherapy.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Immunotherapy/methods
*Gastrointestinal Microbiome/genetics/immunology/drug effects
*Neoplasms/microbiology/therapy/immunology/drug therapy
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology

@article {pmid42896957,
year = {2026},
author = {Newton, JP and Allentoft, ME and Bateman, PW and Ferrier, S and Thomsen, PF and Nevill, P},
title = {Car-Mounted Airborne eDNA Sampling Detects Landscape Scale Biodiversity Turnover Along Environmental Gradients.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70217},
doi = {10.1111/1755-0998.70217},
pmid = {42896957},
issn = {1755-0998},
support = {//Mineral Resources/ ; },
mesh = {*DNA, Environmental/genetics/isolation & purification ; *Biodiversity ; Animals ; Extrachromosomal DNA ; Plants/genetics/classification ; Western Australia ; DNA Barcoding, Taxonomic ; Ecosystem ; *Metagenomics/methods ; },
abstract = {Documenting accelerating global biodiversity decline requires monitoring tools that can operate across large spatial scales and repeated timeframes. Analysis of airborne environmental DNA (eDNA) is an emerging method used to track species distributions, but it is unknown whether airborne eDNA retains coherent ecological signals across terrestrial landscapes, or whether atmospheric mixing and DNA transport make it too spatially diffuse to resolve meaningful macroecological patterns. To address this question, we conducted a biodiversity survey using car-mounted airborne eDNA sampling along a repeated 1155 km route across south-western Western Australia, spanning the Southwest Australian biodiversity hotspot and adjacent inland regions. This extensive and environmentally heterogeneous region faces ongoing pressures from habitat loss, invasive species and climate change, highlighting the need for scalable biodiversity monitoring approaches. Samples were collected at ~26 km intervals and analysed using metabarcoding assays targeting plants, vertebrates and arthropods, with generalised dissimilarity modelling used to assess environmental drivers of community turnover. We detected a broad range of plants and animals, including species of ecological and biosecurity importance. Different taxonomic groups showed distinct spatial scales of airborne eDNA community similarity and beta diversity was structured primarily by habitat and environmental gradients rather than geographic distance alone. This indicates that airborne eDNA did not simply reflect spatially homogenised biological material but retained ecological structure informative of macroecological patterns. Together, these findings demonstrate that car-mounted airborne eDNA can recover ecologically meaningful patterns of community turnover across heterogeneous terrestrial landscapes and support landscape-scale biodiversity assessment.},
}

*DNA, Environmental/genetics/isolation & purification
*Biodiversity
Animals
Extrachromosomal DNA
Plants/genetics/classification
Western Australia
DNA Barcoding, Taxonomic
Ecosystem
*Metagenomics/methods

@article {pmid42897351,
year = {2026},
author = {Vijande, C and Fuentes-González, C and Lazzari, M and Lema, JM and Balboa, S},
title = {Industrial WWTP Sludge as a Reservoir of Putative Plastic-Degrading Enzymes: Insights Into Microbial Community Structure.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42897351},
issn = {1432-184X},
support = {ED481A 2022/391//Xunta de Galicia/ ; ED431F2024/302//Xunta de Galicia/ ; RYC2021-031220-I//Agencia Estatal de Investigación/ ; },
mesh = {*Sewage/microbiology ; *Plastics/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/enzymology/isolation & purification/metabolism ; Biodegradation, Environmental ; Metagenomics ; Biofilms/growth & development ; *Microbiota ; Proteobacteria/genetics/enzymology/isolation & purification ; *Wastewater/microbiology ; },
abstract = {Plastic pollution has emerged as a major environmental challenge. While various microorganisms and enzymatic mechanisms involved in plastic degradation have been described, the microbial communities present in wastewater treatment plants (WWTPs) - particularly those linked to the oil industry - remain largely underexplored as potential reservoirs of plastic-associated metabolic functions. This study evaluated the potential of microbial communities from an industrial WWTP located in an oil refinery complex to colonise different plastic polymers, as well as their genetic potential for plastic-associated transformations. Industrial sewage sludge was incubated with four polymeric substrates: low-density polyethylene, polyamide, polypropylene, and polystyrene. Metagenomic analysis of the inoculum was performed to assess its potential to harbour genes encoding proteins with sequence similarity to enzymes previously associated with plastic transformation or degradation. Additionally, 16S rRNA amplicon sequencing studied changes in microbial community composition during biofilm formation. Proteobacteria accounted for approximately 50% of the microbial relative abundance in the inoculum. Metagenomic screening identified 773 genes encoding proteins with homology to enzymes previously associated with plastic degradation. Biofilms developed on plastic surfaces were dominated by Proteobacteria and Bacteroidota, although differences in dominant classes and orders were observed depending on the polymer type. Correlation analyses further indicated associations between specific microbial taxa and individual plastic types. Overall, the results highlight industrial WWTP sludge as a potential reservoir of microorganisms associated with plastic colonisation, providing new insights into plastisphere community assembly in engineered environments.},
}

*Sewage/microbiology
*Plastics/metabolism
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/enzymology/isolation & purification/metabolism
Biodegradation, Environmental
Metagenomics
Biofilms/growth & development
*Microbiota
Proteobacteria/genetics/enzymology/isolation & purification
*Wastewater/microbiology

@article {pmid42897614,
year = {2026},
author = {Gattei, A and Vettorazzo, S and Pindo, M and Salmaso, N and Manghi, P and Larsen, S and Donati, C},
title = {Metagenomics identifies distinct functional and taxonomic profiles between freshwaters and associated sediments in alpine habitats.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42897614},
issn = {2524-6372},
support = {PNRR, Mission 4 Component 2, Investment 1.4, D.D. 1034 17/06/2022, Project CN00000033//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; },
abstract = {BACKGROUND: Alpine freshwater habitats are biodiversity hotspots, home to uniquely adapted microbial communities. However, our understanding of how taxonomic composition and metabolic potential of microbial communities varies across habitat type and physiography remains limited.

RESULTS: Using metagenomic sequencing, we examined microbial diversity and functions in sediment and water habitats across a physiographic gradient, including deep and shallow lakes, pasture ponds, ponds and peat bogs. Overall, sediments supported more diverse and even microbial communities. Conversely, waters displayed higher heterogeneity across the physiographic gradient in both taxonomic and functional composition. Notably, water communities from small water bodies, especially peat bogs and ponds, showed comparable diversity to their respective sediment communities, with higher taxonomic richness than aquatic communities from larger water bodies. Sediment microbial communities showed higher functional potential for nitrogen and methane metabolism, a pattern related to the likely anoxic conditions. By contrast, water bodies favored higher potential for carbohydrate metabolism, carbon oxidation and photosynthesis. Lastly, we recovered 496 bacterial and archaeal metagenome-assembled genomes and found that 73% could not be assigned at the species level.

CONCLUSIONS: Our findings shed new light on the microbial diversity and metabolic potential of alpine freshwater ecosystems, highlighting the vast and unknown diversity harbored by these fragile alpine ecosystems.},
}

@article {pmid42901642,
year = {2027},
author = {Jiang, W and Li, Z and Dong, Y and Ao, Z and Jia, J and Chen, Z and Song, C and Yang, L and Liu, R and Peng, J and Zhang, S and Feng, Z},
title = {Spatiotemporal dynamics of volatile flavor compounds and associated functional microbial communities during strong-flavor Daqu fermentation.},
journal = {Food microbiology},
volume = {142},
number = {},
pages = {105281},
doi = {10.1016/j.fm.2026.105281},
pmid = {42901642},
issn = {1095-9998},
mesh = {Fermentation ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; *Flavoring Agents/metabolism/chemistry ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; Metagenomics ; *Wine/microbiology/analysis ; RNA, Ribosomal, 16S/genetics ; Taste ; Solid Phase Microextraction ; Fungi/metabolism/genetics/classification/isolation & purification ; },
abstract = {Daqu, the essential fermentation starter for Baijiu production, harbors stratified microbial communities that orchestrate flavor formation. This study integrated headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS), metagenomics, and PacBio full-length 16S rRNA and ITS sequencing to characterize the spatiotemporal heterogeneity of volatile flavor compounds (VFCs) and functional microbial communities across three layers-the surface (QP), middle (HQ), and core (QX) of strong-flavor Daqu over a 90-day fermentation period. A total of 47 VFCs were identified, with alcohols, aldehydes, and esters as the predominant components. VFCs peaked at 2-4 days, then declined and stabilized, showing a progressive accumulation gradient from QP to QX. Aldehydes and pyrazines were enriched in HQ and QX, while esters and acids were highest in QX. Metagenomic analysis demonstrated that the abundance of flavor-related enzyme genes followed spatiotemporal trends of VFCs. Although filamentous fungi and Lactobacillaceae constituted the primary microbial sources of flavor-related enzyme genes across all layers, their community composition and successional dynamics exhibited pronounced spatiotemporal specificity. Positive microbial interactions increased from QP (71.70%) to HQ (76.73%) to QX (89.95%), indicating stronger cooperation in QX. These findings provide mechanistic insights into the ecological underpinnings of flavor stratification in Daqu and offer a scientific framework for future targeted optimization of strong-flavor Baijiu fermentation.},
}

Fermentation
*Volatile Organic Compounds/metabolism/chemistry/analysis
*Flavoring Agents/metabolism/chemistry
*Bacteria/genetics/metabolism/classification/isolation & purification
*Microbiota
Gas Chromatography-Mass Spectrometry
Metagenomics
*Wine/microbiology/analysis
RNA, Ribosomal, 16S/genetics
Taste
Solid Phase Microextraction
Fungi/metabolism/genetics/classification/isolation & purification

@article {pmid42443738,
year = {2026},
author = {Carasso, S and Gefen, T and Bakria, R and Bar-Yoseph, H and Geva-Zatorsky, N},
title = {Microbiome changes associated with FMT-mediated clearance of antibiotic-resistant Klebsiella pneumoniae in a murine carriage model.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42443738},
issn = {1471-2180},
support = {grant 1571/17 and 3165/20//Israeli Science Foundation/ ; grant FL-000969/FL-001245/FL-001381//CIFAR Azrieli Global Scholars/ ; grant CDA00025/2019-C//Human Frontier Science Program Career Development Award/ ; ERC, ExtractABact, 101078712//the European Union/ ; },
mesh = {Animals ; *Klebsiella pneumoniae/drug effects/genetics ; *Fecal Microbiota Transplantation/methods ; Mice ; *Klebsiella Infections/therapy/microbiology ; Feces/microbiology ; Disease Models, Animal ; *Gastrointestinal Microbiome ; *Carrier State/microbiology/therapy ; Anti-Bacterial Agents/pharmacology ; Carbapenem-Resistant Enterobacteriaceae ; Carbapenems/pharmacology ; Female ; Drug Resistance, Bacterial ; Bacteriophages/genetics ; },
abstract = {Carbapenem-resistant Enterobacterales (CRE), including Klebsiella pneumoniae (KP), pose a significant public health threat due to their resistance to last-line antibiotics. Eliminating CRE colonization in asymptomatic carriers is crucial to prevent the spread of resistance, as carriage often serves as a reservoir that enables the transmission of resistant strains to vulnerable populations. Fecal microbiota transplantation (FMT) has emerged as a potential strategy to restore gut microbiome balance and eliminate CRE colonization. However, the mechanisms driving successful decolonization warrant further research. This study investigates the impact of FMT on gut microbiome composition, CRE-KP clearance and host response, in a mouse model of CRE-KP carriage. Mice colonized with CRE-KP, were treated with FMT or left untreated. Shotgun metagenomics of fecal samples were used to monitor changes in microbiome composition and function. FMT resulted in substantial changes in the gut microbiome, with successful clearance correlating with an expansion of commensal bacteria including Bifidobacterium and Lactobacillus species. Notably, a reduction in K. pneumoniae was also observed in some untreated control mice as the microbiome recovered naturally, also associated with Bifidobacterium expansion. Phage profiling revealed distinct viral populations that were associated with successful decolonization. Flow cytometry was employed to quantify bacterial populations bound by immunoglobulins, providing insight into host immune modulation. These findings suggest potential mechanisms for CRE carriage eradication using microbiome targeted therapies. The results emphasize the importance of microbiome resilience in combating antibiotic-resistant infections and suggest that phage-microbiome interactions could play a role in restoring microbial balance.},
}

Animals
*Klebsiella pneumoniae/drug effects/genetics
*Fecal Microbiota Transplantation/methods
Mice
*Klebsiella Infections/therapy/microbiology
Feces/microbiology
Disease Models, Animal
*Gastrointestinal Microbiome
*Carrier State/microbiology/therapy
Anti-Bacterial Agents/pharmacology
Carbapenem-Resistant Enterobacteriaceae
Carbapenems/pharmacology
Female
Drug Resistance, Bacterial
Bacteriophages/genetics

@article {pmid42735830,
year = {2026},
author = {Ma, Y and Ge, Y and Liu, C and Wang, M and Xiao, Z and Liu, X and Song, T and Zhou, Q and Xiao, L},
title = {Pathogenic microbiomes on jellyfish reveal health risks beyond envenomation.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {284},
number = {},
pages = {109307},
doi = {10.1016/j.toxicon.2026.109307},
pmid = {42735830},
issn = {1879-3150},
mesh = {Animals ; *Microbiota ; *Scyphozoa/microbiology ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; },
abstract = {Jellyfish stings pose a growing public health concern in coastal regions, yet secondary bacterial infections arising from venom-induced tissue damage remain largely unexplored. Here we used shotgun metagenomics to characterize the surface microbiomes of Rhopilema esculentum, Chrysaora quinquecirrha and Stomolophus meleagris, profiling bacterial composition, virulence factors, antibiotic resistance genes and mobile genetic elements. We observed distinct host-specific microbiome signatures, with R. esculentum harboring the highest abundance of virulence-associated genes and notable enrichment of WHO priority pathogens including Staphylococcus aureus and Acinetobacter baumannii. Resistance genes conferring tetracycline, glycopeptide and fluoroquinolone resistance were prevalent across all species. Transposases comprised over 45% of mobile genetic elements, indicating substantial horizontal gene transfer potential. Validation using newly developed TaqMan qPCR assays across eight jellyfish species including the three aforementioned and five additional species, confirming that all harbored at least one opportunistic pathogen. These findings establish jellyfish surfaces as underappreciated reservoirs of antibiotic-resistant pathogens and highlight a potential, but as yet unproven, route of pathogen exposure following envenomation.},
}

Animals
*Microbiota
*Scyphozoa/microbiology
Drug Resistance, Bacterial/genetics
Bacteria/genetics

@article {pmid42759892,
year = {2026},
author = {Halmi, MFA and Edinur, HA},
title = {Two decades of microbiome forensics: Bibliometric insights into publication trends, applications and methodological advancements.},
journal = {Journal of microbiological methods},
volume = {250},
number = {},
pages = {107716},
doi = {10.1016/j.mimet.2026.107716},
pmid = {42759892},
issn = {1872-8359},
mesh = {Humans ; *Microbiota ; *Bibliometrics ; *Forensic Microbiology/methods/trends ; *Forensic Sciences/methods ; *Publications/trends ; *Forensic Medicine/methods ; },
abstract = {Microbiome forensics focuses on complex microbial communities for use as unique identification methods for forensic inferences. They include individual identification, crime scene reconstruction, and estimation of post-mortem intervals. This study adopts a bibliometric approach to assess the global scientific output and knowledge structure of the microbiome forensics, applications and methodological advancement in microbiome forensics. A total of 220 documents spanning two decades (2005 to 2024) were retrieved from the Web of Science Core Collection using related keywords. Of the total number of scientific publications, 6306 citations were found, with an average of 28.66 citations per publication. The United States dominated this domain with the most publications, followed by China, Australia, England, and Germany. Although Michigan State University had the highest number of citations, but the works produced by the Centre National de la Recherche Scientifique in Paris, France, had the highest research impact. Research trend mapping of keyword co-occurrence revealed five major clusters of forensic microbiome research: i. post-mortem interval estimation, ii. human identification, iii. Body fluid identification, iv. geolocation and provenance, and v. computational methods. Subsequent analyses indicated that forensic microbiome research has evolved from the use of culture-based and polymerase chain reaction (PCR) amplification of 16S rRNA for microbial identification before 2017 to the application of next generation sequencing (NGS) coupled with machine learning and bioinformatics from 2018 onwards. The findings of this study may be used to strategically inform knowledge gaps and key areas for future investigations in this field. In addition, building partnerships between forensic societies is needed not only to effectively move the field forward through the development of standardised protocols and quality assurance but also in exchanging expertise with developing countries, where knowledge is urgently needed to resolve crime cases.},
}

Humans
*Microbiota
*Bibliometrics
*Forensic Microbiology/methods/trends
*Forensic Sciences/methods
*Publications/trends
*Forensic Medicine/methods

@article {pmid42890506,
year = {2026},
author = {Yang, X and Chen, J and Song, J and Liu, H and Wang, L and Li, T and Yan, H and Gao, X and Ding, S},
title = {A nested case-control study on the relationship between gut microbiota and non-alcoholic fatty liver disease.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1917815},
pmid = {42890506},
issn = {1664-2392},
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology/epidemiology ; Female ; Male ; *Gastrointestinal Microbiome ; Case-Control Studies ; Middle Aged ; Biomarkers/analysis ; Adult ; Metagenomics ; Boosting Machine Learning Algorithms ; },
abstract = {BACKGROUND: The gut microbiota plays an important role in non-alcoholic fatty liver disease (NAFLD). This study aimed to explore gut microbiota-associated biomarkers for incident NAFLD and evaluate their predictive value, providing preliminary evidence for early risk identification.

METHODS: From an initial cohort of 1,772 participants, 404 were included in the final analysis, comprising 101 incident NAFLD cases and 303 age-matched controls (1:3). Gut microbiota composition and function were characterized by metagenomic sequencing. Microbial features were compared between participants who developed NAFLD (NAFLD -/+) and those who did not (NAFLD -/-). A CatBoost model integrating gut microbiota, functional pathways, and clinical indicators was constructed to predict NAFLD, with a random forest (RF) model on the same features for comparison. Progressively enriched feature sets assessed the incremental value of microbiota-related features beyond clinical indicators, and SHapley additive exPlanations (SHAP) values interpreted the model outputs.

RESULTS: The NAFLD (-/+) group had significantly lower species-level beneficial gut microbiota (P < 0.05), and the two groups differed markedly in gut microbiota metabolic enrichment. The CatBoost model achieved an area under the curve (AUC) of 0.762, indicating moderate predictive performance for incident NAFLD. We also identified significant intergroup differences in gut microbiota composition within the diagnostic model, including the key species Coprobacillus unclassified and the metabolic pathway PWY-5030.

CONCLUSION: Gut microbiota alterations may serve as potential early biomarkers for incident NAFLD and contribute to its pathogenesis. The CatBoost model integrating multi-omics and clinical data shows moderate predictive ability, supporting the potential of gut microbiota-based approaches for non-invasive risk stratification.},
}

Humans
*Non-alcoholic Fatty Liver Disease/microbiology/epidemiology
Female
Male
*Gastrointestinal Microbiome
Case-Control Studies
Middle Aged
Biomarkers/analysis
Adult
Metagenomics
Boosting Machine Learning Algorithms

@article {pmid42891333,
year = {2026},
author = {Li, Y and Wang, M and Liu, X and Wu, J and Mao, Y and Zhang, C and Chen, Q and Wang, Z and Jing, G and Han, M},
title = {L-EasyARG: A long-read metagenomics tool for rapid antibiotic-resistance-gene profiling.},
journal = {iMetaOmics},
volume = {3},
number = {2},
pages = {e70098},
pmid = {42891333},
issn = {2996-9514},
abstract = {l-EasyARG is a pipeline for long-read metagenomic profiling of antibiotic resistance genes (ARGs) and their genetic context. It integrates ARG identification, plasmid and mobile genetic element (MGE) detection, taxonomic classification, and further identifies ARGs carried by human bacterial pathogens (HBPs) defined in the WHO and ESKAPE pathogen lists. Benchmarking on simulated datasets with error rates ranging from 0% to 15% demonstrates optimal F1-scores at ≤5% errors, outperforming existing tools such as ARGpore2 and DeepARG. Application to hospital wastewater samples validates its ability to capture disinfection-induced shifts in ARG composition, ARG-MGE co-occurrence, and ARG-host associations. l-EasyARG generates comprehensive outputs including abundance profiles, co-occurrence networks, and interactive visualizations, enabling efficient resistome surveillance and risk assessment. The pipeline is user-friendly and locally executable.},
}

@article {pmid42895014,
year = {2026},
author = {Tian, M and Wang, Y and Li, C and Fan, J and Chen, Q and Bu, H and Fan, X and Liu, Q},
title = {Gut microbial and metabolomic alterations associated with herpetic trigeminal neuralgia: an exploratory multi-omics study.},
journal = {Journal of oral & facial pain and headache},
volume = {40},
number = {5},
pages = {130-145},
doi = {10.22514/jofph.2026.067},
pmid = {42895014},
issn = {2333-0376},
support = {2025M773964//China Postdoctoral Science Foundation/ ; 262300422312//Henan Provincial Natural Science Foundation for Young Scholars (Category C)/ ; LHGJ20250266//Henan Provincial Medical Science and Technology Joint Research Project/ ; },
mesh = {Humans ; *Trigeminal Neuralgia/microbiology/metabolism/virology ; Multiomics ; *Gastrointestinal Microbiome ; *Metabolomics ; Female ; Male ; Middle Aged ; Feces/microbiology ; Aged ; Case-Control Studies ; },
abstract = {BACKGROUND: Herpetic trigeminal neuralgia (HTN) is a neuropathic pain disorder caused by varicella-zoster virus invasion of the trigeminal nerve, but its mechanisms remain poorly elucidated. Accumulating evidence implicates gut microbiota dysbiosis and metabolic perturbations in modulating chronic pain via the gut-brain axis, yet their roles in HTN have not been systematically explored.

METHODS: Integrated multi-omics analysis was performed on 19 patients with HTN and 18 healthy controls. Fecal metagenomic sequencing characterized gut microbial composition and function. Untargeted metabolomics profiled metabolic signatures in fecal and circulating samples. Weighted gene co-expression network analysis (WGCNA) and random forest modeling screened pivotal microbial and metabolic features associated with HTN. Correlation analysis between differential metabolites and clinical pain scores validated the translational potential of identified alterations.

RESULTS: HTN patients showed significantly reduced gut microbial diversity, with enriched Proteobacteria, depleted butyrate-producing bacteria (including Faecalibacterium, Roseburia, and Lachnospira), and expanded opportunistic pathogens (Escherichia coli and [Ruminococcus] gnavus). Microbial pathways for pH homeostasis and oxidative stress defense were downregulated. Metabolomic analysis identified differential metabolites, primarily involving nicotinate/nicotinamide metabolism and retrograde endocannabinoid signaling. WGCNA and random forest analyses suggested fecal metabolites as potential candidate features, with associations between gut microbial dysregulation and systemic metabolic changes. Furthermore, screened metabolites correlated significantly with pain scores.

CONCLUSIONS: This study provides multi-omics evidence of gut microbial and metabolic dysregulation in HTN, generating hypotheses for further mechanistic research. Large-scale, multicenter prospective cohorts with standardized metadata collection are needed to validate these findings.},
}

Humans
*Trigeminal Neuralgia/microbiology/metabolism/virology
Multiomics
*Gastrointestinal Microbiome
*Metabolomics
Female
Male
Middle Aged
Feces/microbiology
Aged
Case-Control Studies

@article {pmid42886419,
year = {2026},
author = {Bagul, SY and Sarkar, R and Suthar, MK and Kumar, V and S, S and Rana, VS and Sircar, D and Reddy, NRR},
title = {Culturomics and amplicon-based insights into the endophytic microbiome of Kalmegh (Andrographis paniculata (Burm.f.) Nees) and its implications in plant growth promotion.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42886419},
issn = {1573-0972},
support = {NASF/MA-10007/2023-24//ICAR - National Agricultural Science Fund/ ; (NASF/MA-10007/2023-24//ICAR - National Agricultural Science Fund/ ; (NASF/MA-10007/2023-24//ICAR-National Agricultural Science Fund (NASF)/ ; },
mesh = {*Endophytes/classification/isolation & purification/genetics/metabolism ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Microbiota/genetics ; *Andrographis/microbiology/growth & development ; Diterpenes/metabolism ; Plant Leaves/microbiology/chemistry ; Plants, Medicinal/microbiology/growth & development ; Plant Development ; Metagenomics ; Phylogeny ; Plant Stems/microbiology ; Andrographis paniculata ; Plant Extracts ; },
abstract = {Leaf and stem endophytic microorganisms play an important role in plant physiology and secondary metabolite biosynthesis of plants, particularly in medicinal plants. Kalmegh (Andrographis paniculata (Burm.f.) Nees) is an important medicinal plant with liver-protective, anti-inflammatory, ovicidal, larvicidal, and anti-urolithatic properties. The medicinal activities are due to presence of andrographolides. This study investigated the culture-independent diversity of endophytic bacteria associated with Kalmegh at nursery, vegetative, and flowering stages using a metagenomic approach. The results revealed that Sphingomonas was the dominant bacterial genus during nursery and vegetative stages, whereas Halobacterium predominated during the flowering stage. Microbial abundance was highest in the nursery stage, followed by flowering and vegetative stages. Functional analysis showed that flowering stage endophytes were enriched with specialized carbon metabolism and aromatic compound degradation pathways, potentially influencing andrographolide biosynthesis. Chemical analysis supported these findings, showing the highest andrographolide content in leaves during flowering (3.1%). Gene expression analysis further demonstrated that increased andrographolide accumulation was associated with upregulation of methyl erythritol phosphate pathway (MEP) pathway and diterpene biosynthetic genes. Bacterial endophytes isolated from flowering-stage leaves exhibited plant growth-promotion, antifungal, and seed germination-enhancing activities. In vitro assays against Fusarium wilt and Rhizoctonia disease showed that Bacillus cereus strains KL11, KL12, and KL5 inhibited pathogen growth by 60-65%. Biopriming with strains KL3 and KL5 of Bacillus cereus improved seed germination and plant growth. Pot trials with Micrococcus luteus KES1 increased herbage yield, plant height, and andrographolide content by 43%. These findings highlight the potential of leaf and stem endophytes for sustainable improvement of Kalmegh productivity and andrographolide content in the plant.},
}

*Endophytes/classification/isolation & purification/genetics/metabolism
*Bacteria/classification/isolation & purification/genetics/metabolism
*Microbiota/genetics
*Andrographis/microbiology/growth & development
Diterpenes/metabolism
Plant Leaves/microbiology/chemistry
Plants, Medicinal/microbiology/growth & development
Plant Development
Metagenomics
Phylogeny
Plant Stems/microbiology
Andrographis paniculata
Plant Extracts

@article {pmid42886573,
year = {2026},
author = {Hou, S and Jiang, Y and Zhang, D and Xu, Z and Li, Y and Liu, X and Zhang, H and Zhang, J and Zhai, Q and Zhang, C and Wang, X and Huang, S},
title = {A high-resolution spatial model of the primate gut microbiome defines niche-specific functions and host-adapted microbial metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2748153},
doi = {10.1080/19490976.2026.2748153},
pmid = {42886573},
issn = {1949-0984},
mesh = {Animals ; Humans ; *Macaca mulatta/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Gastrointestinal Tract/microbiology ; Bile Acids and Salts/metabolism ; Metagenomics ; *Host Microbial Interactions ; },
abstract = {The spatial organization of the gastrointestinal microbiome is shaped by strong physicochemical gradients along the gut, yet many region-associated microbial niches remain poorly resolved in humans. Here, we used the rhesus macaque (Macaca mulatta) as a spatially resolved primate model to profile 148 luminal and mucosal samples across the gastrointestinal tract using shotgun metagenomics, 2bRAD-M sequencing, and targeted bile acid metabolomics, complemented by comparative human datasets. Microbial communities exhibited strong spatial stratification along the gastrointestinal tract, while host species explained greater variation than anatomical location in our comparative datasets. Despite broad phylum-level similarity between humans and monkeys, substantial divergence emerged at species and functional levels. Monkey-associated Segatella copri encoded expanded carbohydrate-active enzyme (CAZyme) repertoires specialized for degradation of complex plant polysaccharides, consistent with dietary and other host-associated adaptation. Along the gastrointestinal tract, microbial load and diversity followed pronounced spatial gradients, although the low-biomass stomach retained unexpectedly high taxonomic and functional diversity. Mucosal communities largely mirrored luminal microbiota at broad taxonomic scales but exhibited distinct species-level signatures associated with niche-specific functional specialization. The monkey large intestine was further enriched in the immunomodulatory bile acid isoallo-lithocholic acid (isoalloLCA), with candidate biosynthetic genes identified in previously uncharacterized microbial lineages. Together, these findings establish a high-resolution framework of the primate gut microbiome and reveal how spatial organization and host-associated selection shape microbial metabolism and host-microbe interactions relevant to gut health.},
}

Animals
Humans
*Macaca mulatta/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Gastrointestinal Tract/microbiology
Bile Acids and Salts/metabolism
Metagenomics
*Host Microbial Interactions

@article {pmid42888449,
year = {2026},
author = {He, P and Zhang, K and Khan, J and Ouyang, H and Hu, S and Qian, S and Shu, B and Li, X and Lin, D},
title = {Metagenomic analysis of developmental-category-associated fungal communities in the gut contents of Achatina fulica, an intermediate host of Angiostrongylus cantonensis.},
journal = {Parasites & vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42888449},
issn = {1756-3305},
support = {18MDZ02//Major Project Cultivation Plan of Xizang Minzu University/ ; XZ202401ZR0017//the Tibet Natural Science Foundation/ ; No. SKXRC2025159//the Youth S&T Talent Support Programme of Guangdong Provincial Association for Science and Technology/ ; 82672963 and 82202560//the National Natural Science Foundation of China/ ; 23360095 and 23360208//College Students' Innovative Entrepreneurial Training Plan Program/ ; },
mesh = {Animals ; Metagenomics ; *Mycobiome ; *Snails/microbiology/parasitology ; *Angiostrongylus cantonensis/physiology ; China ; *Fungi/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: The invasive giant African snail (Achatina fulica) poses serious agricultural and ecological threats and serves as an important intermediate host of the zoonotic parasite Angiostrongylus cantonensis, which causes human eosinophilic meningitis. While its gut bacterial microbiome has been extensively characterized, the gut mycobiome remains largely uncharacterized. In particular, variations in gut fungal communities across developmental stages remain unknown, limiting our understanding of the A. fulica gut holobiont.

METHODS: In November 2025, giant African snails were collected from Guangzhou, Guangdong Province, China. Genomic DNA was extracted from the gut contents of the collected snails. Metagenomic sequencing was conducted to characterize variations in the gut mycobiota across different snail sample types.

RESULTS: Metagenomic sequencing of 18 snail gut samples across three developmental stages showed lower fungal alpha diversity in adults than in juveniles, whereas PCoA visualized differences in community composition among developmental categories and PERMANOVA confirmed that these differences were statistically significant. Ascomycota dominated the mycobiome, with developmental-category-associated differences in taxonomic composition. LEfSe and DESeq2 identified differentially abundant taxa associated with developmental categories, while SIMPER analysis identified several taxa contributing to the observed dissimilarity, including Synchytrium taraxaci, Aspergillus flavus and Cladosporium cladosporioides. These taxa are interpreted as contributors to community dissimilarity rather than as causal drivers of developmental-category-associated differences. Co-occurrence networks analysis identified six highly connected taxa (Hanseniaspora uvarum, Apiospora montagnei, Aureobasidium thailandense, Colletotrichum aenigma, Truncatella angustata, and Calonectria ilicicola) within the inferred fungal association network.

CONCLUSIONS: Gut fungal community composition differed significantly among the sampled developmental categories of A. fulica, although the cross-sectional design does not establish that the host development itself causes these differences. The identified developmental-category-associated and highly connected taxa provide a baseline for gut mycobiota ecology and a foundation for future controlled studies investigating their functional roles and potential relevance to A. cantonensis infection.},
}

Animals
Metagenomics
*Mycobiome
*Snails/microbiology/parasitology
*Angiostrongylus cantonensis/physiology
China
*Fungi/genetics/classification/isolation & purification
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology

@article {pmid42888864,
year = {2026},
author = {Schlager, JG and Stiefel, D and Patzer, K and Schloter, M and Foesel, BU and Zelzer, NM and French, LE and Gschwendtner, S and Hartmann, D},
title = {Basal Cell Carcinoma May Be Associated With Staphylococcus Dysbiosis.},
journal = {Experimental dermatology},
volume = {35},
number = {10},
pages = {e70371},
doi = {10.1111/exd.70371},
pmid = {42888864},
issn = {1600-0625},
support = {//Verein zur Förderung von Wissenschaft und Forschung an der Medizinischen Fakultät der LMU München e.V. (WiFoMed)/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/complications ; *Basal Cell Carcinoma/microbiology ; *Skin Neoplasms/microbiology ; Skin Microbiome ; *Staphylococcus/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Male ; Middle Aged ; Skin/microbiology ; Aged, 80 and over ; Microbiota ; },
abstract = {There is growing evidence that a dysbiosis of the skin microbiome has an impact on carcinogenesis in cutaneous squamous cell carcinoma. However, the role of the microbiome in basal cell carcinoma (BCC) remains unclear due to limited, inconsistent, ex vivo studies. Here, we analysed the skin microbiome of patients with BCC, including the tumour lesion as well as perilesional skin from the same subject. Skin swabs from BCC and perilesional skin were taken prior to tumour surgery. After DNA extraction, we used a metabarcoding approach based on 16S rRNA gene amplicon sequencing to analyse the cutaneous bacterial communities. In total, 63 patients with BCC were included for analysis. Most tumour lesions were located on sun-exposed, sebaceous areas such as the nose, cheeks, and forehead. The genera Corynebacterium, Cutibacterium, and Staphylococcus predominated both in BCC and perilesional skin. However, the microbiome of BCC was reduced in overall bacterial richness, with a significant overabundance of amplicon sequence variants (ASV) assigned to the genus Staphylococcus, resulting in a reduced complexity in microbial networks. The dominating ASV assigned to Staphylococcus was also detected in perilesional skin regions, indicating that the microbial dysbiosis in BCC affected regions is caused by natural members of the healthy skin microbiome. The BCC microbiome is characterised by microbial dysbiosis, reflected by a reduced overall bacterial richness, fewer microbe-microbe interactions and a significant over-representation of Staphylococcus species compared with perilesional skin. Further long-read metagenomics and cultivation-based studies are needed to identify Staphylococcus species driving dysbiosis.},
}

Humans
*Dysbiosis/microbiology/complications
*Basal Cell Carcinoma/microbiology
*Skin Neoplasms/microbiology
Skin Microbiome
*Staphylococcus/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Female
Aged
Male
Middle Aged
Skin/microbiology
Aged, 80 and over
Microbiota

@article {pmid42889534,
year = {2026},
author = {Al-Fatlawi, A and Schroeder, M},
title = {UniProt data pruning and the growing invisibility of the dark proteome.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {4},
pages = {lqag115},
doi = {10.1093/nargab/lqag115},
pmid = {42889534},
issn = {2631-9268},
mesh = {*Proteome/genetics ; *Databases, Protein ; Proteomics/methods ; },
abstract = {The protein resource UniProtKB has undergone a major, multi-stage reorganization of its protein space, implemented from release 2025_04 through release 2026_02. Analysis of UniProtKB and UniParc records accessed on 20 January 2026 showed that 125.9 million entries were last present in UniProtKB in 2025 and are now represented in UniParc, while ~200.0 million entries remained in UniProtKB at the access date. Of these, 58.9 million were designated for removal in release 2026_02, whereas 141.2 million were classified as retained. The reorganization retains all reviewed UniProtKB/Swiss-Prot entries (the expert-curated subset of UniProtKB), along with proteins from selected reference proteomes and unreviewed entries with additional biologically important data, including experimentally determined three-dimensional structures. The expected benefits include reduced redundancy, easier navigation, and a protein set that is more tractable for annotation and routine searches. However, the reorganization may reduce the visibility of protein sequences from uncultured microorganisms and metagenomic surveys, phylogenetically underrepresented lineages, particularly many archaeal groups, proteins belonging to the so-called "dark proteome," and strain-level variants of well-studied species such as Escherichia coli. We argue that the main consequence is not the loss of the sequences themselves, because affected proteins remain recoverable through UniParc and related resources, but a reduction in their discoverability, annotation context, and accessibility within routine workflows. These effects are likely to be most important for biodiversity-oriented analyses, retrospective reuse of older datasets, studies of specialized protein families, and downstream pipelines that rely on UniProtKB as an annotation hub. As UniProt shifts toward a more explicitly reference-proteome-centered model, a critical question arises: What are the implications of UniProtKB contraction for the representation of evolutionary diversity across the tree of life, particularly in under-sampled and uncultured lineages?},
}

*Proteome/genetics
*Databases, Protein
Proteomics/methods

@article {pmid40957978,
year = {2026},
author = {Ocampo-Chih, C and Hendricks, H and Weitkamp, S and Gowda, NS and Singh, H and Banerjee, R and Rajagopala, SV and Weitkamp, JH},
title = {Impact of donor human milk pasteurization methods on the gut microbiome of preterm infants.},
journal = {Pediatric research},
volume = {100},
number = {3},
pages = {1414-1420},
pmid = {40957978},
issn = {1530-0447},
mesh = {Humans ; *Pasteurization/methods ; *Milk, Human/microbiology ; *Infant, Premature ; Infant, Newborn ; Female ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; Gestational Age ; },
abstract = {BACKGROUND: Preterm infants are often fed donor human milk (DHM) when the mother's own milk is insufficient or not available. Holder or Retort pasteurization is used to inactivate potential pathogens in DHM. The effects of DHM pasteurization methods on the infant gut microbiome are unknown.

METHODS: To compare the gut microbiome and clinical outcomes between preterm infants fed Holder- versus Retort-pasteurized DHM, we performed weekly collections of stool samples from infants born <34 weeks' gestation and/or <1500 g birth weight. We analyzed stool samples from 150 patients exclusively fed DHM [Retort (n = 80), Holder (n = 54)] or exclusively fed mother's own milk (n = 16). Whole-metagenome sequencing was performed to assess microbiome composition, diversity, and functional enrichment.

RESULTS: Compared to infants fed Retort-pasteurized DHM, infants fed Holder-pasteurized DHM showed higher alpha-diversity (Chao-1 p = 0.007) and a higher abundance of beneficial anaerobes, such as Bacteroides thetaiotaomicron, Clostridium spp., and Bifidobacterium spp. Functional enrichment analysis revealed significant differences in carbohydrate metabolism, transport systems, and regulatory pathways between feeding groups. There were no statistically significant differences in short-term clinical outcomes, such as necrotizing enterocolitis, length of hospitalization or death.

CONCLUSION: Differences in pasteurization methods for DHM resulted in measurable gut microbiome changes in preterm infants.

IMPACT: It is known that the preterm infant gut microbiota is different in infants fed pasteurized donor milk compared to mother's own milk. However, the impact of different pasteurization methods for donor milk on the infant gut microbiome is unknown. We show that the type of pasteurization of donor human milk influences the gut microbiome and its function in preterm infants. In contrast to feeding Retort-pasteurized donor human milk, feeding Holder-pasteurized donor human milk generates an infant gut microbiome similar to feeding mother's own milk.},
}

Humans
*Pasteurization/methods
*Milk, Human/microbiology
*Infant, Premature
Infant, Newborn
Female
Feces/microbiology
*Gastrointestinal Microbiome
Male
Gestational Age

@article {pmid41519950,
year = {2026},
author = {Ye, X and Zhang, T and Zhou, J and Zhao, C and Wu, J},
title = {The gut microbial profile and circulating metabolism are associated with functional constipation in children.},
journal = {Pediatric research},
volume = {100},
number = {3},
pages = {1301-1312},
pmid = {41519950},
issn = {1530-0447},
mesh = {Humans ; *Constipation/microbiology/blood/metabolism ; Child ; *Gastrointestinal Microbiome ; Bile Acids and Salts/metabolism ; Female ; Male ; Child, Preschool ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Bacteria/genetics ; },
abstract = {BACKGROUND: A growing body of evidence highlights the link between gut microbiome imbalances and constipation. However, the role of gut microbiota and its metabolic interactions in pediatric functional constipation (FC) remains incompletely understood.

METHODS: We recruited a total of 40 children with FC and 40 healthy children (CONT). 16SrRNA and metagenomic sequencing were used to evaluate the changes in the gut microbiota structure and gene function in FC patients. Differences in serum metabolite levels were analyzed via targeted metabolomic sequencing.

RESULTS: The FC group exhibited a decrease in gut microbiota diversity, an increase in Bacteroides and Prevotella abundances, depletion of genera such as Lactobacillus and Bifidobacterium and an imbalance of related metabolic activities. Metabolomic analysis revealed that the levels of several metabolites, including taurine and glycochenodeoxycholic acid, which are involved in bile acid (BA) metabolic pathways, differed between the FC and CONT groups. Differences in metabolite levels were associated with changes in the abundances of specific bacteria and with intestinal dysfunction in FC patients.

CONCLUSION: FC in children is associated with distinct gut microbiota alterations and dysregulated BA metabolism. These findings provide potential therapeutic targets for modulating the gut microbiome and metabolic pathways in FC management.

IMPACT: This study offers a comprehensive perspective on the intricate relationship between microbial composition and metabolic pathways in the context of functional constipation in children. This study focuses on children, highlighting how disruptions in bile acid metabolism due to gut microbiota disorders are linked to the occurrence of functional constipation. These findings suggest that disturbances in bile acid metabolism may play a role in the mechanisms underlying functional constipation by impairing intestinal secretion and transport functions. This study offers a new way to study the effects of the gut microbiota, bile acid metabolism, and the gut‒brain axis.},
}

Humans
*Constipation/microbiology/blood/metabolism
Child
*Gastrointestinal Microbiome
Bile Acids and Salts/metabolism
Female
Male
Child, Preschool
Metabolomics
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Bacteria/genetics

@article {pmid42631930,
year = {2026},
author = {Choi, W and Mangal, U and Cha, JK and Cho, H and Ryu, JH and Kim, JY and Koh, WG and Lee, KJ and Kim, KW and Choi, SH and Traverso, G and Hong, J},
title = {A Mucosa-Inspired Dynamic Biointerface Engineering a Biofilm-Preventive Niche Against Pathogenic Microbiome Dysbiosis.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {38},
number = {58},
pages = {e74745},
doi = {10.1002/adma.74745},
pmid = {42631930},
issn = {1521-4095},
support = {//Korea-US Collaborative Research Fund/ ; RS-2024-00468036//Ministry of Science and ICT and Ministry of Health & Welfare/ ; 2025-RISE-10-101//Regional Innovation System & Education/ ; //Regional Anchor company-Academia Partnership Innovation Development/ ; //Institute for Project-Y Seed/ ; RS-2024-00438634//Korea Health Technology R&D Project through the Korea Health Industry Development Institute/ ; //Nano & Material Technology Development Program through the National Research Foundation of Korea/ ; RS-2024-00449435//Ministry of Science and ICT/ ; RS-2021-NR059601//National Research Foundation of Korea/ ; RS-2023-00217709//National Research Foundation of Korea/ ; RS-2025-00522998//National Research Foundation of Korea/ ; },
mesh = {*Biofilms/drug effects ; *Dysbiosis/prevention & control/microbiology ; *Microbiota ; Humans ; *Mucous Membrane ; Biocompatible Materials/chemistry/pharmacology ; },
abstract = {A stable symbiosis within the microbiome-host axis is essential for human health. However, preventing microbiome dysbiosis using biomaterials remains challenging due to their unpredictable influence on microbiome evolution. Inspired by the defensive niche of symbiotic mucosa, we have developed a biointerface that forms an engineered mucosa-inspired dynamic niche to prevent pathogenic dysbiosis. This biointerface features a dynamic zwitterionic network that emulates the mucosa's biophysical defensive functions. Notably, by leveraging its dynamic niche, the biointerface restricts microbial attachment and aggregation, thereby preventing biofilm formation. Comprehensive metagenomic analyses reveal that microbial communities adapt to this biofilm-preventive dynamic biointerface compositionally and functionally. In particular, Gram-negative bacteria were relatively reduced, along with decreased abundance of pathways associated with virulence and biofilm formation. Consequently, the mucosa-inspired biointerface intrinsically prevents the development of pathogenic dysbiosis. This study demonstrates the groundbreaking potential of material-based niche engineering to guide the ecological shifts of microbial communities from the material scale.},
}

*Biofilms/drug effects
*Dysbiosis/prevention & control/microbiology
*Microbiota
Humans
*Mucous Membrane
Biocompatible Materials/chemistry/pharmacology