@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

@article {pmid42879678,
year = {2026},
author = {Lin, ZR and Shi, JC and Qiu, CC and Wu, ZX and Lin, XQ and He, GQ and Liu, SD and Du, QW and Lin, HB and Wu, LP and Sun, F and Jiang, XG},
title = {Metagenomic insights into the pulmonary microbiome of drug-sensitive and multidrug-resistant tuberculosis patients.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2720327},
doi = {10.1080/07853890.2026.2720327},
pmid = {42879678},
issn = {1365-2060},
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Tuberculosis, Multidrug-Resistant/microbiology/drug therapy ; Female ; Male ; Metagenomics ; *Lung/microbiology ; Middle Aged ; Adult ; Prospective Studies ; Antitubercular Agents/therapeutic use/pharmacology ; },
abstract = {BACKGROUND: While the pulmonary microbiota may influence TB pathogenesis, direct comparisons between drug-sensitive (DS-TB) and multidrug-resistant (MDR-TB) patients remain scarce. This study explored microbiome differences between these groups.

METHODS: Bronchoalveolar lavage fluid (BALF) from 30 prospective patients (11 DS-TB, 19 MDR-TB) was analysed via metagenomic sequencing.

RESULTS: Patients with MDR-TB showed lower α-diversity and distinct β-diversity compared with patients with DS-TB. Streptococcus and Prevotella were relatively enriched in DS-TB, whereas Staphylococcus, Cutibacterium, and Mycobacterium were more abundant in MDR-TB. DS-TB showed enrichment of 45 carbohydrate-active enzyme families and core metabolic annotations, whereas MDR-TB showed enrichment of infection- and immunity-related functional annotations and a less connected taxonomic network. An exploratory random forest analysis identified six candidate genera and yielded an internally cross-validated AUC of 0.957.

CONCLUSIONS: MDR-TB was associated with lower pulmonary microbial diversity, altered community composition, and shifts in predicted microbial functions. These findings characterise lower-airway microbiome differences between DS-TB and MDR-TB and provide a basis for further validation.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Tuberculosis, Multidrug-Resistant/microbiology/drug therapy
Female
Male
Metagenomics
*Lung/microbiology
Middle Aged
Adult
Prospective Studies
Antitubercular Agents/therapeutic use/pharmacology

@article {pmid42880064,
year = {2026},
author = {Sun, P and Tan, Y and Jia, R and Lian, J and Yang, T and Li, H and Zhu, Z and Xi, C},
title = {Impacts and mechanisms of oyster farming on denitrification and anammox in coastal sediments from Tieshan Bay, China.},
journal = {Marine environmental research},
volume = {222},
number = {},
pages = {108453},
doi = {10.1016/j.marenvres.2026.108453},
pmid = {42880064},
issn = {1879-0291},
abstract = {Oyster aquaculture is widely recognized as an effective way to mitigate coastal eutrophication, but critical knowledge gaps remain regarding how it modulates nitrogen removal processes, which requires further investigation. In this study, sediments from oyster farming (OY) and non-oyster farming (NOY) areas in Tieshan Bay, China, were analyzed to explore the impacts of oyster farming on denitrification and anammox in coastal sediments. OY sediments exhibited significantly higher sediment oxygen demand (SOD), total organic carbon (TOC), ammonium (NH4[+]), ferrous iron (Fe[2+]), and sulfide than NOY sediments (P < 0.05), collectively creating hypoxic conditions favorable for nitrogen removal. Denitrification dominated nitrogen removal in both areas (OY: 91.84%; NOY: 90.19%). Potential denitrification and anammox rates in OY areas were 2.25 and 1.80 times higher than those in NOY areas, respectively (P < 0.01). Redundancy analysis (RDA) identified TOC, SOD, sulfide, Fe[2+], Fe[3+], and NH4[+] as key drivers of these processes. Metagenomic analysis revealed that OY sediments were enriched in Bacillota and Bacteroidota at the phylum level, and key functional genes (nirS, nosZ, hzsB) were significantly more abundant in OY areas (P < 0.05), suggesting enhanced genetic potential for nitrogen removal. The stronger promotion of denitrification over anammox was attributed to the combined effects of TOC (electron donors), Fe[2+] (electron carrier), and sulfide (alternative electron donor for denitrification but inhibitor for anammox). These findings demonstrate that oyster aquaculture enhances the functional capacity for sedimentary nitrogen removal through physicochemical modification, microbial community selection, and enrichment of key functional genes.},
}

@article {pmid42881160,
year = {2026},
author = {Fernandes, N and Cai, M and Warren, FJ and Duncan, A and Harris, H and Serrano Contreras, JI and Sidorczuk, K and Bernal, A and Castillo, A and Petropoulou, K and Blunt, D and Perez-Moral, N and Garcia-Perez, I and Edwards, C and Hildebrand, F and Holmes, E and Wist, J and Frost, G},
title = {Effect of dietary chickpea structures on the small intestine metabolome and microbiome: a randomised crossover trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42881160},
issn = {2041-1723},
support = {BB/X018857/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Humans ; Cross-Over Studies ; *Metabolome ; Glucagon-Like Peptide 1/metabolism ; Postprandial Period ; *Cicer/chemistry ; *Intestine, Small/metabolism/microbiology ; Peptide YY/metabolism ; Female ; Adult ; Gastric Inhibitory Polypeptide/metabolism ; *Gastrointestinal Microbiome/physiology ; Ileum/microbiology/metabolism ; *Diet ; Young Adult ; },
abstract = {The human gastrointestinal tract (GIT) is central to human physiology, yet our understanding of the metabolite, microbial, and hormonal spatiotemporal dynamics in humans is limited. How these environments respond to complex food structures and homeostatic mechanisms they generate is unknown in humans. In this randomised study, ten participants consumed chickpea-based meals with intact versus broken cellular structures, with sampling of oral, gastric, duodenal and ileal fluids. The primary outcome was the postprandial enteroendocrine hormone responses (GIP, GLP-1 and PYY); secondary outcomes were GIT metabolite profiles ([1]H NMR) and ileal microbiota (shotgun metagenomics). We observed that food structure markedly altered the spatiotemporal trajectories of metabolites and dominant microbe, driving distinct enteroendocrine hormone responses. Broken-cell meals produced early GIT glucose and maltose peaks associated with rapid GIP responses, whereas intact-cell meals elevated duodenal amino acids and ileal sugars, amino acids and formate, enhancing GLP-1 and PYY responses. Microbial profiles exhibited rapid spatial reorganisation, with evidence that oral bacterial strains transmitted to the ileum, where their abundance was associated with local metabolites and PYY responses. These findings identify food structure as a determinant of postprandial gastrointestinal metabolism and enteroendocrine responses and suggest an underappreciated route for oral bacteria to reach the ileum via the food bolus and impact metabolism. ISRCTN registration: ISRCTN18097249.},
}

Humans
Cross-Over Studies
*Metabolome
Glucagon-Like Peptide 1/metabolism
Postprandial Period
*Cicer/chemistry
*Intestine, Small/metabolism/microbiology
Peptide YY/metabolism
Female
Adult
Gastric Inhibitory Polypeptide/metabolism
*Gastrointestinal Microbiome/physiology
Ileum/microbiology/metabolism
*Diet
Young Adult

@article {pmid42883692,
year = {2026},
author = {Zhang, W and Zhu, Y and Chu, X and Zhang, X and Pan, Z and Li, A},
title = {Co-Enrichment of Desulfovibrio and Erysipelotrichaceae and Dysregulation of Multiple Amino Acid Pathways in HFpEF: Insights into TXG-Associated Metabolic Changes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198445},
pmid = {42883692},
issn = {1422-0067},
support = {82174080//National Natural Science Foundation of China/ ; H2022423333//Hebei Provincial Department of Science and Technology/ ; },
mesh = {Animals ; *Amino Acids/metabolism/blood ; *Heart Failure/metabolism/microbiology/drug therapy ; *Desulfovibrio/genetics/isolation & purification ; Mice ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Male ; *Eubacteriales/genetics ; Diet, High-Fat/adverse effects ; Metabolome ; Metagenomics ; },
abstract = {Gut enrichment of Desulfovibrio and Erysipelotrichaceae may be associated with systemic amino acid metabolic dysfunction, myocardial injury, and heart failure with preserved ejection fraction (HFpEF). These taxa appear to influence host amino acid metabolism through distinct processes, but the functional implications of their co-enrichment in HFpEF remain unclear. Total xanthones from Gentianella acuta (TXG) have documented cardioprotective effects, although their effects on gut microbiota and systemic metabolism remain unexplored. We established a mouse model of HFpEF using a high-fat diet (HFD) combined with Nω-nitro-L-arginine methyl ester (L-NAME). We integrated 16S rRNA sequencing, fecal metagenomics, and targeted serum amino acid metabolomics to examine microbe-metabolite associations, with echocardiography and histopathology providing complementary phenotypic evidence. Microbial and metabolomic analyses revealed pronounced enrichment of Desulfovibrio and Erysipelotrichaceae (particularly Dubosiella), accompanied by elevated serum isoleucine, tryptophan, and homocysteine levels. TXG treatment was associated with lower abundance of both taxa, altered serum amino acid profiles, preserved colonic barrier integrity, and reduced myocardial inflammation and fibrosis. These changes coincided with improved diastolic function. Together, these findings associate co-enrichment of the two taxa with dysregulation of multiple amino acid pathways in HFpEF. TXG treatment was accompanied by attenuated cardiac and metabolic injury as well as shifts in gut-microbiota profiles, with these correlative observations motivating further investigation of Gentianella acuta for metabolic heart failure.},
}

Animals
*Amino Acids/metabolism/blood
*Heart Failure/metabolism/microbiology/drug therapy
*Desulfovibrio/genetics/isolation & purification
Mice
Gastrointestinal Microbiome/drug effects
RNA, Ribosomal, 16S/genetics
Metabolomics/methods
Male
*Eubacteriales/genetics
Diet, High-Fat/adverse effects
Metabolome
Metagenomics

@article {pmid42883703,
year = {2026},
author = {Pérez-Castro, S and Carballo-Quinta, M and Rodríguez-Costas, N and Freire-Rodríguez, A and Davina-Nunez, C and Bellas-Pereira, A and Taboada-Rodríguez, P and Pérez-Schoch, M and Cabrera-Alvargonzález, JJ and Muller-Arteaga, CA and Sánchez-García, JF and Cespón-Outeda, E and López-Díez, ME},
title = {Gut Microbiota Signatures Associated with Metastatic Prostatic Cancer Treated with Androgen Receptor Pathway Inhibitor (ARPI) Therapy.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198454},
pmid = {42883703},
issn = {1422-0067},
support = {Leonardo de la Peña 2022 Grant//Urological Research Foundation/ ; GAIN IN607B-2022-19//Axencia Galega de Innovacion/ ; },
mesh = {Humans ; Male ; *Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Androgen Receptor Antagonists/therapeutic use/pharmacology ; *Receptors, Androgen/metabolism ; Neoplasm Metastasis ; Aged ; Disease Progression ; Metagenomics/methods ; },
abstract = {Metastatic prostate cancer (MPCa) remains an aggressive disease despite the introduction of androgen receptor pathway inhibitors (ARPIs), and biomarkers predicting progression are still lacking. The aim of this study was to investigate gut microbiota (GM) composition and functional potential associated with advanced disease and progression under ARPI therapy. The GM of 15 patients with metastatic PCa receiving ARPIs, including 5 patients with disease progression, was compared with that of 39 patients with untreated (UT) PCa using shallow shotgun metagenomic sequencing. The metastatic PCa cohort receiving ADT plus ARPI therapy showed reduced microbial alpha diversity and significant taxonomic and functional differences compared with the untreated, clinically localized PCa reference cohort. In patients with advanced disease, microbial functions related to dietary carbohydrate utilization, fermentation, epithelial interaction, and microbial structural maintenance were predominantly underrepresented, whereas stress-responsive and redox-associated functions were overrepresented. These alterations may reflect reduced metabolic and ecological versatility alongside increased adaptation to host-associated stress conditions. Compared with the UT group, in patients with progression we found that Bifidobacterium longum, Anaerobutyricum hallii, Ruminococcus sp., and Blautia obeum (LinDA coefficients 5.7, 2.6, 2.6 and 2.4, respectively) were enriched, whereas Sutterella wadsworthensis, Butyricimonas, Bilophila wadsworthia, Alistipes indistinctus, and Intestinimonas were depleted (LinDA coefficients -8.4, -5.9, -5, -5 and -3, respectively). Together, these findings identify distinct taxonomic and functional features associated with metastatic PCa under systemic therapy and microbial features observed in patients experiencing progression during ARPI treatment, providing potential candidates for biomarker development and generating testable hypotheses regarding microbiome-host metabolic interactions in treatment resistance. The GM may therefore represent a potential source of biomarkers for advanced PCa and progression under ARPI therapy, although longitudinal and multi-omics studies are required to determine their predictive value and functional relevance.},
}

Humans
Male
*Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism
*Gastrointestinal Microbiome/drug effects
*Androgen Receptor Antagonists/therapeutic use/pharmacology
*Receptors, Androgen/metabolism
Neoplasm Metastasis
Aged
Disease Progression
Metagenomics/methods

@article {pmid42883729,
year = {2026},
author = {Liu, N and Zhang, S and Li, Y},
title = {Molecular Mechanisms of the Gut-Liver-Placenta Axis in Intrahepatic Cholestasis of Pregnancy: Microbiota-Associated Pathogenesis and Next-Generation Therapeutic Strategies.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198481},
pmid = {42883729},
issn = {1422-0067},
support = {XLYC2412033//LiaoNing Revitalization Talents Program/ ; },
mesh = {Humans ; Female ; *Cholestasis, Intrahepatic/metabolism/microbiology/therapy/etiology/pathology ; Pregnancy ; *Pregnancy Complications/metabolism/microbiology/therapy/etiology ; *Placenta/metabolism ; Bile Acids and Salts/metabolism ; Animals ; *Liver/metabolism/pathology ; *Gastrointestinal Microbiome ; Dysbiosis ; },
abstract = {Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder characterized by elevated maternal bile acid concentrations and an increased risk of adverse perinatal outcomes. Genetic susceptibility, hormonal changes, and impaired bile acid transport contribute to its development but do not fully explain the variability in disease severity and fetal outcomes. Increasing evidence suggests that gut microbiota dysbiosis and altered bile acid metabolism are associated with ICP and may participate in disease development through the gut-liver-placenta axis. In this review, we integrate evidence on bile acid-microbiota interactions during pregnancy, ICP-associated microbial and metabolic alterations, and their possible links to placental and fetal outcomes. Human studies primarily support associations among microbial alterations, bile acid profiles, and disease severity, whereas the microbiota-mediated effects on placental function and fetal injury proposed to date are supported largely by experimental models. We further discuss potential links among gut microbial dysfunction, placental oxidative stress, fetal cardiac injury, neurodevelopmental risk, offspring metabolic susceptibility, and iatrogenic prematurity. Although ursodeoxycholic acid (UDCA) improves maternal pruritus and selected biochemical indices, its effect on major perinatal outcomes remains uncertain. Ileal bile acid transporter (IBAT) inhibitors and microbiota-targeted interventions remain investigational, with insufficient pregnancy-specific evidence regarding their efficacy and maternal-fetal safety. Future studies should clarify the associated causal mechanisms and integrate metagenomic, metabolomic, and placental data to identify clinically relevant biomarkers and therapeutic targets.},
}

Humans
Female
*Cholestasis, Intrahepatic/metabolism/microbiology/therapy/etiology/pathology
Pregnancy
*Pregnancy Complications/metabolism/microbiology/therapy/etiology
*Placenta/metabolism
Bile Acids and Salts/metabolism
Animals
*Liver/metabolism/pathology
*Gastrointestinal Microbiome
Dysbiosis

@article {pmid42883733,
year = {2026},
author = {Abdulkhakov, SR and Safina, DD and Markelova, MI and Ponomareva, ER and Siniagina, MN and Khusnutdinova, DR and Kupriyanova, OV and Abdulkhakov, RA and Grigoryeva, TV},
title = {Metagenomic and Metabolomic Signatures of Gut Microbiota After Helicobacter pylori Eradication Therapy Supplemented with Butyric Acid and Inulin: Observational Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198485},
pmid = {42883733},
issn = {1422-0067},
support = {12/2025-PD-KFU//Tatarstan Academy of Sciences/ ; },
mesh = {Humans ; *Inulin/pharmacology/therapeutic use/administration & dosage ; *Helicobacter pylori/drug effects ; *Helicobacter Infections/drug therapy/microbiology/metabolism ; Adult ; *Butyric Acid/pharmacology/therapeutic use/administration & dosage ; Middle Aged ; Metagenomics/methods ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Female ; Male ; Fatty Acids, Volatile/metabolism ; Metabolomics/methods ; *Metabolome ; Young Adult ; Anti-Bacterial Agents/therapeutic use ; Metagenome ; },
abstract = {The long-term impact of eradication therapy for Helicobacter pylori on the gut microbiota is a subject of significant interest. To evaluate the influence of the bismuth-based quadruple H. pylori eradication therapy supplemented with butyrate and inulin on functional alterations within the gut microbial community, metagenomic and metabolomic profiling were performed. Fecal samples were collected from 15 patients (aged 19-64 years) prior to the treatment, immediately after the treatment, and one month after the therapy. A significant decrease in the relative abundance of Actinobacteria, such as Bifidobacterium and Collinsella, was observed after the therapeutic intervention. In contrast, the levels of Faecalibacterium prausnitzii remained consistent, while Roseburia faecis levels exhibited a substantial decline, suggesting a disruption in key butyrate-producing bacteria. A moderate increase in the relative abundance of opportunistic Proteobacteria, Firmicutes, and Bacteroides was observed. A comprehensive analysis of short-chain fatty acids (SCFAs) levels in the feces of the patients revealed a decline in the butyric acid concentration in response to the therapy, followed by a return to baseline levels. However, the level of valeric acid declined, and there was no tendency for it to increase after a month-long course of therapy. It is important to note that these shifts persisted for a period of four weeks. Consequently, the H. pylori eradication therapy intervention promotes a persistent microbial reorganization, and the observed recovery is unlikely to be spontaneous and probably reflects the protective effect of butyrate and inulin supplementation. To confirm the conclusions, a larger sample size and longer-duration studies are required.},
}

Humans
*Inulin/pharmacology/therapeutic use/administration & dosage
*Helicobacter pylori/drug effects
*Helicobacter Infections/drug therapy/microbiology/metabolism
Adult
*Butyric Acid/pharmacology/therapeutic use/administration & dosage
Middle Aged
Metagenomics/methods
*Gastrointestinal Microbiome/drug effects
Feces/microbiology
Female
Male
Fatty Acids, Volatile/metabolism
Metabolomics/methods
*Metabolome
Young Adult
Anti-Bacterial Agents/therapeutic use
Metagenome

@article {pmid42883741,
year = {2026},
author = {Zhukov, IS and Alnefeesi, Y and Gladyshev, NS and Zolkin, A and Zalicheva, AB and Chalabiani, Y and Miklya, I and Ermolenko, EI and Gainetdinov, RR},
title = {Gut Microbiome Alterations in TAAR5 Knockout Mice and In Silico Ligand Prediction.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198493},
pmid = {42883741},
issn = {1422-0067},
support = {148723091//St Petersburg University/ ; },
mesh = {Animals ; *Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry ; Mice, Knockout ; Trace Amine-Associated Receptors ; Mice ; *Gastrointestinal Microbiome/genetics ; Molecular Docking Simulation ; Ligands ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Trace amine-associated receptors (TAARs) are a class of G protein-coupled receptors with roles in olfaction, behaviour, and immunity. Known best as an olfactory receptor, TAAR5 has been linked to emotional behaviour and hippocampal neurogenesis, yet its peripheral mechanisms remain poorly understood. Given bidirectional influences between the gut microbiota and the host, we investigated whether TAAR5 deletion alters the gut microbiome in mice. Using 16S rRNA sequencing, we compared the gut microbiota of TAAR5-knockout (TAAR5-KO) and wild-type mice. While alpha-diversity remained unchanged, beta-diversity analysis revealed significant separation between genotypes, with TAAR5-KO mice exhibiting markedly increased inter-individual variability. Taxonomically, KO mice showed a significant reduction in Ruminococcus and ASF356, alongside an enrichment of specific Lachnospiraceae and Prevotellaceae lineages. Functional metagenomic prediction (PICRUSt2) implied a reduction in the metagenomic capacity for central metabolic pathways (glycolysis, TCA cycle, fatty acid β-oxidation) and an increase in the capacity for guanosine nucleotide degradation pathways; these hypotheses remain untested. Molecular docking identified candidate microbial metabolites, including small amines (2-aminophenol, aminoacetone, butan-1-amine), with ligand efficiencies comparable to the known TAAR5 agonist trimethylamine. These findings suggest that TAAR5 may influence gut microbiome composition and function, with particular impact on Ruminococcus-a genus linked to intestinal inflammation. The increased compositional variability in TAAR5-KO mice suggests that TAAR5 may act as a homeostatic gatekeeper in gut microbial ecology. Our in silico results offer testable hypotheses for future validation of microbial metabolites as novel TAAR5 ligands.},
}

Animals
*Receptors, G-Protein-Coupled/genetics/metabolism/deficiency/chemistry
Mice, Knockout
Trace Amine-Associated Receptors
Mice
*Gastrointestinal Microbiome/genetics
Molecular Docking Simulation
Ligands
RNA, Ribosomal, 16S/genetics

@article {pmid42883855,
year = {2026},
author = {Dessalegn, B and Debelo, M and Palmieri, N and Dublecz, K and Hess, M and Awad, WA},
title = {Early-Life Oat Supplementation Is Associated with Altered Cecal Microbiota and Microbial Metabolic Profiles and Reduced Campylobacter jejuni Colonization in Broiler Chickens.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198607},
pmid = {42883855},
issn = {1422-0067},
support = {FWF; P 36720//FWF Austrian Science Fund/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology/metabolism ; *Campylobacter jejuni ; *Avena/chemistry ; *Dietary Supplements ; *Campylobacter Infections/veterinary/microbiology ; Animal Feed ; *Gastrointestinal Microbiome/drug effects ; Amino Acids/metabolism ; Fatty Acids, Volatile/metabolism ; Diet ; *Metabolome ; *Poultry Diseases/microbiology/prevention & control ; },
abstract = {Campylobacter jejuni is a leading foodborne pathogen that commonly colonizes the intestinal tract of broiler chickens and represents a significant food safety concern. Dietary intervention may provide a practical approach to modulate the gut microbiota and reduce pathogen colonization. This study investigated the effects of oat supplementation on C. jejuni colonization and dissemination, cecal microbiota and predicted functions, and cecal short-chain fatty acids (SCFAs) and ileal amino acid profiles during early-life infection in broiler chickens. One-day-old Ross 308 broiler chickens were fed a basal diet or diets containing 10% oat (MDF) or 20% oat (HDF) and orally infected with C. jejuni at 2 days of age. C. jejuni loads in the cecum, jejunum, liver, and spleen were quantified by culture. Cecal microbiota composition and predicted functional profiles were characterized by shotgun metagenomic sequencing, while cecal SCFAs and ileal amino acids were quantified at 21 and 35 dpi using gas chromatography and an automatic amino acid analyzer, respectively. Oat supplementation reduced intestinal C. jejuni loads and limited dissemination to the liver and spleen, with the MDF diet reducing cecal loads by up to 3.3 log10 CFU/g at 35 dpi (p < 0.05). Infection altered cecal microbial diversity and community structure, while oat supplementation modified these infection-associated microbial patterns, with MDF showing the most consistent effects. Differential abundance analysis identified changes in taxa, including Bacteroides, Parabacteroides, and Phocaeicola, together with changes in predicted functions related to motility and chemotaxis, iron acquisition, and dormancy/sporulation. These microbial changes coincided with alterations in cecal isobutyrate and ileal amino acids, particularly glutamate, serine, proline, and aspartate, in MDF-fed infected chickens. Overall, MDF supplementation was most consistently associated with reduced C. jejuni colonization and dissemination and concurrent changes in the developing cecal microbial and metabolic profiles.},
}

Animals
*Chickens/microbiology
*Cecum/microbiology/metabolism
*Campylobacter jejuni
*Avena/chemistry
*Dietary Supplements
*Campylobacter Infections/veterinary/microbiology
Animal Feed
*Gastrointestinal Microbiome/drug effects
Amino Acids/metabolism
Fatty Acids, Volatile/metabolism
Diet
*Metabolome
*Poultry Diseases/microbiology/prevention & control

@article {pmid42884152,
year = {2026},
author = {Jenkins Sánchez, L and Poppe, J and Baudot, A and Vu, LD and Villella, W and Van den Abbeele, P},
title = {Impact of Triacetin- and Tributyrin-Based Formulations on IBS Microbiome Composition and SCFA Profiles: A Preclinical Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198910},
pmid = {42884152},
issn = {1422-0067},
mesh = {Humans ; *Triglycerides/pharmacology ; *Fatty Acids, Volatile/metabolism ; *Triacetin/pharmacology ; *Irritable Bowel Syndrome/microbiology/drug therapy/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; Adult ; Male ; Prebiotics/administration & dosage ; Female ; Butyrates/metabolism ; },
abstract = {Irritable bowel syndrome (IBS) is a prevalent yet poorly understood functional gut disorder frequently associated with microbial dysbiosis, making microbiome-targeting interventions a promising management strategy. In this study, we evaluated the microbiome-modulating potential of three doses of triacetin (TA; ReBiome™; 100, 200 and 300 mg/day) and two finished formulations containing TA and/or tributyrin (TB): Active Biome™ (AB) and Bio Complete 3™ (BC3). Inulin served as a benchmark prebiotic. The validated ex vivo Systemic Intestinal Fermentation Research (SIFR[®]) technology pipeline was applied using fecal microbiota from eight adults with IBS. TA dose-dependently increased short-chain fatty acid (SCFA) levels from 100 mg/day, significantly increasing acetate and butyrate while maintaining low gas formation. In addition to acetate and butyrate, AB and BC3 also promoted propionate while BC3 induced a particularly pronounced butyrate increase. Overall, both formulations induced stronger SCFA but milder gas increases than inulin. TA, AB and BC3 enriched IBS-depleted, butyrate-associated OTUs related to Faecalibacterium and Anaerobutyricum species. AB and BC3 increased microbial diversity (community modulation score (CMS)) by promoting Bifidobacteriaceae, Lachnospiraceae and Bacteroidaceae. Overall, TA and TA/TB-containing formulations promoted butyrate production, potentially helping mitigate IBS symptom severity by inducing a favorable fermentation profile with limited gas formation.},
}

Humans
*Triglycerides/pharmacology
*Fatty Acids, Volatile/metabolism
*Triacetin/pharmacology
*Irritable Bowel Syndrome/microbiology/drug therapy/metabolism
Feces/microbiology
*Gastrointestinal Microbiome/drug effects
Fermentation
Adult
Male
Prebiotics/administration & dosage
Female
Butyrates/metabolism

@article {pmid42884177,
year = {2026},
author = {Rodríguez-Costas, N and Rodríguez-Blanco, A and Expósito, CR and Cubiella, J and Stompel, ES and Fernández-de-Ana Portela, C and Martín, AID and Taboada-Rodríguez, P and Silva, BF and Fernández, MDR and Zarraquiños, S and Remedios, D and Gómez, CAS and Lorenzo, SA and Poceiro, RF and Parga, MLC and Ramírez, VH and Pérez-Castro, S},
title = {Beyond Taxonomy: Fungal Nutraceutical Supplementation Modifies the Functional Potential of the Gut Microbiome in Colorectal Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198936},
pmid = {42884177},
issn = {1422-0067},
support = {N.º Solicitud SOL-00105490, N.º Expediente EXP0010549//Centre for Industrial Technological Development/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Fungi/chemistry ; Female ; Male ; Feces/microbiology ; Metagenomics/methods ; Middle Aged ; Aged ; },
abstract = {The gut microbiome is increasingly recognized as an important determinant of host immune regulation, intestinal homeostasis, and recovery after colorectal cancer (CRC) surgery. Although our previous randomized, double-blind, placebo-controlled clinical trial demonstrated that fungal nutraceutical supplementation with Micodigest[®] was associated with favorable taxonomic and systemic inflammatory changes in patients undergoing CRC surgery with curative intent, the functional consequences of this intervention remain poorly understood. Here, we performed a functional metagenomic analysis of fecal samples collected from patients enrolled in the original clinical trial to investigate whether Micodigest[®] supplementation was associated with changes in the functional potential of the gut microbiome. A total of 37 patients were analyzed, including 24 receiving Micodigest[®] and 13 receiving placebo, with paired samples collected before supplementation and after 4-6 weeks of intervention. Shallow shotgun metagenomic sequencing was performed, and microbial functional potential was characterized using KEGG Orthologues (KOs). Differential abundance analysis identified 14 significantly different KOs between groups at baseline and 23 after intervention, with no overlap between the two sets of orthologues. Following supplementation, Micodigest[®]-treated patients exhibited increased representation of functions related to CRISPR-associated systems, bacteriophage biology, and chitin-derived carbohydrate utilization, together with reduced representation of nutrient acquisition systems, conjugative transfer, sulfur metabolism, and components of the Wood-Ljungdahl pathway. These functional signatures suggest coordinated changes in microbial ecological adaptation, nutrient utilization, genetic exchange, and metabolic activity following fungal nutraceutical supplementation. Integration with previously reported taxonomic and inflammatory findings supports the hypothesis that Micodigest[®] may promote coordinated remodeling of the gut microbiome and host-microbiota interactions during the perioperative period. Although the present study cannot establish causality or directly infer microbial activity from metagenomic potential, these findings provide novel functional insights into the microbiome response to fungal nutraceutical supplementation in patients with CRC and highlight functional metagenomics as a valuable complement to taxonomic profiling.},
}

Humans
*Colorectal Neoplasms/microbiology
*Dietary Supplements
*Gastrointestinal Microbiome/drug effects
*Fungi/chemistry
Female
Male
Feces/microbiology
Metagenomics/methods
Middle Aged
Aged

@article {pmid42884562,
year = {2026},
author = {Xu, Z and Lau, RI and Qi, H and Wong, MCS and Chan, KHN and Lau, ISF and Ching, JYL and Cheong, PK and Chan, FKL and Ng, SC},
title = {Synbiotic HQP08 Supplementation for Hair Loss and Depressive Symptoms: An Open-Label Pilot Study of Clinical Outcomes and Gut Microbiome Changes.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193111},
pmid = {42884562},
issn = {2072-6643},
support = {//InnoHK/ ; },
mesh = {Humans ; Pilot Projects ; *Alopecia/microbiology/therapy ; Female ; Male ; Adult ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; *Synbiotics/administration & dosage ; Treatment Outcome ; *Depression/therapy/microbiology ; *Bifidobacterium longum ; Dietary Supplements ; Young Adult ; },
abstract = {Background: Gut microbiota dysregulation has been implicated in hair loss via the gut-skin axis, but human interventional data are limited. We previously showed that Bifidobacterium longum HK003 reverses alopecia-like phenotypes in mice. Methods: We conducted an open-label, single-arm pilot study to evaluate an HK003-containing synbiotic (HQP08) in 32 adults with self-reported hair loss over 8 weeks. The primary endpoint was the proportion of participants reporting improvement on the Patient Global Impression of Change (PGI-C) scale at week 8. Secondary outcomes included changes in hair loss severity, 60 s hair count, depressive symptoms (PHQ-9), safety, and gut microbiome composition (Chinese Clinical Trial Registry ChiCTR2500112698). Results: At week 8, 62.5% (20/32) of participants reported PGI-C improvement. Significant reductions were observed in hair loss severity (p = 0.0008), 60 s hair count (p = 0.0048), and PHQ-9 scores (p = 0.002). Younger age was associated with PGI-C response (OR per year 0.86, 95% CI: 0.73-0.98, p = 0.037). Metagenomic analysis identified engraftment of B. longum HK003-like profiles in a subset of participants at week 12. Changes in microbial pathways related to thiamine metabolism, vitamin B12 salvage, and lipopolysaccharide biosynthesis were associated with ΔPHQ-9 (FDR-adjusted p < 0.05), but not with hair-related endpoints. No serious adverse events occurred. Conclusions: This first-in-human pilot study suggests that HQP08 was well tolerated and was associated with within-participant changes in hair-loss measurements and PHQ-9 scores. Randomized controlled trials are warranted to confirm efficacy and further elucidate mechanisms within the gut-brain-skin axis.},
}

Humans
Pilot Projects
*Alopecia/microbiology/therapy
Female
Male
Adult
*Gastrointestinal Microbiome/drug effects
Middle Aged
*Synbiotics/administration & dosage
Treatment Outcome
*Depression/therapy/microbiology
*Bifidobacterium longum
Dietary Supplements
Young Adult

@article {pmid42884650,
year = {2026},
author = {Zhao, X and Yang, C and Gao, L and Gao, Y and Qian, W and Liu, H and Sun, Z and Wang, G and Zhao, F},
title = {Heat-Inactivated Lacticaseibacillus paracasei PC-01 Alleviates DSS-Induced Colitis in Mice by Modulating Gut Microbiota and Intestinal Barrier Function.},
journal = {Nutrients},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/nu18193199},
pmid = {42884650},
issn = {2072-6643},
support = {23402050//National Natural Science Foundation of China/ ; 2024YFA1307002//National Key Research and Development Program of China/ ; 2024QN03052//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; SPKJ202206//Science and technology project of the Food Science and Engineering College, Inner Mongolia Agricultural University/ ; },
mesh = {Animals ; Mice, Inbred C57BL ; *Lacticaseibacillus paracasei/physiology ; *Gastrointestinal Microbiome ; Mice ; Intestinal Barrier Function ; Dextran Sulfate ; *Colitis/chemically induced/microbiology/therapy ; Cytokines/blood/metabolism ; Disease Models, Animal ; Male ; Hot Temperature ; *Probiotics/pharmacology ; Intestinal Mucosa/microbiology/metabolism ; },
abstract = {Background: Inflammatory bowel disease (IBD) is a chronic, progressive, immune-mediated inflammatory disorder of the gastrointestinal tract. Methods: This study used C57BL/6J mice induced by DSS to construct an intestinal inflammation model, and explored the alleviating effect and potential mechanism of heat inactivated Lactobacillus paracasei PC-01 (PC-01) on intestinal inflammation. Results: The results showed that heat-inactivated PC-01 significantly decreased the Disease Activity Index and H&E histopathological scores (p < 0.05). It also reduced the serum levels of pro-inflammatory cytokines, including IL-6, IL-1β, TNF-α, and malondialdehyde (p < 0.01), increased the levels of the anti-inflammatory factor IL-10 (p < 0.001) and antioxidant enzymes SOD and GSH-Px (p < 0.01), and restored the integrity of the intestinal epithelial barrier in DSS-induced colitis mice. Metagenomic analysis showed that PC-01 treatment restored the abundance of beneficial bacteria, including Barnesiella and Muribaculum, and reduced the enrichment of opportunistic pathogens such as Angelakisella and Lawsonibacter (p < 0.05). Further functional annotation of the microbial community indicated that PC-01 significantly enriched pathways related to the TCA cycle, riboflavin metabolism, Toll and Imd signaling, and lipopolysaccharide biosynthesis. In addition, the relative abundances of auxiliary activities, polysaccharide lyases, and S-layer homology modules were lower than those in the DSS group, whereas those of glycoside hydrolases, glycosyltransferases, and carbohydrate esterases were higher. At the transcriptional level, intervention with heat-inactivated PC-01 resulted in a downward trend in the expression of TLR4, Nfkb1, and Rela, accompanied by reduced expression of the chemokines MCP-1 and Cxcl10, and inflammasome-related genes NLRP3, Casp1, and IL-1β. Conclusions: In summary, heat-inactivated Lacticaseibacillus paracasei PC-01 effectively alleviated intestinal inflammatory injury in mice by regulating gut microbiota homeostasis and suppressing intestinal inflammatory responses.},
}

Animals
Mice, Inbred C57BL
*Lacticaseibacillus paracasei/physiology
*Gastrointestinal Microbiome
Mice
Intestinal Barrier Function
Dextran Sulfate
*Colitis/chemically induced/microbiology/therapy
Cytokines/blood/metabolism
Disease Models, Animal
Male
Hot Temperature
*Probiotics/pharmacology
Intestinal Mucosa/microbiology/metabolism

@article {pmid42885240,
year = {2026},
author = {Ghosh, SK and Wassel, MA and Wong, MK and Hyodo, S and Hamasaki, K},
title = {Functional Metagenomics Reveals Gut Microbial Biosynthetic Potential for Essential Nutrients in Juvenile Chum Salmon.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70448},
doi = {10.1111/1462-2920.70448},
pmid = {42885240},
issn = {1462-2920},
support = {//University of Tokyo/ ; //Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {Animals ; *Oncorhynchus keta/microbiology/metabolism/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; Amino Acids/biosynthesis ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenome ; },
abstract = {The fish gut microbiota contributes to host nutrition, immunity and homeostasis, yet how its metabolic capacity relates to gaps in the host genome remains poorly characterized. Here we used shotgun metagenomic sequencing and KEGG module completion analysis to compare the biosynthetic potential of the gut microbiome with that of the host genome in juvenile chum salmon (Oncorhynchus keta) at 35 days posthatching, when exogenous feeding begins. Because small juvenile guts yield low microbial biomass and a high proportion of host DNA, we first optimized a protocol combining enzymatic lysis with NEBNext-based host DNA depletion. This raised the bacterial sequence fraction from 11.3% to 41.2% and increased the number of KEGG Orthology identifiers mapped to modules from 1128 to 1532. Module Completion Ratio analysis revealed complementation in functional potential: the chum salmon genome was incomplete for de novo biosynthesis of essential amino acids (threonine, leucine, valine/isoleucine, lysine) and B-vitamins (thiamine, riboflavin, biotin), whereas the gut metagenome encoded complete or near-complete modules for these pathways. Sequences assigned to Bartonella-like, Acinetobacter and Enterococcus lineages contributed most. These observations indicate that the gut microbiome encodes biosynthetic potential the host genome lacks, although demonstrating a nutritional benefit to the host will require experimental manipulation.},
}

Animals
*Oncorhynchus keta/microbiology/metabolism/genetics
Metagenomics
*Gastrointestinal Microbiome
Amino Acids/biosynthesis
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenome

@article {pmid42482126,
year = {2026},
author = {Zhai, Y and Kim, Y and Ban, GH and Kim, YM and Kim, SC and Bae, D and Jeong, KC and Kim, SA},
title = {Environmental reservoirs and transmission pathways of antimicrobial resistance across the pork production continuum.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42482126},
issn = {2049-2618},
mesh = {Animals ; Swine ; Gene Transfer, Horizontal ; Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Abattoirs ; Microbiota/genetics ; Acinetobacter/genetics/drug effects/isolation & purification ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Pseudomonas/genetics/drug effects/isolation & purification ; *Drug Resistance, Bacterial/genetics ; Farms ; *Pork Meat/microbiology ; Humans ; Metagenome ; Genes, Bacterial ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major One Health challenge linking human, animal, and environmental health, yet the contribution of food production environments to resistance transmission remains poorly understood.

RESULTS: We conducted a longitudinal shotgun metagenomic study across the pork production continuum from farm to retail to identify environmental AMR reservoirs and transmission pathways of antimicrobial resistance genes (ARGs). Assembly-based, genome-resolved, and source-tracking analyses were integrated to characterize resistomes, microbial communities, and horizontal gene transfer dynamics. ARG abundance and diversity were highest at farms, slaughterhouses, and processing plants and declined toward retail, although clinically relevant resistance determinants persisted throughout processing. Slaughterhouse environments emerged as major contributors to ARG contamination on carcasses, highlighting the importance of environmental exposure at intermediate stages. Resistome structure was closely linked to microbial community composition, with persistent taxa such as Acinetobacter and Pseudomonas serving as key ARG carriers, including genes conferring resistance to tetracycline, aminoglycosides, macrolide-lincosamide-streptogramin, and β-lactams, multidrug efflux. Co-localization of ARGs with mobile genetic elements demonstrated ongoing potential for horizontal transfer across production stages, and genome-resolved metagenome-assembled genome analyses revealed overlapping resistance and virulence profiles between slaughterhouse- and processing plant-associated bacteria, indicating adaptive persistence within pork production environments.

CONCLUSIONS: Resistome composition across the pork production chain is largely shaped by stage-specific environmental sources, highlighting potential intervention points to mitigate AMR transmission. Video Abstract.},
}

Animals
Swine
Gene Transfer, Horizontal
Metagenomics/methods
Anti-Bacterial Agents/pharmacology
Abattoirs
Microbiota/genetics
Acinetobacter/genetics/drug effects/isolation & purification
*Bacteria/genetics/drug effects/classification/isolation & purification
Pseudomonas/genetics/drug effects/isolation & purification
*Drug Resistance, Bacterial/genetics
Farms
*Pork Meat/microbiology
Humans
Metagenome
Genes, Bacterial

@article {pmid42525291,
year = {2026},
author = {Gutiérrez-Ávila, JL and Gutiérrez-Rebolledo, GA and Avila-Bonilla, RG and Pardo, MES},
title = {Functional Equivalence and Conserved Sexual Dimorphism in the Gut Microbiome: A Cross-Species Meta-analysis.},
journal = {Journal of molecular evolution},
volume = {94},
number = {5},
pages = {814-834},
pmid = {42525291},
issn = {1432-1432},
mesh = {Animals ; Humans ; Female ; Male ; Sex Characteristics ; Mice ; *Gastrointestinal Microbiome/genetics/physiology ; Drosophila melanogaster/genetics ; Metagenome/genetics ; Metagenomics/methods ; Metabolic Networks and Pathways ; },
abstract = {The murine model is a standard system in translational microbiome research, yet its functional equivalence to the human microbiome remains debated. To evaluate its translational validity, we conducted a comparative whole-genome shotgun (WGS) metagenomic meta-analysis, integrating an initial retrieval of 520 datasets from 5 independent cohorts (BioProjects) across Homo sapiens (n = 202), Mus musculus (n = 75), and Drosophila melanogaster (n = 243) samples. Taxonomic and functional profiles were evaluated using strict bioinformatic quality control and batch-effect mitigation. Taxonomic profiling revealed pronounced divergence driven by host-specific ecological constraints and filtering. However, metabolic reconstruction demonstrated substantial functional equivalence, supporting the functional redundancy hypothesis for core mammalian metabolic circuits. We also noted a methodological vulnerability in our dataset: a low-depth murine sample clustered with invertebrate profiles, suggesting that technical noise or insufficient depth might artificially compress mammalian functional diversity. Comparative analysis identified sex-biased metabolic pathways conserved across mammalian hosts. Specifically, we observed a consistent enrichment of steroid metabolism in females and mineralocorticoid regulation in males. These findings indicate that functional conservation between humans and mice is modular rather than global. Consequently, the translational value of the murine model lies in domain-specific functional equivalence rather than taxonomic imitation. Moreover, the conservation of sex-specific metabolic signatures suggests that biological sex is a fundamental organising principle of microbiome function. This study highlights the necessity of mapping conserved metabolic modules and rigorously controlling inter-study variance to effectively deploy murine models in biomedical research.},
}

Animals
Humans
Female
Male
Sex Characteristics
Mice
*Gastrointestinal Microbiome/genetics/physiology
Drosophila melanogaster/genetics
Metagenome/genetics
Metagenomics/methods
Metabolic Networks and Pathways

@article {pmid42660482,
year = {2026},
author = {Li, X and Yang, H and Xu, Z and Peng, L and Jiang, Z and Zhou, X and Xiang, J and Cui, B},
title = {Artificial light pollution alters epilithic microbial communities and functional biodeterioration-related functional potentials in subterranean sandstone environments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {409},
number = {},
pages = {129056},
doi = {10.1016/j.envpol.2026.129056},
pmid = {42660482},
issn = {1873-6424},
mesh = {Bacteria/classification/genetics ; *Microbiota ; *Caves/microbiology ; *Light Pollution/adverse effects ; China ; *Soil Microbiology ; RNA, Ribosomal, 16S ; Light ; Biodegradation, Environmental ; },
abstract = {Artificial light pollution represents an important anthropogenic disturbance in subterranean heritage environments, yet its associations with epilithic microbial communities and biodeterioration processes remain poorly understood. In tourist-accessible subterranean caves, artificial light creates persistent illuminated areas on stone surfaces that may alter microbial community assembly and biogeochemical functions associated with biofilm development. Here, the Longyou Grottoes, a large underground sandstone cave complex in Zhejiang, China, were investigated using 16S rRNA gene sequencing and metagenomics. Bacterial communities dominated all samples (>98% relative abundance). Cyanobacteriota were enriched under artificial light and sunlight (>40%), whereas Pseudomonadota and Actinomycetota prevailed in darkness. Dark sites exhibited higher bacterial alpha diversity and more complex co-occurrence networks. Compared with sunlight and dark environments, the artificial-light environment was associated with greater stochasticity in bacterial community assembly, broader niche breadth, and lower niche overlap. Metabolic potential analysis further revealed light-dependent metabolic shifts: artificial light enhanced assimilatory nitrogen and sulfur metabolism, sunlight promoted nitrogen fixation, and darkness favored nitrification, denitrification, and sulfur oxidation. However, bacterial community patterns were also associated with temperature, humidity, pH, and soluble salts, indicating that the observed differentiation reflected the combined influence of light and environmental heterogeneity. These findings identify artificial lighting as an important and manageable environmental factor associated with epilithic bacterial communities and provide a basis for integrating lighting management with environmental control in the preventive conservation of subterranean sandstone heritage.},
}

Bacteria/classification/genetics
*Microbiota
*Caves/microbiology
*Light Pollution/adverse effects
China
*Soil Microbiology
RNA, Ribosomal, 16S
Light
Biodegradation, Environmental

@article {pmid42665077,
year = {2026},
author = {Fan, Q and Bai, J and Wang, X and Zhao, Z and Zhao, X},
title = {Metagenomic characterization of potential exposure to genetic hazards at the interface between grazing livestock and Przewalski's gazelle.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {409},
number = {},
pages = {129059},
doi = {10.1016/j.envpol.2026.129059},
pmid = {42665077},
issn = {1873-6424},
mesh = {Animals ; *Livestock/microbiology ; *Antelopes/microbiology ; Metagenomics ; Sheep ; *Metagenome ; Microbiota ; Cattle ; },
abstract = {Livestock and endangered wildlife increasingly share grazing landscapes, yet the sources, mobility-associated contexts, and bacterial hosts of livestock-associated genetic hazards in wildlife microbiomes remain poorly resolved. We analyzed metagenomes from yak, Tibetan sheep, Przewalski's gazelle, and local topsoil within an Acquired Genetic Risk (AGR) conceptual framework integrating genetic hazard burden, compositional source attribution, mobility-associated evidence, and bacterial genomic context. MRGs and Rank I and Rank III ARGs were more abundant in livestock than in Przewalski's gazelle, whereas VF abundance was highest in yak. FEAST attributed approximately 64% of the Przewalski's gazelle resistome composition to the two livestock source profiles, less than 1% to sampled topsoil, and approximately 36% remained unassigned. MGE profiles were associated with ARGs, MRGs, and VFs, while tnpA ranked highest in random forest models and was associated with total ARG abundance (R[2] = 0.618). Short-read contigs containing hazard genes and MGE markers provided localized mobility-associated sequence context. Genome-resolved analysis identified distinct bacterial contexts: TS.Bin143, an Escherichia coli MAG from Tibetan sheep, contained ARGs, MRGs, VFs, tnpA, and IS91, whereas PG.Bin275, a Hylemonella sp. MAG from Przewalski's gazelle, contained tnpA. These findings extend wildlife resistome assessment beyond abundance profiling toward source attribution, mobility-associated sequence context, and bacterial host resolution, supporting multilevel surveillance of genetic hazard exposure at livestock-wildlife interfaces.},
}

Animals
*Livestock/microbiology
*Antelopes/microbiology
Metagenomics
Sheep
*Metagenome
Microbiota
Cattle

@article {pmid42863410,
year = {2027},
author = {Villa-Rodríguez, E and Ferguson, S and Stougaard, J and Radutoiu, S},
title = {Understanding genetic determinants of bacterial adaptation to plant niches: Toward more robust bioinoculant design.},
journal = {Microbiological research},
volume = {314},
number = {},
pages = {128760},
doi = {10.1016/j.micres.2026.128760},
pmid = {42863410},
issn = {1618-0623},
mesh = {*Bacteria/genetics/metabolism/growth & development ; Soil Microbiology ; *Plants/microbiology ; Plant Roots/microbiology ; *Adaptation, Physiological/genetics ; Rhizosphere ; *Bacterial Physiological Phenomena ; Microbiota/genetics ; Biofilms/growth & development ; },
abstract = {Plant-associated bacteria offer a sustainable alternative to chemical inputs in agriculture, yet the field performance of microbial inoculants remains inconsistent. A central but frequently overlooked cause is that bioprospecting pipelines still select strains on the basis of plant-growth-promoting activities, while the bacterial genetic traits that determine whether a strain can reach, colonise and persist in a given root compartment are rarely assessed. Previous reviews have largely catalogued growth-promoting functions or described root microbiome assembly from the plant's perspective, here we take the bacterium's. We trace the journey of a bacterium from bulk soil to its final niche and, at each stage, identify the genes and pathways (genetic determinants) that encode key bacterial traits involved, such as chemotaxis and motility, nutrient acquisition and metabolic independence, competitive and defensive arsenals, attachment and biofilm formation, evasion of plant immunity, and endophytic entry and persistence. Throughout, we use evidence from comparative genomics and metagenomics, (meta)transcriptomics, targeted mutagenesis and genome-wide screens such as Tn-seq, obtained in systems ranging from binary interactions to synthetic communities and natural soils. For each stage we examine the current state of knowledge, identify critical gaps, and propose avenues to deepen our mechanistic understanding of the bacterial traits involved in plant colonisation. We argue that this mechanistic understanding is the missing foundation for developing inoculants with more consistent and robust performance across diverse agroecosystems.},
}

*Bacteria/genetics/metabolism/growth & development
Soil Microbiology
*Plants/microbiology
Plant Roots/microbiology
*Adaptation, Physiological/genetics
Rhizosphere
*Bacterial Physiological Phenomena
Microbiota/genetics
Biofilms/growth & development

@article {pmid42874540,
year = {2026},
author = {Dara, M and Calabrisotto, LS and Bisanti, L and Torreagrossa, N and La Corte, C and Bertini, F and Catania, V and Quatrini, P and Parrinello, D and Piazzese, D and Cammarata, M and Banni, M and Parisi, MG},
title = {Integrated assessment of bioplastic materials effects on microbial communities and macroinvertebrate model, Mytilus galloprovincialis, in marine ecosystems.},
journal = {Marine pollution bulletin},
volume = {234},
number = {Pt 1},
pages = {120459},
doi = {10.1016/j.marpolbul.2026.120459},
pmid = {42874540},
issn = {1879-3363},
abstract = {The increasing use of biopolymer derivatives raises concerns about their actual environmental sustainability, which remains insufficiently understood. In this study, we adopted an integrated approach combining microbial and ecotoxicological perspectives to evaluate their impact in marine ecosystems. We investigated the plastisphere composition of conventional petroleum-based High Density Polyethylene (HDPE) and polyhydroxyalkanoates (PHA), polyhydroxybutyric acid (PHB), and polylactic acid (PLLA) scaffolds after 60 days of exposition in marine ecosystem or microcosm, by high throughput metagenomics 16S rRNA gene sequencing and culture dependent approach. A variation in terms of composition and abundance of plastisphere, between petroleum-derived and bio-based degradable scaffolds, was observed. A high abundance of Proteobacteria was detected in all polymers, with Alpha and Gamma Proteobacteria dominant. At the genera level, high abundance of sequences assigned to hydrocarbon-degrading bacteria (i.e. Oleibacter, Labrenzia, Alcanivorax) was detected in biopolymeric plastic compared to petroleum-based plastic. To link microbial colonization and material degradation with biological effects on marine fauna, the impact of biopolymer-derived micro- and nanoparticles on the mussel Mytilus galloprovincialis was assessed. Both in vitro and in vivo assays demonstrated immune system activation through phagocytosis and encapsulation, while in vivo exposures influenced several biomarkers (phagocytosis, haemocyte density, lysozyme, glutathione peroxidase, phenoloxidase, alkaline phosphatase, esterase), suggesting potential detrimental effects after 72 h. By bridging microbial ecology with immunological responses in a bioindicator species, this multidisciplinary study provides novel insights into the complex ecological footprint of biodegradable plastics in marine environments.},
}

@article {pmid42875131,
year = {2026},
author = {Kang, C and Zheng, X and Liu, Z and Wang, W and Zeng, W and He, Y and Huang, J and Nie, W and Wang, J and Wang, F},
title = {Cryptic microheterogeneity of the casing-layer microbiome and metabolome is associated with primordium fate in Phallus rubrovolvatus.},
journal = {Fungal biology},
volume = {130},
number = {7},
pages = {101864},
doi = {10.1016/j.funbio.2026.101864},
pmid = {42875131},
issn = {1878-6146},
mesh = {*Microbiota ; *Metabolome ; *Agaricales/growth & development/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Multiomics ; },
abstract = {Commercial cultivation of Phallus rubrovolvatus relies on casing layers, yet yields remain unstable, with primordium development varying among individual microsites. This cryptic microheterogeneity is masked by conventional bulk sampling, limiting insight into casing-layer performance. Here, we combined phenotype-guided back-tracing with multi-omics to characterize microecological signatures associated with primordium fate. We identified two contrasting ecological regimes associated with reproductive outcomes. Productive microsites were characterized by a "Cooperative state" enriched in oligotrophic bacteria (e.g., Hyphomicrobium) and basidiomycetes (e.g., Clathrus columnatus). Productive microsites also showed lower available potassium (K[+]) and elevated catalase activity. Conversely, non-productive microsites were characterized by a Rhizopus-dominated "Disruptive state". This state was associated with elevated urease activity, lower catalase activity, and stress-associated metagenomic functional signatures. Overall, primordium fate was associated with distinct local microbial, functional, and metabolic configurations that were not fully explained by bulk physicochemical properties. We propose the "Cooperative vs. Disruptive" model as a conceptual framework and identify candidate microbial and metabolic features for future validation in microbiome-informed cultivation management.},
}

*Microbiota
*Metabolome
*Agaricales/growth & development/metabolism
Bacteria/classification/genetics/metabolism/isolation & purification
Multiomics

@article {pmid42876779,
year = {2026},
author = {Cleanclay, WD and Kernyuy, FB and Kintung, IF and Yensii, NG and Obi, AMM and Nguema, OAM},
title = {The mosquito gut microbiome and Plasmodium development: a scoping review of molecular approaches and implications for malaria vector control.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1906816},
pmid = {42876779},
issn = {2235-2988},
mesh = {Animals ; *Malaria/prevention & control/transmission/parasitology ; *Plasmodium/growth & development ; *Mosquito Vectors/microbiology/parasitology ; *Gastrointestinal Microbiome ; *Anopheles/microbiology/parasitology ; *Mosquito Control/methods ; Metagenomics ; Humans ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Malaria remains a major health burden, with an estimated 282 million cases and approximately 610,000 deaths recorded in 2024. The increasing prevalence of insecticide-resistant Anopheles vectors and drug-resistant Plasmodium strains has substantially eroded the efficacy of conventional control strategies, underscoring the critical need for innovative approaches. Accumulating evidence suggest that the mosquito midgut microbiome exerts a significant influence on Plasmodium sporogonic development; however, no scoping investigation has fully mapped the metagenomic evidence base in this field.

METHODS: Adhering to the Arksey and O'Malley framework and PRISMA-ScR guidelines, a systematic search was conducted across PubMed, Scopus, and Web of Science for publications from January 2000 to April 2026. Studies that used microbiological, molecular, or metagenomic techniques to study the gut microbiota of mosquito species related to Plasmodium were included. Descriptive mapping was used to synthesize the data in a thematic manner.

RESULTS: Thirteen primary studies met the inclusion criteria, comprising both observational field surveys and experimental infection studies. Four themes emerged: (1) gut microbiota diversity and composition are associated with Plasmodium infection status, though the direction varies by mosquito species, geography, and season; (2) several taxa, including Burkholderia, Asaia, Sphingomonas, Pseudomonas, and Serratia, are consistently associated with reduced infection or are experimentally inhibitory; (3) the Enterobacteriaceae and Serratia spp. show context-dependent, bidirectional relationships with Plasmodium that are best explained by strain-level variation; and (4) a smaller set of taxa, including Elizabethkingia, Chryseobacterium, Methylobacterium, and Pantoea, is positively associated with infection, on observational evidence only. The evidence relied predominantly on 16S rRNA amplicon sequencing, with a minority of studies adding whole-genome sequencing, transcriptomics, or metabolomics; none used shotgun metagenomics.

CONCLUSIONS: The mosquito gut microbiome exerts a net inhibitory effect on Plasmodium development, with translational potential for microbiome-based vector control, including paratransgenesis. However, the microbiota is not uniformly antagonistic to the parasite, and taxa positively associated with infection remain observational. The field is limited by a near-exclusive reliance on 16S rRNA profiling, few functional and longitudinal studies, and geographically narrow evidence. Multi-omics approaches, longitudinal designs, and broader geographic coverage will be essential to translate these associations into sustainable malaria control.},
}

Animals
*Malaria/prevention & control/transmission/parasitology
*Plasmodium/growth & development
*Mosquito Vectors/microbiology/parasitology
*Gastrointestinal Microbiome
*Anopheles/microbiology/parasitology
*Mosquito Control/methods
Metagenomics
Humans
Bacteria/classification/genetics

@article {pmid42876851,
year = {2026},
author = {Xie, W and Lu, S and Liu, Z and Zheng, J and Mo, F and Zhang, K and Huang, Z},
title = {Gut microbiome profiles of two limestone forest-dwelling langurs show stronger influence of host-associated factors than environment.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1953526},
pmid = {42876851},
issn = {1664-302X},
abstract = {BACKGROUND: Host-associated factor and the environment play crucial roles in shaping the composition and function of the gut microbiome. Considerable debate exists regarding the relative influence of host-associated and environmental factors on the gut microbiome. To determine the relative importance of host-associated factors and environmental factors in langurs, we employed metagenomic sequencing to examine differences in the gut microbiome of the white-headed langurs (Trachypithecus leucocephalus) and François' langurs (T. francoisi).

RESULTS: The results revealed that the alpha diversity of the gut microbiome significantly differed between white-headed langurs and François' langurs in similar habitats. However, there was no significant variation in the alpha diversity between the wild and captive François' langurs. Similarly, the proportion of Bacillota differed between the langur species, with a higher proportion in the white-headed langurs than the François' langurs. In addition, significant separation in gut microbiome functions also occurred between the two species. The functional genes related to metabolism (e.g., carbohydrate metabolism and amino acid metabolism) and Glycoside Hydrolases in wild François' langurs were more abundant than in the other langurs. The results of PCoA showed that the pathways were significantly separated between white-headed langurs and François' langurs at four levels in the KEGG database, whereas the pathways showed no significant differences between the wild and captive François' langurs except for module level. The proportion of ARGs related to multidrug resistance was higher in wild François' langurs, likely associated with the utilization of poultry manure and antibacterial biocides in the langur's habitat.

CONCLUSION: Our study demonstrates that the host-associated factors have stronger influence on shaping the gut microbiome of langurs than environmental factors. These findings provide data on the relative contributions of host-associated factors and environmental factors to the gut microbiome of langurs and identify potential driving factors for antibiotic resistance genes. In addition, these findings provide crucial insights into the influence of host-associated factors on the gut microbiome, offering a theoretical basis for future langur conservation strategies.},
}

@article {pmid42877104,
year = {2026},
author = {Tang, H and Xiong, Q and Qian, G},
title = {Exploratory microbiota-metabolite alterations associated with cognitive impairment after repeated low-dose sevoflurane exposure in mice.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1869293},
pmid = {42877104},
issn = {2235-2988},
mesh = {Animals ; *Sevoflurane/adverse effects/administration & dosage ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Cognitive Dysfunction/chemically induced/microbiology ; Mice, Inbred C57BL ; Metabolomics ; Disease Models, Animal ; Maze Learning/drug effects ; *Microbiota/drug effects ; *Metabolome/drug effects ; },
abstract = {BACKGROUND: Repeated low-dose sevoflurane exposure may affect cognition, but the relationship between such exposure, gut microbial composition, and circulating metabolites remains unclear. This study examined an experimental proof-of-concept exposure model and treated microbiota-metabolite findings as exploratory associations.

METHODS: Mice were exposed to 100 ppm sevoflurane for 2 h/day over 7 consecutive days, followed by Morris water maze testing without a long-term recovery follow-up. Gut microbiota and serum metabolites were profiled by shotgun metagenomic sequencing and LC-MS metabolomics, respectively, and machine-learning analyses were used only for exploratory feature ranking.

RESULTS: Sevoflurane-exposed mice exhibited poorer Morris water maze performance (Day 6 escape latency: 28.6 ± 3.4 s vs. 12.5 ± 1.8 s in controls, p < 0.01), although interpretation is limited by unequal behavioral sample sizes. Serum metabolomics suggested nominal and exploratory alterations in bile acid- and sphingolipid-related pathways. Shotgun metagenomics (n = 3/group) identified preliminary relative-abundance shifts, including a lower Bacteroidota/Bacillota ratio and lower relative abundance of Akkermansia.

CONCLUSIONS: In this proof-of-concept model, repeated low-dose sevoflurane exposure was associated with impaired spatial learning and memory and with exploratory serum metabolic and gut microbial alterations. The findings do not establish persistent long-term deficits, routine occupational risk, or causal microbiota-metabolite mediation. Larger cage-aware studies, an ambient-air comparison group, targeted validation, and interventional experiments are required.},
}

Animals
*Sevoflurane/adverse effects/administration & dosage
Mice
Male
*Gastrointestinal Microbiome/drug effects
Metagenomics
*Cognitive Dysfunction/chemically induced/microbiology
Mice, Inbred C57BL
Metabolomics
Disease Models, Animal
Maze Learning/drug effects
*Microbiota/drug effects
*Metabolome/drug effects

@article {pmid42877526,
year = {2026},
author = {Fang, YH and Liu, HN and Chen, YJ and Hsu, TW and Chiu, CA and Chiang, PN and Huang, CL},
title = {Metagenomic profiling reveals that divergent fire-adaptive strategies drive distinct fungal succession in pine litter decomposition.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e201414},
pmid = {42877526},
issn = {2210-6340},
abstract = {Decomposing litter is a critical driver of fuel bed formation and forest fire regimes, yet how divergent plant fire-adaptive strategies influence litter chemistry and subsequent fungal decomposition dynamics remains poorly understood. Here, we conducted a 6-month reciprocal litterbag experiment by incubating litter from two contrasting pine species-the fire-tolerant Pinus taiwanensis and the fire-avoiding P. morrisonicola-in both their own native habitat and that of the other species, coupled with genome-resolved metagenomics to track fungal succession and lignocellulolytic functional profiles. We found that the fire-avoiding P. morrisonicola exhibited significantly accelerated decomposition, driven by inherently lower initial C:N ratio and less recalcitrant litter, whereas the fire-tolerant P. taiwanensis exhibited slower decomposition rates. Metagenomic profiling revealed a distinct functional succession underlying this process. Early decomposition was dominated by Ascomycota (e.g., Leotiomycetes), which rapidly colonized the litter to initiate biopolymer breakdown. As easily decomposable substrates depleted, a functional shift occurred. Specifically, the highly recalcitrant P. taiwanensis litter selectively recruited Basidiomycota (e.g., Agaricales and Trechisporales) equipped with diverse lignin-modifying enzymes, reflected by a late-stage temporal surge in ligninolytic gene abundances. Ultimately, these findings demonstrate that plant fire-adaptive strategies act as a strong filter, shaping litter chemistry to drive specific taxonomic and functional fungal succession. This study provides a mechanistic understanding of the eco-evolutionary linkage between plant traits, microbiome assembly, and ecosystem-level fire dynamics.},
}

@article {pmid42878177,
year = {2026},
author = {Vliex, LMM and Godinho Mimoso, IF and Le, GN and Blaak, EE and Penders, J},
title = {Modulation of the gut microbiome and resistome by antibiotic use, but not by subsequent 2'-fucosyllactose intake, in adults with overweight or obesity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2746814},
doi = {10.1080/19490976.2026.2746814},
pmid = {42878177},
issn = {1949-0984},
mesh = {Humans ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Vancomycin/administration & dosage/therapeutic use ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Obesity/microbiology/drug therapy ; *Trisaccharides/administration & dosage ; Double-Blind Method ; *Overweight/microbiology/drug therapy ; Female ; Adult ; Male ; Middle Aged ; Prebiotics/administration & dosage ; Feces/microbiology ; Drug Resistance, Bacterial ; },
abstract = {Antibiotics are widely used to treat bacterial infections, yet overuse and misuse causes disruption of the gut microbiome and spread of antibiotic-resistant bacteria. Presence of antibiotic resistance genes (ARGs) could be a determinant of the response to antibiotics. Supplementation with prebiotics may limit the detrimental antibiotic-induced effects on the microbiome, but whether this results in changes in the gut resistome is unclear. This study investigated the impact of eight-week 2'-fucosyllactose (2'-FL) supplementation after seven-day vancomycin use in 18 adults with overweight/obesity, a subset from a double-blind placebo-controlled randomized intervention. Whole-metagenome shotgun sequencing was used to characterize the gut microbiome and resistome at baseline, after vancomycin use and after supplementation. Seven-day vancomycin use disrupted microbial richness and diversity (p < 0.001) and changed microbial composition. No improvements in microbial recovery were detected after eight week 2'-FL supplementation compared to placebo. Resistome richness and diversity were not affected by vancomycin use, although the presence of specific ARGs changed. No differential impact of 2'-FL supplementation on resistome richness, diversity and composition was detected. While vancomycin use disrupted the gut microbiome and affected the resistome, the detectable effects of 2'-FL supplementation were limited. Future research should investigate antibiotic- and prebiotic-induced changes in the gut resistome in more detail.},
}

Humans
*Anti-Bacterial Agents/administration & dosage/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Vancomycin/administration & dosage/therapeutic use
*Bacteria/genetics/drug effects/classification/isolation & purification
*Obesity/microbiology/drug therapy
*Trisaccharides/administration & dosage
Double-Blind Method
*Overweight/microbiology/drug therapy
Female
Adult
Male
Middle Aged
Prebiotics/administration & dosage
Feces/microbiology
Drug Resistance, Bacterial

@article {pmid42878179,
year = {2026},
author = {Shin, MG and Park, SJ and Kang, W and Bae, Y and Kim, S and Yoo, D and Yoon, S and Park, SM and Kwon, ES and Chang, J and Yoon, JH and Park, DG and Lee, EJ},
title = {Escherichia coli hns and methylglyoxal link gut microbial metabolism to host neuronal gene regulation in Parkinson's disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2739674},
doi = {10.1080/19490976.2026.2739674},
pmid = {42878179},
issn = {1949-0984},
mesh = {Animals ; *Parkinson Disease/metabolism/microbiology/genetics ; Humans ; *Escherichia coli/metabolism/genetics ; Caenorhabditis elegans/genetics/microbiology ; *Gastrointestinal Microbiome ; *Pyruvaldehyde/metabolism/blood ; Dopaminergic Neurons/metabolism ; *Escherichia coli Proteins/metabolism/genetics ; Gene Expression Regulation ; Male ; Disease Models, Animal ; Female ; Neurons/metabolism ; Feces/microbiology ; },
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by dopaminergic neuron loss in the substantia nigra (SN). Although the gut microbiota has been implicated in PD pathogenesis, how defined bacterial genes and their metabolites influence host neuronal gene regulation remains unclear. Here, we identify a gut microbial hns-methylglyoxal (MG) pathway linking Escherichia coli (E. coli) metabolism to host neuronal gene regulation. In the stool metagenomic cohort, hns, a bacterial gene encoding the histone-like nucleoid structuring protein and primarily derived from E. coli, was enriched particularly in body-first PD, a subtype associated with gut-originating pathology. In a separate plasma MG cohort, plasma levels of MG, a reactive metabolite whose bacterial production was hns-dependent in our model system, were higher in body-first than in brain-first PD and were nominally inversely associated with cardiac meta-iodobenzylguanidine (MIBG) uptake within the body-first group. Using Caenorhabditis elegans (C. elegans) PD models, we found that feeding with Δhns E. coli protected dopaminergic neurons, whereas exogenous MG abolished this neuroprotection. Transcriptomic and neuronal RNAi analyses identified rig-5 as a host mediator of hns deletion-induced neuroprotection. Cross-species analyses identified LSAMP as a candidate mammalian ortholog of rig-5. MG suppressed LSAMP expression in human neuronal cells, and LSAMP expression was reduced in the post-mortem SN of patients with PD. Conversely, Lsamp expression was increased in the SN of mice colonized with Δhns E. coli. Together, these findings delineate a microbial gene-metabolite-host gene pathway through which E. coli hns and MG modulate rig-5-dependent dopaminergic vulnerability in C. elegans, with corresponding changes of LSAMP expression in mammalian systems.},
}

Animals
*Parkinson Disease/metabolism/microbiology/genetics
Humans
*Escherichia coli/metabolism/genetics
Caenorhabditis elegans/genetics/microbiology
*Gastrointestinal Microbiome
*Pyruvaldehyde/metabolism/blood
Dopaminergic Neurons/metabolism
*Escherichia coli Proteins/metabolism/genetics
Gene Expression Regulation
Male
Disease Models, Animal
Female
Neurons/metabolism
Feces/microbiology

@article {pmid42477662,
year = {2026},
author = {Chao-Chao, Q and Zhi-Ruo, L and Xiao-Qing, L and Yan-Hong, M and Yue-Ying, Z and Ning, P and Ji-Chan, S and Xian-Gao, J},
title = {Exploring differences in alveolar microbiome between pulmonary tuberculosis patients with different treatment outcomes: a metagenomic study from China.},
journal = {BMC pulmonary medicine},
volume = {26},
number = {1},
pages = {},
pmid = {42477662},
issn = {1471-2466},
mesh = {Humans ; *Tuberculosis, Pulmonary/drug therapy/microbiology ; *Microbiota/genetics ; Female ; Bronchoalveolar Lavage Fluid/microbiology ; China ; Male ; *Antitubercular Agents/therapeutic use ; Metagenomics ; Adult ; Treatment Outcome ; Middle Aged ; *Pulmonary Alveoli/microbiology ; },
abstract = {This study aimed to investigate differences in the composition and functional characteristics of alveolar microbiota in patients with pulmonary tuberculosis (PTB) exhibiting differential therapeutic responses. Thirty-two patients with drug-sensitive PTB who had completed standard anti-tuberculosis therapy were enrolled and classified into good-response (n = 16) and poor-response (n = 16) groups. Bronchoalveolar lavage fluid (BALF) samples were collected and analysed using metagenomic sequencing to characterize microbial community and functional pathways. No significant differences were observed in α-diversity between the two groups; however, β-diversity analysis demonstrated moderate but significant in microbial community structure (ANOSIM, R = 0.381, P < 0.001). The good efficacy group was characterized by enrichment of Prevotella, Staphylococcus, and oral commensal bacteria including Fusobacterium and Rothia, together with significantly increased pathways related to peptidoglycan biosynthesis, glutathione metabolism, energy production, and DNA repair. In contrast, the poor efficacy group was characterised by enrichment of Microbacterium and activation of functional pathways associated with biofilm formation. These findings suggest that both the taxonomic composition and functional activity of the pulmonary microbiome are closely associated with anti-tuberculosis treatment outcomes.},
}

Humans
*Tuberculosis, Pulmonary/drug therapy/microbiology
*Microbiota/genetics
Female
Bronchoalveolar Lavage Fluid/microbiology
China
Male
*Antitubercular Agents/therapeutic use
Metagenomics
Adult
Treatment Outcome
Middle Aged
*Pulmonary Alveoli/microbiology

@article {pmid42671175,
year = {2026},
author = {Schärer, MR and Yu, Y and Grawe, A and Christenson, JK and Robinson, SL and Bokulich, NA},
title = {Laccase-mediated biotransformation potential for fluorinated compounds by geographically diverse human gut microbiota.},
journal = {mBio},
volume = {17},
number = {10},
pages = {e0102626},
doi = {10.1128/mbio.01026-26},
pmid = {42671175},
issn = {2150-7511},
support = {23-2 ETH-047//ETH Research Grants/ ; //Uniscientia Foundation/ ; PZPGP2_209124/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Humans ; *Laccase/metabolism/genetics ; Biotransformation ; *Gastrointestinal Microbiome ; Phylogeny ; *Bacteria/classification/genetics/enzymology/metabolism ; Metagenome ; *Hydrocarbons, Fluorinated/metabolism ; },
abstract = {The growing prevalence of synthetic organofluorine substances in agrochemicals, food packaging, and consumer products has led to increasing gastrointestinal exposure, with potential consequences for human health. Despite the extreme stability of fluorinated compounds, several microbial pathways for their transformation are known, including those involving laccases, a type of multicopper oxidase. However, the functionality of laccases in the gut microbiome, a natural contact point between food-associated chemicals and microbial biotransformation pathways, is poorly defined. Through a multi-study analysis of 1,578 human gut metagenomes spanning a global gradient from hunter-gatherer societies to industrialized urban populations, we found that laccase-coding gene homologs are widely distributed in the human gut microbiome. We identified a significant association between both the abundance and phylogenetic diversity of laccase homologs and the degree of urbanization. As human gut microbial laccase activity has not been experimentally demonstrated, eight gut metagenome-derived laccases were heterologously expressed and screened for activity with a redox mediator system. Six of the eight laccases demonstrated activity. One of these gut microbial laccases, derived from Veillonella, and three previously characterized laccases were then tested for their capacity to deplete 11 different food-associated chemicals. The Veillonella laccase depleted the agrochemicals cyflumetofen and fluazinam, as well as the industrial chemical bisphenol AF, to a lesser extent. By linking global gut metagenomes with activity assays, this work demonstrates the untapped potential of mining human gut metagenomes for laccases and other microbial enzymes that can actively modify various agricultural and industrial chemicals.IMPORTANCEAs adverse effects of fluorinated compounds on human health are emerging, the responsible enzymes from the human gut microbiome of geographically diverse human cohorts mediating interactions with fluorinated compounds in the gastrointestinal tract remain poorly characterized. In a multi-study analysis of publicly available microbiome sequencing data, we linked the abundance, diversity, and phylogeny of laccases within the gut microbiome to the degree of urbanization of human cohorts and experimentally demonstrated the ability of these laccases to deplete a range of food-associated fluorochemicals. Another significant contribution of our study is in the integration of rural catchment areas as a quantitative metric of urbanization in gut microbiome metagenomics and enzyme activity surveys.},
}

Humans
*Laccase/metabolism/genetics
Biotransformation
*Gastrointestinal Microbiome
Phylogeny
*Bacteria/classification/genetics/enzymology/metabolism
Metagenome
*Hydrocarbons, Fluorinated/metabolism

@article {pmid42700718,
year = {2026},
author = {Maglione, A and Rosso, R and Tortarolo, D and Pantini, F and Pernice, S and Contaldo, SG and Lanzillo, R and Spiezia, AL and Cordioli, C and Virgilio, E and Masuzzo, F and Matta, M and Malucchi, S and Cavalla, P and Cocolin, L and Sirovich, R and Beccuti, M and Ferrocino, I and Cordero, F and Clerico, M and Rolla, S},
title = {Gut microbiome profiling at multiple sclerosis onset as a potential early prognostic marker of disease course: evidence from an observational cohort study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106470},
doi = {10.1016/j.ebiom.2026.106470},
pmid = {42700718},
issn = {2352-3964},
mesh = {Humans ; *Multiple Sclerosis/diagnosis/microbiology/etiology ; Prognosis ; Female ; Disease Progression ; *Gastrointestinal Microbiome ; Adult ; Male ; Biomarkers ; Metagenomics/methods ; Middle Aged ; Magnetic Resonance Imaging ; Metagenome ; Cohort Studies ; },
abstract = {BACKGROUND: Alterations in gut microbiome composition have been associated with multiple sclerosis (MS), but their impact on disease severity and early progression remains poorly understood. In this study we investigated whether gut microbiome profiling at diagnosis could identify microbial signatures associated with clinical and radiological features of early MS and provide prognostic information.

METHODS: We analysed the gut microbiome of 53 treatment-naïve patients with MS (pwMS) and 55 healthy donors (HD) using shotgun metagenomic sequencing, combined with clinical features collected over 1 year from diagnosis. To clarify whether gut microbiome composition at MS onset could have prognostic relevance, pwMS were stratified according to lesion burden, lesion localisation, and magnetic resonance imaging (MRI) activity.

FINDINGS: Overall beta diversity in Bacteria, Archaea, and Eukarya differed significantly between pwMS and HD (p-value <0.001, <0.02, <0.03, respectively). Within the MS group, glucocorticoid treatment at disease onset was the clinical factor most strongly associated with gut microbiota diversity. Stratification according to lesion burden, lesion localisation, and MRI activity identified two clinically distinct MS subgroups with different baseline clinical characteristics at onset (p-value <0.03) and different risk of early disease progression. The cluster associated with an unfavourable prognosis showed greater progression within 12 months and was enriched for motor symptoms and spinal cord lesions at diagnosis.

INTERPRETATION: Our findings suggest that gut microbiome alterations are detectable at the earliest stages of MS and are associated with clinical and radiological features linked to short-term disease evolution. Gut microbial profiling may therefore represent a promising early prognostic biomarker and may help to identify candidate targets for early intervention and therapeutic development in MS, although further validation in larger longitudinal cohorts is needed.

FUNDING: This study was supported by grants from the Italian Multiple Sclerosis Foundation, the Cassa di Risparmio di Torino Foundation, and the Italian Ministry of University and Research.},
}

Humans
*Multiple Sclerosis/diagnosis/microbiology/etiology
Prognosis
Female
Disease Progression
*Gastrointestinal Microbiome
Adult
Male
Biomarkers
Metagenomics/methods
Middle Aged
Magnetic Resonance Imaging
Metagenome
Cohort Studies

@article {pmid42716835,
year = {2026},
author = {Zhao, K and Vignolle, GA and Labus, JS and Mayer, EA and Vaughan, A and Dy, M and Vora, P and Hung, MW and Vossel, K and Gill, C and Del Rio, D and Stanton, C and Ross, RP and Cryan, JF and Kaddurah-Daouk, R and Zhang, Y and Church, A},
title = {Brain-gut crosstalk associated with brain ageing in young and mid-life adults: a multicohort cross-sectional study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106468},
pmid = {42716835},
issn = {2352-3964},
support = {R01 AG046171/AG/NIA NIH HHS/United States ; U01 AG088562/AG/NIA NIH HHS/United States ; R01 MH108348/MH/NIMH NIH HHS/United States ; R21 AG080425/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; RF1 AG059093/AG/NIA NIH HHS/United States ; K23 DK106528/DK/NIDDK NIH HHS/United States ; U01 AG061359/AG/NIA NIH HHS/United States ; RF1 AG057452/AG/NIA NIH HHS/United States ; R01 AG081322/AG/NIA NIH HHS/United States ; R01 AG081768/AG/NIA NIH HHS/United States ; R03 DK121025/DK/NIDDK NIH HHS/United States ; R01 MD015904/MD/NIMHD NIH HHS/United States ; U19 AG074879/AG/NIA NIH HHS/United States ; UH2 AG083254/AG/NIA NIH HHS/United States ; U24 AG056270/AG/NIA NIH HHS/United States ; R01 AG085518/AG/NIA NIH HHS/United States ; RF1 NS033310/NS/NINDS NIH HHS/United States ; UH3 AG083254/AG/NIA NIH HHS/United States ; RF1 AG058942/AG/NIA NIH HHS/United States ; RF1 AG051550/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Brain/physiology/diagnostic imaging/metabolism ; *Aging/physiology ; Female ; Magnetic Resonance Imaging ; Cross-Sectional Studies ; Male ; Adult ; Middle Aged ; Young Adult ; Cognition ; Gastrointestinal Microbiome ; Metabolomics/methods ; },
abstract = {BACKGROUND: Brain age deviation is a promising neuroimaging biomarker of brain health, but its relevance in young and mid-life adults and its biological underpinnings remain insufficiently characterised. We aimed to test whether a functional-connectivity-derived brain ageing index (BAI) captures reproducible variability in early brain ageing and whether it is associated with cognitive-affective function and gut-derived biological signatures.

METHODS: We analysed resting-state fMRI from a discovery cohort (n = 674) with validation in a replication cohort (n = 444) and an independent cohort (n = 344). Whole-brain functional connectivity was computed using a 100-region Schaefer parcellation, and Bayesian ridge regression was used to predict chronological age; BAI was defined as the age-bias-corrected residual (predicted brain age minus chronological age). We tested associations between BAI and cognitive and affective measures across cohorts. In the independent cohort, we applied multi-view sparse partial least squares to integrate stool metagenomic and metabolomic profiles with BAI, and performed KEGG pathway enrichment analyses on features with non-zero weights.

FINDINGS: Predicted brain age correlated with chronological age across cohorts (r = 0.50-0.59). Higher BAI was consistently associated with connectivity patterns involving posterior cingulate/praecuneus and medial frontal regions, poorer cognitive performance, particularly working memory and executive function, and greater depressive symptoms. Multi-omics integration identified microbial taxa and stool metabolites, including ceramides, 24-hydroxycholesterol, dicarboxylic acids, and inverse associations with estetrol, linked to BAI. Enrichment analyses suggested involvement of neuroimmune, vascular, synaptic, and mitochondrial pathways.

INTERPRETATION: A connectivity-derived BAI captures reproducible variability in early brain ageing and links large-scale brain network organisation to gut-derived biological signatures. These findings suggest that BAI captures individual variability associated with brain health-related phenotypes and support the potential association of peripheral brain-gut biological pathways in early brain ageing.

FUNDING: National Institutes of Health, National Institute on Ageing.},
}

Humans
*Brain/physiology/diagnostic imaging/metabolism
*Aging/physiology
Female
Magnetic Resonance Imaging
Cross-Sectional Studies
Male
Adult
Middle Aged
Young Adult
Cognition
Gastrointestinal Microbiome
Metabolomics/methods

@article {pmid42742206,
year = {2026},
author = {Boldogkői, Z and Tombácz, D},
title = {The canine gut microbiome as a translational model for human health and aging.},
journal = {mBio},
volume = {17},
number = {10},
pages = {e0195126},
doi = {10.1128/mbio.01951-26},
pmid = {42742206},
issn = {2150-7511},
support = {K 142674//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; ADV 152705//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; LP2020-8/2020//Magyar Tudományos Akadémia/ ; FK 142676//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; },
mesh = {Animals ; Dogs/microbiology ; *Aging ; Humans ; *Gastrointestinal Microbiome ; Translational Research, Biomedical ; Disease Models, Animal ; Models, Animal ; One Health ; },
abstract = {The domestic dog is increasingly recognized as a complementary translational model for microbiome research relevant to human health while also offering direct benefits for veterinary medicine. Dogs share environments and dietary exposures with humans and show substantial taxonomic and gene-content similarity to the human gut microbiome, although the apparent degree of similarity depends strongly on whether read recruitment, gene-catalog overlap, or functional overlap is assessed. Dogs also develop spontaneous chronic enteropathies, obesity-associated metabolic dysfunction, cancers, cognitive dysfunction, and behavioral disorders in which gut microbial changes can be examined under clinically realistic conditions. Their shorter, breed- and body-size-dependent lifespan permits repeated sampling across development, aging, disease progression, and treatment within practical timeframes. Breed structure, full-sibling cohorts, controlled dietary interventions, and access to clinically indicated samples from multiple anatomical compartments can strengthen selected study designs, although they do not provide the tighter genetic, environmental, and microbial control achievable in rodents. Here, we evaluate the research questions for which canine cohorts are especially informative, synthesize evidence linking canine and human disease-associated microbiomes, and critically assess aging, causal inference, and One Health applications. Major limitations include the need for breed and body-size stratification, heterogeneous diet and husbandry, incomplete treatment histories, the lack of routinely available gnotobiotic canine systems, and gaps in canine-specific reference resources. The canine system is therefore most informative when study designs exploit its clinical realism while acknowledging the tighter experimental control offered by reductionist models, positioning the dog as a complementary rather than a universally superior model.},
}

Animals
Dogs/microbiology
*Aging
Humans
*Gastrointestinal Microbiome
Translational Research, Biomedical
Disease Models, Animal
Models, Animal
One Health

@article {pmid42767310,
year = {2026},
author = {Guo, Y and Song, Z and Xie, H and Kong, Q and Bai, L and Zhang, J},
title = {Coupled salinity-redox gradients shape dissolved organic matter characteristics and its linkages with microbial functional potential in intertidal sediments.},
journal = {Environmental research},
volume = {309},
number = {Pt 1},
pages = {125713},
doi = {10.1016/j.envres.2026.125713},
pmid = {42767310},
issn = {1096-0953},
mesh = {*Geologic Sediments/microbiology/chemistry ; Seashore ; *Salinity ; Oxidation-Reduction ; *Dissolved Organic Matter/analysis/chemistry ; Estuaries ; *Microbiota ; },
abstract = {Estuarine intertidal sediments occur in freshwater-seawater mixing zones where hydrological processes simultaneously alter salinity and redox conditions, potentially regulating dissolved organic matter (DOM) transformation and microbial processes. However, how DOM and its interactions with microbial communities respond to salinity and redox gradients in natural intertidal environments remains poorly understood. Here, surface sediments and porewater from the Yellow River Estuary were analyzed by integrating constructed composite salinity and redox indicators, spectroscopy-based two-dimensional correlation analysis, metagenomics, and multivariate statistics. Results showed that overall DOM variation was significantly associated with both gradients, with redox showing stronger links to chromophoric and protein-like components, molecular-weight properties, and redox-sensitive aromatic, phenolic, oxygen-containing structures. In contrast, neither gradient was significantly associated with whole-community taxonomic composition or functional potential, whereas carbon- and nitrogen-related taxa and functions showed environmental associations. Multiple analyses consistently indicated that DOM covaried with selected functional modules, with more reducing conditions linked to DOM accumulation and fermentation-related functions, and higher salinity linked to microbially derived DOM and substrate-utilization functions. Variation partitioning attributed 20.7% of DOM variation and 39.6% of the main joint DOM-microbe pattern to the shared salinity-redox fraction, while redox retained a significant unique association with DOM (20.3%). Exploratory path models further suggested that DOM characteristics may link salinity-redox gradients to selective rather than community-wide microbial functional variation. Together, these findings support considering salinity and redox as a coupled environmental background and highlight DOM chemistry as a potential interface between their variation and selective microbial functional responses in intertidal sediments.},
}

*Geologic Sediments/microbiology/chemistry
Seashore
*Salinity
Oxidation-Reduction
*Dissolved Organic Matter/analysis/chemistry
Estuaries
*Microbiota

@article {pmid42785295,
year = {2026},
author = {Ziemski, M and Gehret, L and Simard, A and Castro Dau, S and Risch, V and Grabocka, D and Matzoros, C and Wood, C and Cabrera, PM and Hernández-Velázquez, R and Schärer, MR and Sandberg, F and Herman, C and Evans, K and Robeson, MS and Bolyen, E and Caporaso, JG and Bokulich, NA},
title = {MOSHPIT: Accessible, reproducible metagenome data science on the QIIME 2 framework.},
journal = {Cell genomics},
volume = {6},
number = {10},
pages = {101366},
doi = {10.1016/j.xgen.2026.101366},
pmid = {42785295},
issn = {2666-979X},
mesh = {*Metagenome/genetics ; *Software ; *Metagenomics/methods ; Microbiota/genetics ; Reproducibility of Results ; *Data Science ; Computational Biology/methods ; Humans ; },
abstract = {Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems but is fraught with technical hurdles. We introduce MOSHPIT (MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking; https://moshpit.qiime2.org)-software built on the QIIME 2/rachis framework (Q2F) that integrates best-in-class CAMI II- and LEMMI-validated metagenome tools with robust provenance tracking and multiple user interfaces-enabling streamlined, reproducible metagenome analysis for all expertise levels. By building on Q2F, MOSHPIT enhances scalability, interoperability, and reproducibility in complex workflows, democratizing and accelerating discovery at the frontiers of metagenomics.},
}

*Metagenome/genetics
*Software
*Metagenomics/methods
Microbiota/genetics
Reproducibility of Results
*Data Science
Computational Biology/methods
Humans

@article {pmid42785505,
year = {2026},
author = {Jiang, Y and Liu, B and Ding, Y and Li, L and Li, Z and Ren, Y and Zhong, C and Chen, J and Cui, X and Lu, A and Liu, J},
title = {Mineral-supported microbial functional differentiation across a vertical gradient in a vanadium-titanium magnetite mine.},
journal = {Environmental research},
volume = {309},
number = {Pt 1},
pages = {125725},
doi = {10.1016/j.envres.2026.125725},
pmid = {42785505},
issn = {1096-0953},
mesh = {*Mining ; *Vanadium ; *Ferrosoferric Oxide ; *Titanium ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification ; *Microbiota ; China ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Vanadium-titanium magnetite (VTM) mines are often associated with metal contamination, organic carbon depletion, and ecological degradation, yet how indigenous microbiomes respond to vertical geochemical heterogeneity remains poorly understood. Here, we investigated a ∼260 m vertical gradient in the Zhulan Iron Mine, China, by integrating elemental and mineralogical analyses with 16S rRNA gene amplicon and metagenomic profiling. Pronounced vertical stratification was observed. The lower-elevation section was enriched in vanadium (V) and Fe(II)-bearing minerals and harbored microbial communities with lower diversity but a more highly connected co-occurrence network. Representative lower-section taxa, including Thiobacillus, Sulfuricaulis, and Chloroflexota members, were linked to functional potentials for V-associated redox transformation, Fe/S metabolism, extracellular electron transfer, and autotrophic carbon fixation. These patterns suggest that Fe(II)-bearing minerals, particularly magnetite, may serve as potential inorganic electron sources supporting mineral-based lithotrophy and carbon fixation under metal-rich and organic-carbon-limited conditions. In contrast, the upper-elevation section exhibited lower V stress, higher microbial diversity, sparse vegetation, and enrichment of heterotrophic and plant-associated taxa, such as Sphingomonas, Flavisolibacter, and Actinomycetota, indicating a shift toward plant-supported microbial functions during early ecological recovery. Overall, this study links vertical geochemical stratification to microbial functional differentiation and highlights indigenous mineral-microbe interactions as a potential basis for targeted, low-input restoration strategies in metal-contaminated mining ecosystems.},
}

*Mining
*Vanadium
*Ferrosoferric Oxide
*Titanium
*Soil Microbiology
*Bacteria/genetics/metabolism/classification
*Microbiota
China
RNA, Ribosomal, 16S/genetics

@article {pmid42822627,
year = {2026},
author = {Zhou, L and Sha, H and Han, H and Wang, S and Li, S and Peng, X},
title = {Oxygen-associated differentiation of TBBPA-transforming activated sludge consortia and characterization of a cultivable Klebsiella degrader.},
journal = {Environmental research},
volume = {309},
number = {Pt 1},
pages = {125834},
doi = {10.1016/j.envres.2026.125834},
pmid = {42822627},
issn = {1096-0953},
mesh = {*Sewage/microbiology ; *Polybrominated Biphenyls/metabolism ; *Klebsiella/metabolism/genetics ; *Oxygen/metabolism ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; Anaerobiosis ; *Flame Retardants/metabolism ; *Microbial Consortia ; },
abstract = {Tetrabromobisphenol A (TBBPA), a widely used brominated flame retardant, poses increasing environmental and health concerns, yet how oxygen availability is associated with the assembly and degradation potential of TBBPA-transforming microbiomes remains poorly resolved. Here, ten enrichment consortia (six aerobic and four anaerobic) were established from activated sludge collected at six municipal wastewater treatment plants, achieving up to 63.46% TBBPA removal at an initial concentration of 5 mg/L. Metagenomic analysis revealed marked community divergence between the aerobic and anaerobic enrichment conditions, with Burkholderia predominating in the aerobic consortia and Klebsiella predominating in the anaerobic consortia. Read-mapping-based abundance profiling detected the HY4.102-affiliated Klebsiellapneumoniae population under both oxygen conditions, with higher relative abundance in the anaerobic consortia. Strain NCHT, isolated from the aerobic consortium NC_H, shared >99% ANI and AAI with HY4.102 and transformed TBBPA under both aerobic and anaerobic batch conditions. During aerobic incubation, strain NCHT transformed 51.0-68.4% of TBBPA across the tested concentrations, and UHPLC-MS/MS analysis yielded 17 putatively identified transformation intermediates consistent with an interconnected network involving debromination, hydroxylation, O-methylation, and β-scission. Molecular docking further prioritized DhmA, GSTs, CbdA/B, and PobB as candidate enzymes for debromination and downstream aromatic transformation, broadly consistent with the dehalogenation-related genes annotated in MAG HY4.102. Together, these findings provide an integrated community-to-strain framework for investigating TBBPA transformation.},
}

*Sewage/microbiology
*Polybrominated Biphenyls/metabolism
*Klebsiella/metabolism/genetics
*Oxygen/metabolism
Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism
Anaerobiosis
*Flame Retardants/metabolism
*Microbial Consortia

@article {pmid42862088,
year = {2026},
author = {Hoque, MN and Rahman, MS and Hossain, MG and Rahman, MT and Islam, T and Hossain, MA},
title = {Subclinical Mastitis and Antibiotic Exposure Reshape the Milk Bacteriome, Resistome, and Metabolic Functional Profiles in Dairy Cows.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70440},
pmid = {42862088},
issn = {2045-8827},
support = {LS20221764//Bangladesh Bureau of Educational Information & Statistics (BANBEIS), Ministry of Education/ ; },
mesh = {Animals ; *Milk/microbiology ; Female ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Cattle ; *Bacteria/drug effects/classification/genetics/isolation & purification ; *Mastitis, Bovine/microbiology/drug therapy ; Metagenomics ; *Microbiota/drug effects ; Drug Resistance, Bacterial ; },
abstract = {Subclinical mastitis (SCM) reduces milk yield and promotes antibiotic use, contributing to antimicrobial resistance. However, information on milk microbiome dysbiosis and resistome alterations in dairy cows remains limited. We performed shotgun metagenomic sequencing of 30 milk samples from 20 cows classified as SCM (n = 10), antibiotic-treated (ANT; n = 10), and healthy milk (HM; n = 10). Bacteriome, resistome, and metabolic functions were analyzed using bioinformatic tools. Microbial alpha diversity was significantly higher in HM than SCM and ANT samples (p < 0.05), with the greatest richness observed in Local Zebu and Middle-aged (5-8 years) cows. However, beta diversity did not differ significantly among groups (PERMANOVA, p > 0.05). A total of 665 bacterial species belonging to 15 phyla were identified, with Pseudomonadota, Actinomycetota, and Bacillota comprising 90%-99% of total abundance. SCM milk was dominated by Actinoalloteichus sp. (40.55%) and Vibrio furnissii (37.01%), while Staphylococcus aureus was enriched (1.74%) compared with HM and ANT (< 0.01%). ANT milk showed increased abundance of Acinetobacter johnsonii (10.52%), whereas HM samples contained beneficial commensals, including Pseudomonas lundensis, Bacteroides thetaiotaomicron, and Lactococcus lactis. Similar taxonomic shifts were observed across breeds and age groups. In total, 194 antimicrobial resistance genes (ARGs) were detected, with SCM harboring the largest repertoire (n = 161). Nevertheless, macrolide-, aminoglycoside-, and β-lactam-resistance genes were significantly enriched in ANT samples (p < 0.01). Correlation analyses linked Escherichia coli and A. johnsonii with multiple ARGs, while Acinetobacter and Pseudomonas were associated with lipid metabolism, membrane transport, and xenobiotic biodegradation pathways. These findings reveal bacteriome disruption, ARG enrichment, and functional alterations in SCM and antibiotic-exposed milk.},
}

Animals
*Milk/microbiology
Female
*Anti-Bacterial Agents/pharmacology/therapeutic use
Cattle
*Bacteria/drug effects/classification/genetics/isolation & purification
*Mastitis, Bovine/microbiology/drug therapy
Metagenomics
*Microbiota/drug effects
Drug Resistance, Bacterial

@article {pmid42865259,
year = {2026},
author = {Doane, MP and Martin, B and Kerr, E and Dinsdale, EA and Rangers, MM and Guida, L and Kyne, PM},
title = {Patterns of Functional Redundancy and Anaerobic Metabolic Potential Characterise the Skin Microbiome of a Critically Endangered Sawfish.},
journal = {Environmental microbiology},
volume = {28},
number = {10},
pages = {e70442},
pmid = {42865259},
issn = {1462-2920},
support = {//Charles Darwin University 2021 Institute of Advanced Studies (IAS) Rainmaker Start Up/ ; //Australian Marine Conservation Society (AMCS)/ ; //Flinders Accelerator for Microbiome Exploration/ ; },
mesh = {Animals ; *Skin Microbiome ; Anaerobiosis ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Endangered Species ; *Microbiota ; Metagenomics ; *Skin/microbiology ; Phylogeny ; },
abstract = {Using shotgun metagenomics of largetooth sawfish (Pristis pristis) skin and paired pool water samples, we provide the first taxonomic and functional characterisation of a sawfish skin microbiome and assess its ecological distinctiveness, assembly, and resilience relative to the surrounding water column. The skin microbiome was strongly host-associated and compositionally distinct, with lower taxonomic richness than the water column but dominated by Bacillota, particularly spore-forming Bacilli. Functional profiling revealed genes associated with sporulation, dormancy, anaerobic metabolism, and peptide transport, consistent with low-oxygen, low-flow conditions. In contrast, water-column microbiomes were more taxonomically diverse and enriched in phototrophic and polysaccharide-utilisation pathways. Sawfish skin communities exhibited patterns consistent with greater functional redundancy, with gene functions accumulating more rapidly per taxon. Together with greater among-individual taxonomic dispersion, this pattern is consistent with a host-filtered, lottery-like assembly process in which taxonomically variable communities maintain similar functional potential. The enrichment of dormancy and anaerobic pathways suggests the skin microbiome persists through periods of host quiescence and environmental stress while maintaining metabolic potential. Together, these results demonstrate that the sawfish skin supports a resilient, functionally robust microbiome distinct from ambient aquatic communities, highlighting the potential for integrating microbial functional data into conservation strategies for Critically Endangered vertebrates.},
}

Animals
*Skin Microbiome
Anaerobiosis
*Bacteria/classification/genetics/isolation & purification/metabolism
Endangered Species
*Microbiota
Metagenomics
*Skin/microbiology
Phylogeny

@article {pmid42869831,
year = {2026},
author = {Li, T and Song, ZX and Yang, DM and Ren, GX and Yin, Y and Yan, YG and Gao, J and Jiang, D and Liu, CS},
title = {[Diversity of endophytes in licorice from different habitats based on metagenomics and analysis of their correlation with accumulation of active ingredients].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {51},
number = {18},
pages = {5253-5261},
doi = {10.19540/j.cnki.cjcmm.20260415.406},
pmid = {42869831},
issn = {1001-5302},
mesh = {*Endophytes/genetics/classification/metabolism/isolation & purification ; *Glycyrrhiza/microbiology/chemistry/metabolism ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Ecosystem ; Glycyrrhizic Acid/metabolism/analysis ; Biodiversity ; },
abstract = {Licorice is an important TCM. Its medicinal quality mainly depends on the accumulation of active ingredients such as flavonoids(such as liquiritin and isoliquiritin) and triterpenoids(such as glycyrrhizic acid), and the endogenous microbial community is considered an important environmental factor influencing the synthesis of these components. To analyze the regulatory effect of endophytes on secondary metabolites of licorice, metagenomic sequencing and ultra-high performance liquid chromatography were used to compare and analyze the composition and function of endophytes in wild and cultivated licorice roots as well as their relationship with the main active ingredients. The results showed that the content of liquiritin, isoliquiritin, and glycyrrhizic acid in wild licorice was significantly higher than that in cultivated licorice. The metagenomic analysis annotated that the endophytes in wild licorice belonged to 31 phyla and 315 genera, while those in cultivated licorice belonged to 24 phyla and 125 genera. Among them, Rathayibacter, Plantibacter, and other genera were significantly enriched in wild licorice, while only Lysobacter was significantly enriched in cultivated licorice. Functional annotations indicated that the endophytes in wild licorice were enriched in pathways such as two-component systems, nitrogen metabolism, and aminoacyl tRNA synthesis, while those in cultivated licorice were enriched in pathways such as photosynthesis and carbon fixation. Further correlation analysis revealed that some endophyte genera(such as Phenylobacterium and Microbacterium) and functional pathways(such as signal transduction and terpenoid metabolism) were significantly positively correlated with the content of glycyrrhizic acid and liquiritin. In addition, the abundance of glycosyltransferases and cytochrome P450 in endophytes in wild licorice was significantly higher than that in cultivated licorice. This indicated that they had an enzymatic basis for participating in the synthesis of host glycosides. This research systematically reveals the differences in endophytic community structure, function, and accumulation of active ingredients between wild and cultivated licorice, providing a theoretical basis for understanding the microbial mechanism of endophytes regulating the quality of licorice, and also offering references for developing microbial fertilizers to improve the quality of licorice.},
}

*Endophytes/genetics/classification/metabolism/isolation & purification
*Glycyrrhiza/microbiology/chemistry/metabolism
Metagenomics
*Bacteria/classification/genetics/isolation & purification/metabolism
Ecosystem
Glycyrrhizic Acid/metabolism/analysis
Biodiversity

@article {pmid42870454,
year = {2026},
author = {Khafagy, ES and El-Kimary, GI and Al Saqr, A and Hegazy, WAH},
title = {The Oral Virome in Dental Caries: From Ecological Disruptors to Therapeutic Opportunities.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2604028},
doi = {10.4014/jmb.2604.04028},
pmid = {42870454},
issn = {1738-8872},
mesh = {*Dental Caries/therapy/virology/microbiology ; Humans ; Biofilms/growth & development ; *Virome ; *Mouth/virology/microbiology ; Bacteriophages/physiology/genetics ; Animals ; Dysbiosis ; Streptococcus mutans/virology ; Microbiota ; },
abstract = {Dental caries results from ecological dysbiosis of oral biofilms driven by frequent sugar exposure, yet the role of viruses, particularly bacteriophages, in this process remains underexplored. This review synthesizes current evidence on how the oral virome contributes to caries pathogenesis and examines emerging phage-based therapeutic strategies. The oral cavity harbors diverse viral communities, including eukaryotic viruses (herpesviruses, papillomaviruses) and prokaryotic viruses (bacteriophages). While herpesviruses like EBV, CMV, and HSV-1 do not directly demineralize teeth, they may act as ecological stressors by modulating host immunity, altering gingival crevicular fluid composition, and promoting inflammation that favors cariogenic bacterial activity. Bacteriophages function as key ecological regulators through "kill-the-winner" dynamics, maintaining microbial diversity by preying on dominant species. However, temperate phages can horizontally transfer genes encoding acidogenicity, biofilm formation, or antibiotic resistance, potentially accelerating dysbiosis. Metagenomic studies reveal distinct salivary phage signatures associated with caries, suggesting diagnostic potential. Preclinical evidence demonstrates that lytic phages targeting Streptococcus mutans (e.g., SMHBZ8, ΦAPCM01) disrupt biofilms in vitro and prevent caries in ex vivo and murine models. Phage-derived enzymes (endolysins, depolymerases) and peptides offer additional precision antimicrobials with minimal commensal disruption. Despite promising advances, significant translational gaps remain, including limited well-characterized phages, insufficient polymicrobial model testing, and absence of human clinical trials. Integrating virome ecology into caries management represents a paradigm shift from pathogencentric approaches toward ecosystem-based therapeutics, with phages offering targeted, self-replicating, and evolutionarily dynamic tools for restoring oral health.},
}

*Dental Caries/therapy/virology/microbiology
Humans
Biofilms/growth & development
*Virome
*Mouth/virology/microbiology
Bacteriophages/physiology/genetics
Animals
Dysbiosis
Streptococcus mutans/virology
Microbiota

@article {pmid42870579,
year = {2026},
author = {Zhu, YH and Li, X and Liu, Z and Liu, J and Ye, R and Xue, W and Jiang, G},
title = {DecBin: Bayesian-optimized deep clustering for long-read metagenomic binning.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
doi = {10.1093/bib/bbag571},
pmid = {42870579},
issn = {1477-4054},
support = {2025AIYJSZX-YB006//Fundamental Research Funds for the Central Universities/ ; BK20230102//Natural Science Foundation of Jiangsu Province/ ; 62402227//National Natural Science Foundation of China/ ; 42677660//National Natural Science Foundation of China/ ; 42477122//National Natural Science Foundation of China/ ; },
mesh = {*Metagenomics/methods ; Bayes Theorem ; Clustering Algorithms ; *Metagenome ; Microbiota ; Cluster Analysis ; Algorithms ; Autoencoder ; },
abstract = {Accurate metagenomic binning is essential for reconstructing microbial genomes, thereby facilitating the discovery of novel taxa, the identification of pathogens, and the characterization of antimicrobial resistance genes. Most existing methods are designed for assembled contigs and cannot be directly applied to raw long reads. Although a few dedicated long-read binning methods have emerged, challenges remain in bin-number estimation and representation learning. Here, we propose Deep Embedded Clustering for Long-read Binning (DecBin), an adaptive method for directly binning raw long reads through integrating a variational autoencoder (VAE), Bayesian optimization, and deep embedded clustering within a unified framework. Computational experiments on large-scale simulated and mock-community datasets demonstrate that DecBin outperforms state-of-the-art methods in both long-read binning and metagenome-assembled genome recovery, while also achieving strain-level resolution in a low-complexity natural microbiome. Further analysis shows that the advantage of DecBin is partly attributable to its Davies-Bouldin index-guided Bayesian optimization, which explicitly evaluates candidate cluster numbers using a global cluster-validity criterion, thereby improving bin-number estimation across communities of varying complexity. Meanwhile, joint fine-tuning of the VAE encoder and clustering layer enables clustering feedback to refine the latent space, yielding representations better aligned with genome partitions. These findings highlight the potential of adaptive deep clustering for metagenomic binning directly from raw long reads without prior assembly. The source code of DecBin is freely available at https://github.com/LorMeBioAI/DecBin.},
}

*Metagenomics/methods
Bayes Theorem
Clustering Algorithms
*Metagenome
Microbiota
Cluster Analysis
Algorithms
Autoencoder

@article {pmid42871043,
year = {2026},
author = {Zou, Y and Zhang, W and Gao, A and Fu, J and Sui, Y},
title = {Beyond community state types: vaginal microbial diversity and CST-IV signatures are associated with pregnancy in euploid embryo transfer cycles.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1881146},
pmid = {42871043},
issn = {1664-2392},
mesh = {Female ; Humans ; *Embryo Transfer/methods ; *Vagina/microbiology ; Pregnancy ; *Microbiota ; Pregnancy Outcome ; Adult ; Fertilization in Vitro ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Pregnancy Rate ; },
abstract = {BACKGROUND: Despite significant progress in assisted reproductive technology, in vitro fertilization (IVF) pregnancy rates remain suboptimal. Although the vaginal microbiome has been implicated in IVF outcomes, prior studies often overlooked embryonic aneuploidy, a major confounder. This study aimed to investigate the association between the vaginal microbiome and pregnancy outcomes in euploid embryo transfer cycles.

METHODS: This prospective study included 109 single euploid blastocyst transfer cycles. Upper vaginal swabs were collected on the transfer day and subjected to 16S rRNA gene sequencing. Microbial α- and β-diversity, community state types (CSTs), and differentially abundant taxa were compared between the clinical pregnancy (CP, n = 55) and non-clinical pregnancy (NCP, n = 54) groups.

RESULTS: The NCP group exhibited significantly higher vaginal microbial richness (Chao1, p = 0.029; ACE, p = 0.029) and distinct β-diversity compared with the CP group (R² = 0.049, p = 0.002), whereas CST distribution did not differ between groups. Within the non-Lactobacillus-dominant CST-IV subgroup, the CP group was relatively enriched in Bifidobacteriaceae (LDA = 5.0) with predicted fermentative pathways, whereas the NCP group showed higher relative abundances of Prevotella (LDA = -4.1), Dialister (LDA = -3.6), and Peptoniphilus (LDA = -2.3), accompanied by predicted tryptophan degradation and oxidative stress pathways.

DISCUSSION: These findings, derived mainly from computational prediction, suggest that fine-scale taxonomic and functional composition, rather than broad CST classification, may influence pregnancy outcomes following euploid embryo transfer, offering preliminary insights for microbiome-informed strategies to optimize reproductive outcomes. Future longitudinal studies incorporating shotgun metagenomics and metabolomics in independent cohorts are warranted to validate these preliminary observations and to clarify the dynamic association between vaginal microbiota and IVF pregnancy outcomes.},
}

Female
Humans
*Embryo Transfer/methods
*Vagina/microbiology
Pregnancy
*Microbiota
Pregnancy Outcome
Adult
Fertilization in Vitro
Prospective Studies
RNA, Ribosomal, 16S/genetics
Pregnancy Rate

@article {pmid42873652,
year = {2026},
author = {Pulvino, AT and Sardaro, MLS and Quinn, WG and Christopher, ER and Koenig, S and Lucore, JM and Vidal-Cruchez, O and Mallott, EK and Kuthyar, S and Lee, W and Chitta, S and Gray, S and Williams, LE and Curley, JP and Liechty, ER and Ben-Sahra, I and Amato, KR},
title = {Bile, sulphur and carbohydrate metabolic variation co-occur with host adiposity in mice colonized with primate microbiota.},
journal = {Microbial genomics},
volume = {12},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001848},
pmid = {42873652},
issn = {2057-5858},
mesh = {Animals ; Mice ; Humans ; *Adiposity ; *Bile/metabolism ; Macaca mulatta ; *Sulfur/metabolism ; *Carbohydrate Metabolism ; Multiomics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Cecum/microbiology ; Liver/metabolism ; Metagenomics ; Primates/microbiology ; Microbiota ; },
abstract = {Although mechanistic links between the microbiome and chronic disease are increasingly well defined, how microbiomes facilitate normal variation in host metabolism remains less clear. Building on our recent demonstration that pooled faecal inocula from different primate species can cause relative differences in mouse host adiposity, we define potential mechanisms by which this could occur. Using existing samples from germ-free mice inoculated with faecal samples from humans (Homo sapiens), rhesus macaques (Macaca mulatta) and squirrel monkeys (Saimiri boliviensis), we integrate shotgun metagenomics of caecal contents, liquid chromatography-MS-MS metabolomics of serum and caecal contents and hepatic RNA-sequencing. Our multi-omic analysis reveals that the relative increase in adiposity previously observed in macaque-donor mice is associated with differences in hepatic cysteine catabolism and bile metabolism pathway features. These data suggest that bile and sulphur co-metabolic variation may mediate increased bile pool hydrophobicity. We also observed variation in caecal microbiome composition as well as host hepatic retinol signalling and lipid metabolism between treatments. When considered together with the observation that macaque-donor mice consumed less food than the other treatment groups, our results support the hypothesis that increased bile pool hydrophobicity results in increased dietary energy extraction. Our findings provide a foundation for future mechanistic testing of new hypotheses for understanding how the intestinal microbiomes of different primate species regulate lipid homeostasis in a mouse host.},
}

Animals
Mice
Humans
*Adiposity
*Bile/metabolism
Macaca mulatta
*Sulfur/metabolism
*Carbohydrate Metabolism
Multiomics
Feces/microbiology
*Gastrointestinal Microbiome
Cecum/microbiology
Liver/metabolism
Metagenomics
Primates/microbiology
Microbiota

@article {pmid42152807,
year = {2026},
author = {Jing, M and Chen, X and Jiang, M and Fang, H and Zhu, X and Jin, X and Jiao, Y and Hou, N and Gong, W and Liu, A},
title = {Microbial and Metabolic Correlates of Endometrial Dysfunction in Polycystic Ovary Syndrome: A Translational Study.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {133},
number = {12},
pages = {2092-2102},
doi = {10.1111/1471-0528.70266},
pmid = {42152807},
issn = {1471-0528},
support = {//Hangzhou Joint Fund of the Zhejiang Provincial Natural Science Foundation of China/ ; //Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
mesh = {Female ; Humans ; *Polycystic Ovary Syndrome/microbiology/physiopathology/complications/metabolism ; Animals ; Pregnancy ; Adult ; *Gastrointestinal Microbiome/physiology ; Rats ; *Endometrium/physiopathology/metabolism ; Prospective Studies ; *Abortion, Spontaneous/microbiology/etiology ; *Dysbiosis/microbiology/complications ; Disease Models, Animal ; Case-Control Studies ; Pregnancy Outcome ; Isoleucine/blood ; Cellular Senescence ; Rats, Sprague-Dawley ; Stromal Cells ; Amino Acids, Branched-Chain/blood ; },
abstract = {OBJECTIVE: Women with polycystic ovary syndrome (PCOS) exhibit a substantially increased risk of miscarriage, yet the underlying mechanisms remain inadequately understood. This study aimed to investigate whether specific gut microbial dysbiosis and metabolic disturbance are associated with and may potentially contribute to endometrial dysfunction and adverse pregnancy outcomes in women with PCOS.

DESIGN: Prospective cohort study integrated with mechanistic experiments.

SETTING: Women's Hospital, School of Medicine, Zhejiang University, China (2022-2024).

POPULATION: A total of 110 women with PCOS and 110 age- and body mass index-matched controls were enrolled.

METHODS: We performed 16S rRNA and metagenomic sequencing of gut microbiota, with untargeted and targeted serum metabolomics. Functional validation was conducted using primary human endometrial stromal cells and a PCOS rat model intervened with Parabacteroides merdae (P. merdae) supplementation or faecal microbiota transplantation.

MAIN OUTCOME MEASURES: Gut microbiota composition, serum metabolites, endometrial senescence markers, and pregnancy outcomes.

RESULTS: Women with PCOS exhibited significantly higher miscarriage rates than controls, accompanied by a marked depletion of P. merdae abundance and elevated serum levels of branched-chain amino acids, particularly isoleucine. Exogenous isoleucine induced cellular senescence in human endometrial stromal cells in a dose-dependent manner. Restoration of P. merdae levels in the PCOS rat model resulted in decreased serum isoleucine levels, amelioration of the senescent endometrial phenotype, and reduction in the fetal resorption rate.

CONCLUSIONS: These findings suggest that P. merdae depletion and the concurrent accumulation of isoleucine may be associated with endometrial senescence and elevated risk of miscarriage, suggesting the possible involvement of a gut microbiota-metabolite pathway in PCOS-related reproductive dysfunction. These results also provide a mechanistic basis for future translational investigations.},
}

Female
Humans
*Polycystic Ovary Syndrome/microbiology/physiopathology/complications/metabolism
Animals
Pregnancy
Adult
*Gastrointestinal Microbiome/physiology
Rats
*Endometrium/physiopathology/metabolism
Prospective Studies
*Abortion, Spontaneous/microbiology/etiology
*Dysbiosis/microbiology/complications
Disease Models, Animal
Case-Control Studies
Pregnancy Outcome
Isoleucine/blood
Cellular Senescence
Rats, Sprague-Dawley
Stromal Cells
Amino Acids, Branched-Chain/blood

@article {pmid42861600,
year = {2026},
author = {Liu, Y and Ning, X and Liu, Y and Yu, Z and Liu, J and Xu, X and Zhao, J and Sun, S},
title = {Potential Roles of Escherichia coli in IgA Nephropathy: Evidence, Mechanistic Hypotheses and Microbiota-Targeted Strategies.},
journal = {Microbial biotechnology},
volume = {19},
number = {10},
pages = {e70455},
pmid = {42861600},
issn = {1751-7915},
support = {82470735//National Natural Science Foundation of China/ ; 2023TD-02//Shaanxi Provincial Health Commission/ ; 2023-ZDLSF-15//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLSF03-12//Key Research and Development Projects of Shaanxi Province/ ; },
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/therapy/pathology ; *Escherichia coli/pathogenicity ; Animals ; *Gastrointestinal Microbiome ; Immunoglobulin A/metabolism ; },
abstract = {IgA nephropathy (IgAN), the most common primary glomerular disease, involves mucosa-kidney axis dysregulation, with gut dysbiosis increasingly implicated in its pathogenesis. Certain Escherichia coli (E. coli) strains harbour virulence-associated features that promote intestinal colonization, barrier disruption and immune activation. Recent microbiome and metagenomic studies have reported an enrichment of E. coli in patients with IgAN, suggesting a potential link to the mucosa-kidney axis. Nevertheless, E. coli may contribute to IgAN through two major pathways. First, sustained LPS exposure may induce aberrant production of galactose-deficient IgA1 (Gd-IgA1) by stimulating B cells and activate the NLR family pyrin domain containing 3 (NLRP3) inflammasome in macrophages, thereby amplifying systemic and renal inflammation. Second, metabolic reprogramming is associated with increased circulating sphingosine-1-phosphate (S1P) and altered production of indole and trimethylamine (TMA); S1P may promote mesangial proliferation and fibrosis, whereas indole- and TMA-related pathways may contribute to tubulointerstitial injury and chronic kidney disease (CKD) progression. Beyond conventional gut microbiota-targeted interventions, emerging precision therapeutic strategies offer promising new directions for the etiological treatment of IgAN. This review summarizes E. coli virulence factors, pathogenesis, and host, environmental, and ecological factors driving its gut expansion in IgAN patients and outlines corresponding therapeutic strategies.},
}

Humans
*Glomerulonephritis, IGA/microbiology/therapy/pathology
*Escherichia coli/pathogenicity
Animals
*Gastrointestinal Microbiome
Immunoglobulin A/metabolism

@article {pmid42336879,
year = {2026},
author = {Feng, C and Lu, H and Bian, J and Wang, H and Jia, H and Li, X and Yang, M and Song, H and Tan, W and Wang, L},
title = {Phage-mediated expansion of the virulence gene types and enhanced ecological integration of pathogens in wild mice from human-impacted environments.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42336879},
issn = {2055-5008},
support = {2025ZD01900200//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; },
mesh = {Animals ; *Bacteriophages/genetics/physiology ; Mice ; *Virulence Factors/genetics ; Humans ; Metagenomics/methods ; Virulence/genetics ; *Bacteria/genetics/pathogenicity/classification/virology ; Microbiota ; Ecosystem ; Animals, Wild/microbiology ; },
abstract = {Wild mice are crucial in the transmission of infectious diseases; however, quantitative indicators for evaluating risk of virulence factors transmission are still lacking. We combined metagenomics and network analysis to evaluate ecological connectivity and functional gene profiles of microbial communities in wild mice from human-impacted environments (HE) and woodland environments (WE). We found that the pathogen centrality was significantly higher in HE than in WE (p < 0.001). Random Forest Model suggested habitats, phage abundances, and antibiotic resistance genes (ARGs) counts were crucial factors influencing virulence factor genes (VFGs) counts (p < 0.05). Structural Equation Model revealed that habitats affected VFGs (p < 0.01) via phages mediation (p < 0.05), while ARGs directly affected VFGs (p < 0.001). Although VFG counts were significantly higher in HE (p < 0.001), their expression levels did not differ between two habitats (p = 0.2952), indicating that VFG diversity was not necessarily accompanied by higher virulence expression. This study highlights the mediating role of phages and the direct contribution of ARGs in shaping the virulence-associated genetic repertoire, underscoring the importance of a One Health perspective that considers human impacts on microbial communities in infectious disease surveillance.},
}

Animals
*Bacteriophages/genetics/physiology
Mice
*Virulence Factors/genetics
Humans
Metagenomics/methods
Virulence/genetics
*Bacteria/genetics/pathogenicity/classification/virology
Microbiota
Ecosystem
Animals, Wild/microbiology

@article {pmid42458473,
year = {2026},
author = {Gupta, E and Sharma, S and Tikar, SN and Dash, PK},
title = {Exploration of viral diversity in Aedes mosquitoes employing different shotgun metagenomic data analysis pipelines.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {42458473},
issn = {1743-422X},
mesh = {Animals ; *Aedes/virology ; *Metagenomics/methods ; India ; Computational Biology/methods ; Genome, Viral ; *Virome ; *Mosquito Vectors/virology ; *Viruses/classification/genetics/isolation & purification ; *Genetic Variation ; Larva/virology ; Shotgun Sequencing ; },
abstract = {Metagenomics or metaviromics is emerging as a powerful technology for pathogen surveillance and pandemic preparedness. Mosquitoes are important vectors for transmission of many emerging viruses responsible for numerous outbreaks. Monitoring mosquitoes becomes essential to investigate its virome which leads to understanding of disease dynamics and allow preventive actions. In this study, shotgun metagenomic methodology using Ion GeneStudio S5 System was optimized for exploration of viral diversity. A total of 1913 Aedes larvae were collected from Central India during post monsoon season of 2024. Aedes larvae reared to adulthood and processed for sequencing using Ion Torrent S5 platform. Computational analyses were performed using three bioinformatic pipelines: Chan Zuckerberg ID (CZ ID), Genome Detective Platform and the Galaxy Platform. A mock database of 11 known viruses was created as well as publicly available NCBI Sequence Read Archive (SRA) datasets were used to validate all three pipelines. In terms of detection accuracy, Genome Detective and CZ ID performed exceptionally well and therefore may be suitable for future mosquito virome surveillance studies. We found presence of viruses viz. Alphamesonivirus cavallynense and Phasivirus phasiense dominating in all samples. Dengue virus was detected in one sample by CZ ID, whereas Wenzhou sobemo-like virus, Hubei mosquito virus 2, Cell fusing agent virus found most commonly among samples. Other viruses found like Aedes anphevirus (AeAV; genus Glybovirus), Aedes totivirus, Verdadero virus and Chaq-like virus. Variation in the result among different pipelines are likely attributable to incorporation of different viral reference databases, classification algorithms, metrics and analysis parameters. To the best of our knowledge, this study represents the first metagenomic study of mosquitoes using Ion GeneStudio S5 platform in India. The findings provide a comparative evaluation of the metagenomic pipelines and elucidates detailed information of each pipeline and its working for future studies.},
}

Animals
*Aedes/virology
*Metagenomics/methods
India
Computational Biology/methods
Genome, Viral
*Virome
*Mosquito Vectors/virology
*Viruses/classification/genetics/isolation & purification
*Genetic Variation
Larva/virology
Shotgun Sequencing

@article {pmid42464266,
year = {2026},
author = {He, C and Du, Y and Lloyd, KG and Vishnivetskaya, TA and Rivkina, EM and Jiang, H and Liang, R},
title = {Diversity and potential ecological roles of viruses in Pleistocene permafrost.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {},
pmid = {42464266},
issn = {1741-7007},
mesh = {*Permafrost/virology ; Siberia ; *Viruses/classification/genetics/isolation & purification ; Arctic Regions ; *Biodiversity ; Metagenomics ; },
abstract = {BACKGROUND: Ancient permafrost, formed during past glacial periods, is widespread in Siberia and other Arctic regions. Even though these soils have remained below 0 °C over geological time periods, the widespread presence of bacteria and archaea in permafrost is well documented. However, the diversity of viruses in ancient permafrost of different geological ages and their potential ecological roles are still poorly understood.

RESULTS: We applied metagenomics to characterize viruses from Middle to Late Pleistocene permafrost sediments from Siberia. A total of 2697 viral operational taxonomic units (vOTUs) were recovered through metagenomic assembly and virus identification. Viral diversity in the Middle Pleistocene permafrost was much higher than that in the Late Pleistocene. The virus communities at different depths of the Middle Pleistocene permafrost showed great similarity to each other but were significantly different from those of the Late Pleistocene, with Azeredovirinae, Peduoviridae, and Fiersviridae being the predominant viruses in Pleistocene permafrost. The viruses were predicted to carry auxiliary metabolic genes potentially involved in cold adaptation and elemental (C and N) biogeochemical cycling in ancient permafrost. The virus-host prediction revealed that microorganisms such as bacteria and archaea are the main hosts and only a few eukaryotic hosts were identified.

CONCLUSIONS: Our results show that permafrost viral communities in Siberia exhibit remarkable diversity and may have played a significant ecological role in ancient permafrost over geological time. While the release of viruses from thawing deep permafrost could pose a relatively small risk to human health and environment, it could have significant impacts on the carbon cycle, potentially influencing climate change feedback in permafrost regions.},
}

*Permafrost/virology
Siberia
*Viruses/classification/genetics/isolation & purification
Arctic Regions
*Biodiversity
Metagenomics

@article {pmid42571869,
year = {2026},
author = {Manzoor, M and Leskelä, J and Könönen, E and Lahti, L and Putaala, J and Pussinen, PJ and Paju, S},
title = {Shotgun Metagenomic Analysis Reveals Taxonomic and Functional Transitions in the Salivary Microbiome During Periodontal Disease Progression.},
journal = {Journal of clinical periodontology},
volume = {53},
number = {11},
pages = {1650-1662},
doi = {10.1111/jcpe.70184},
pmid = {42571869},
issn = {1600-051X},
support = {296541//Research Council of Finland/ ; 316777//Research Council of Finland/ ; 355532//Research Council of Finland/ ; 340750//Research Council of Finland/ ; 369310//Research Council of Finland/ ; 286246//Research Council of Finland/ ; 318075//Research Council of Finland/ ; 322656//Research Council of Finland/ ; //Finnish Dental Society Apollonia/ ; //Sigrid Juselius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; },
mesh = {Humans ; *Saliva/microbiology ; Disease Progression ; *Metagenomics/methods ; Cross-Sectional Studies ; *Microbiota/genetics ; Female ; Adult ; Male ; *Periodontal Diseases/microbiology ; Gingivitis/microbiology ; Periodontitis/microbiology ; },
abstract = {AIM: To characterise multi-kingdom salivary microbiome profiles across clinically defined periodontal states and identify stage-specific taxonomic and functional alterations using shotgun metagenomic sequencing.

MATERIALS AND METHODS: In this cross-sectional study, 204 adults (mean age 40.3 ± 7.6 years) from the SECRETO study (NCT01934725) underwent clinical and radiographic oral examinations and were classified into six periodontal groups: periodontal health, localised gingivitis, generalised gingivitis, gingivitis with pockets, mild periodontitis (Stages I-II) and severe periodontitis (Stages III-IV). Saliva samples were analysed using shotgun metagenomic sequencing to evaluate microbial diversity, taxonomic composition and functional pathways.

RESULTS: Beta diversity differed between periodontal health and the different disease states (Bray-Curtis: p = 0.049; Jaccard: p = 0.043). Gingivitis with pockets and severe periodontitis showed a significant enrichment of disease-associated species Porphyromonas gingivalis , Tannerella forsythia , Treponema denticola , Porphyromonas endodontalis , Fusobacterium nucleatum and Parvimonas micra . Among non-bacterial taxa, Candida, Moineauvirus, Pyricularia and Roseolovirus were the predominant genera. A composite metagenomic classifier showed high discriminative performance for gingivitis with pockets (AUC = 0.90; 95% CI: 0.770-1.000) and severe periodontitis (AUC = 0.865; 95% CI: 0.762-0.968).

CONCLUSION: Salivary multi-kingdom microbiome transitions closely reflect the progression of periodontal disease and provide promising biomarkers for identifying at-risk individuals.},
}

Humans
*Saliva/microbiology
Disease Progression
*Metagenomics/methods
Cross-Sectional Studies
*Microbiota/genetics
Female
Adult
Male
*Periodontal Diseases/microbiology
Gingivitis/microbiology
Periodontitis/microbiology