@article {pmid41633490,
year = {2026},
author = {Kelly, MS and Huang, CY and Kim, M and Haghnazari, D and Baig, A and Sun, Y and Lenneman, BR and Tisza, MJ and Cunningham, A and Gold, D and Phipatanakul, W and Lai, PS},
title = {Nasal microbiome and phageome profiles are associated with prospective respiratory viral infection risk in school-age children.},
journal = {The Journal of allergy and clinical immunology},
volume = {158},
number = {2},
pages = {408-420},
pmid = {41633490},
issn = {1097-6825},
support = {U01 AI110397/AI/NIAID NIH HHS/United States ; F32 AI194859/AI/NIAID NIH HHS/United States ; R21 AI175965/AI/NIAID NIH HHS/United States ; R01 AI144119/AI/NIAID NIH HHS/United States ; R21 AI178155/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Child ; *Microbiota ; Female ; *Respiratory Tract Infections/microbiology/epidemiology/virology ; Male ; *Asthma/microbiology/epidemiology/virology ; Prospective Studies ; *Virome ; *Virus Diseases/epidemiology/microbiology ; *Nose/microbiology ; Rhinovirus ; },
abstract = {BACKGROUND: Respiratory viral infections are common and can trigger asthma exacerbations in children. The roles of the nasal microbiome and phageome (viruses that infect microbes) are not well understood.

OBJECTIVE: We sought to characterize the epidemiology of respiratory viral infections and the interplay between the nasal microbiome, phageome, and viral infections in school-age children with asthma.

METHODS: We performed metagenomic sequencing and quantitative RT-PCR detection of respiratory viruses on 375 nasal samples from 227 school-age children with asthma collected routinely 3 times over a year. Surveys on parent-reported cold and asthma symptoms were administered routinely every 2 months. We evaluated multikingdom changes to the nasal microbiome during infection. A sparse partial least-squares discriminant analysis model identified microbial signatures associated with prospective viral infection risk.

RESULTS: Respiratory viruses were identified in 124 (33%) samples, with rhinovirus being the most prevalent. Cold and asthma symptoms within the previous 14 days had a sensitivity of 79% and 59%, respectively, for quantitative RT-PCR-confirmed infection. Respiratory viral infection increased asthma symptoms and was accompanied by loss of nasal bacterial diversity and a reproducible bloom of pathobionts with no change in the mycobiome or phageome. A baseline bacteriome-dominated profile was protective (adjusted odds ratio, 0.41 [95% CI, 0.25-0.67]; P < .001), whereas phageome profiles increased risk (adjusted odds ratio, 3.74 [95% CI, 1.85-7.55]; P < .001) of viral infection. Specific phages inversely correlated with Staphylococcus epidermidis abundance, the most protective commensal against infection risk.

CONCLUSIONS: The nasal microbiome and phageome exert opposing influences on respiratory viral infection risk, highlighting their potential roles in modulating susceptibility to viral infections.},
}

Humans
Child
*Microbiota
Female
*Respiratory Tract Infections/microbiology/epidemiology/virology
Male
*Asthma/microbiology/epidemiology/virology
Prospective Studies
*Virome
*Virus Diseases/epidemiology/microbiology
*Nose/microbiology
Rhinovirus

@article {pmid41819166,
year = {2026},
author = {Zhao, X and Zhang, J and Li, Y and Wang, Q and Li, J and Xia, Y and Zha, M and Chen, Y},
title = {Elucidating the microbiota-metabolite interplay in Hurood and Chula: An integrated multiomics investigation.},
journal = {Journal of dairy science},
volume = {109},
number = {8},
pages = {7965-7980},
doi = {10.3168/jds.2025-28134},
pmid = {41819166},
issn = {1525-3198},
mesh = {Volatile Organic Compounds/analysis/metabolism ; *Microbiota ; *Cheese/microbiology/analysis ; Multiomics ; Gas Chromatography-Mass Spectrometry ; Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {The differences in flavor and quality between Hurood and Chula, two traditional Xilingol cheeses, are primarily due to variations in their production processes. Therefore, how heating and kneading affect their microbial, nonvolatile metabolite, and volatile organic compound (VOC) composition warrants exploration. In this study, shotgun metagenomic sequencing revealed the differential micro-organisms between Hurood and Chula. Ultra-performance liquid chromatography-tandem MS identified 47 differential metabolites. Among these, organic acids and their derivatives, benzene and substituted derivatives, free fatty acids (FFA), and lysophosphatidylcholines showed the highest content in Chula, whereas lactose, melibiose, and histamine were significantly enriched in Hurood, suggesting that the heating and kneading process affected galactose and histidine metabolic pathways. In contrast, headspace solid-phase microextraction GC-MS identified 4 differential VOC with elevated levels in Hurood. These compounds functioned as key aroma contributors, imparting richer and more complex aroma characteristics that included creamy, oily, fatty, caramel, coconut, woody, spice, and maple notes. Correlation analysis indicated that the differential micro-organisms were involved in metabolite dynamics and VOC accumulation and further revealed that they drove the directed accumulation of VOC through regulating FFA release and transformation and by regulating the Maillard reaction of small peptides, thereby underpinning their distinct flavor profiles. This study provides important insights into the heating- and kneading-induced formation of flavor and quality in traditional Xilingol cheeses, thereby facilitating the precise control of traditional processes and subsequent product quality improvement.},
}

Volatile Organic Compounds/analysis/metabolism
*Microbiota
*Cheese/microbiology/analysis
Multiomics
Gas Chromatography-Mass Spectrometry
Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid41871943,
year = {2026},
author = {Awoniyi, M and El Hag, M and Hernandez, J and Yang, Q and Evans, N and Nemet, I and Ngo, B and Coskuner, D and Zhou, J and Farmer, M and Su, L and Zhou, H and Roach, J and Stappenbeck, T and Sartor, RB},
title = {Dysbiotic microbiota trigger colitis-associated colorectal cancer and imprint a distinctive bile acid profile in a PSC-IBD model.},
journal = {Gut},
volume = {75},
number = {9},
pages = {1711-1725},
doi = {10.1136/gutjnl-2025-336675},
pmid = {41871943},
issn = {1468-3288},
support = {U01 CA280829/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice ; *Cholangitis, Sclerosing/complications/microbiology ; Mice, Knockout ; *Dysbiosis/complications/microbiology ; Disease Models, Animal ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/physiology ; *Colitis-Associated Neoplasms/microbiology/metabolism/etiology ; *Colorectal Neoplasms/microbiology/etiology ; *Colitis, Ulcerative/microbiology/complications ; Male ; Mice, Inbred C57BL ; Colitis/microbiology ; Humans ; },
abstract = {BACKGROUND: Primary sclerosing cholangitis-associated UC (PSC-UC) carries excess colorectal neoplasia despite often mild-appearing endoscopy, implicating persistent microscopic inflammation and microbiota-bile acid (BA) dysfunction.

OBJECTIVE: To test whether PSC-UC neoplasia is driven by transferable microbiota-mediated inflammation linked to secondary BA loss.

DESIGN: Surveillance colonoscopies (2012-2022) from PSC-UC (n=251) and UC-only (n=8839) were compared for segmental endoscopic/histological activity and dysplasia. We generated multidrug resistance protein 2 (MDR2)[-/-] × interleukin (IL)-10[-/-] double-knockout (DKO) mice and used germ-free (GF) derivation, faecal microbiota transplantation (FMT), antibiotic conditioning and cohousing with shotgun metagenomics and liquid chromatography-tandem mass spectrometry BA profiling.

RESULTS: PSC-UC showed greater inflammatory activity and a right-shifted dysplasia burden versus UC-only. Under specific-pathogen-free conditions, DKO mice developed early right-predominant colitis and multifocal dysplasia progressing with age. DKO communities were depleted of 7α-dehydroxylation capacity with near absence of deoxycholic and lithocholic acids and no enrichment of canonical bacterial genotoxins. GF DKO mice were protected, whereas live DKO donor FMT reinstated severe colitis and dysplasia; sterile-filtered stool supernatant was inactive. IL-10[-/-] donor FMT or cohousing attenuated colitis and increased recipient secondary BA, whereas wild-type/MDR2[-/-] donor transfers were non-colitogenic. In GF DKO mice, direct deoxycholic acid repletion caused hepatotoxicity.

CONCLUSION: PSC-UC neoplasia associates with transmissible microbiota-dependent inflammation and secondary BA deficiency. Controlled restoration of BA-transforming microbial functions, rather than indiscriminate secondary BA replacement, is a rational translational direction.},
}

Animals
*Bile Acids and Salts/metabolism
Mice
*Cholangitis, Sclerosing/complications/microbiology
Mice, Knockout
*Dysbiosis/complications/microbiology
Disease Models, Animal
Fecal Microbiota Transplantation
*Gastrointestinal Microbiome/physiology
*Colitis-Associated Neoplasms/microbiology/metabolism/etiology
*Colorectal Neoplasms/microbiology/etiology
*Colitis, Ulcerative/microbiology/complications
Male
Mice, Inbred C57BL
Colitis/microbiology
Humans

@article {pmid42104558,
year = {2026},
author = {Luo, X and Lei, Z and Fang, D and Chen, H and Qian, L and Jin, C and Wang, X and Liu, X and Liu, H and Wang, Y},
title = {Integrated multi-omics decipher the complex nodule microbiota and distinct Frankiaceae symbiotic traits in wild actinorhizal plants.},
journal = {The New phytologist},
volume = {251},
number = {5},
pages = {2832-2851},
pmid = {42104558},
issn = {1469-8137},
support = {32300265//Young Scientists Fund of the National Natural Science Foundation of China/ ; },
mesh = {*Symbiosis/genetics ; Multiomics ; *Root Nodules, Plant/microbiology ; *Microbiota/genetics ; Phylogeny ; Frankia/genetics ; Fabaceae/microbiology ; Transcriptome/genetics ; },
abstract = {Actinorhizal plants are ecologically important pioneer species in temperate regions, capable of nitrogen-fixing root nodule symbiosis with Frankiaceae bacteria. Despite their significance within the nitrogen-fixing clades (NFC), multi-omics studies of actinorhizal symbiosis remain scarce. We profiled prokaryotic communities in the rhizosphere, root, and/or nodule compartments from five phylogenetically representative actinorhizal species, three legumes, and four nonnodulated NFC species using 16S rDNA sequencing. Transcriptomic and metagenomic analyses were performed on actinorhizal roots and nodules, respectively. Metagenome-assembled genomes revealed four novel Frankiaceae species. Frankiae relative abundance levels in nodules were generally lower than rhizobia in legumes. Actinorhizal nodules harbour diverse bacterial taxa, which exhibit predominantly positive interactions, with Frankiae forming a tightly interacting subgroup. Actinorhizal plants engage actively with soil microbiota, recruiting a specific rhizosphere community enriched with beneficial microbes, including ammonia-oxidising archaea. Many symbiotic mechanisms in nodulating host plants are conserved and derived from pre-existing molecular modules. Our analysis suggests the phosphoinositide signalling likely functions in actinorhizal symbiotic signal transduction. However, Frankiae exhibit fundamentally different symbiotic functional characteristics compared to rhizobia, reflecting less intimate symbiosis, which might favour the life-history strategies of temperate perennial actinorhizal plants.},
}

*Symbiosis/genetics
Multiomics
*Root Nodules, Plant/microbiology
*Microbiota/genetics
Phylogeny
Frankia/genetics
Fabaceae/microbiology
Transcriptome/genetics

@article {pmid42162897,
year = {2026},
author = {Wang, C and Liu, X and Wan, S and Xie, F and Dai, J and Chen, W and Qu, L and Zhang, L and Li, N and Du, X and Zhu, H and Hua, J},
title = {BLOS1 overexpression enhances goat immune response to Brucella LPS through augmented autophagy with associated gut microbiota remodeling.},
journal = {Veterinary journal (London, England : 1997)},
volume = {318},
number = {},
pages = {106706},
doi = {10.1016/j.tvjl.2026.106706},
pmid = {42162897},
issn = {1532-2971},
mesh = {Animals ; *Goats/immunology/genetics ; *Autophagy/genetics ; *Lipopolysaccharides/immunology/pharmacology ; *Gastrointestinal Microbiome/immunology ; Macrophages/immunology ; *Brucellosis/immunology/veterinary/microbiology ; *Goat Diseases/immunology/microbiology ; Immunity, Innate ; Leukocytes, Mononuclear/immunology ; },
abstract = {Biogenesis of lysosome-related organelles complex 1 subunit 1 (BLOC1S1, also known as BLOS1) is a key gene involved in phagosome-lysosome maturation, transport, and autophagosome fusion, and it plays a crucial role in host resistance to Brucella infection. This study aimed to examine the effects of BLOS1 overexpression (oeBLOS1) on the stress response of goat macrophages and on intestinal microbiota composition. Peripheral blood mononuclear cells (PBMCs) were isolated from oeBLOS1 and wild-type (WT) goats and differentiated into macrophages. These macrophages were then stimulated with Brucella LPS to assess cytokine secretion and autophagy levels. Metagenomic sequencing was also performed to analyze the structural and functional profiles of the rectal fecal microbiota in these goats. After Brucella LPS stimulation, oeBLOS1 goat macrophages rapidly activated the NF-κB and TLR4 signaling pathways, promoting the synthesis and secretion of cytokines such as TNF-α (P < 0.05). Brucella LPS challenge also significantly increased the transcription of autophagy-related genes such as LAMP2 and BECN1, enhancing autophagic activity and bacterial clearance (P < 0.05). Furthermore, oeBLOS1 altered the intestinal microbiota, significantly enriching pathways linked to membrane transport and cell motility, and reducing the abundance of virulence factors and opportunistic pathogens, which may contribute to intestinal immune homeostasis. In summary, oeBLOS1 may help counteract Brucella LPS-induced infection by promoting the immune response, enhancing autophagy. In addition, it is associated with remodeling gut microbial function, suggesting a potential role in disease resistance.},
}

Animals
*Goats/immunology/genetics
*Autophagy/genetics
*Lipopolysaccharides/immunology/pharmacology
*Gastrointestinal Microbiome/immunology
Macrophages/immunology
*Brucellosis/immunology/veterinary/microbiology
*Goat Diseases/immunology/microbiology
Immunity, Innate
Leukocytes, Mononuclear/immunology

@article {pmid42210528,
year = {2026},
author = {Zhou, X and Zhang, M and Zhou, J and Han, J},
title = {Multi-target effects of Limosilactobacillus reuteri RE225 on hyperuricemia through xanthine oxidase inhibition, nucleoside degradation, gut microbiota modulation, and renal TLR4-NF-κB suppression.},
journal = {Journal of the science of food and agriculture},
volume = {106},
number = {12},
pages = {7197-7208},
pmid = {42210528},
issn = {1097-0010},
support = {2024S138//Ningbo Public Welfare Research Program/ ; //K.C. Wong Magna Fund of Ningbo University/ ; },
mesh = {Animals ; *NF-kappa B/metabolism/genetics ; *Xanthine Oxidase/metabolism/antagonists & inhibitors/genetics ; *Toll-Like Receptor 4/genetics/metabolism ; Mice ; *Kidney/metabolism/drug effects ; *Hyperuricemia/metabolism/microbiology/genetics/drug therapy ; *Gastrointestinal Microbiome/drug effects ; Male ; *Limosilactobacillus reuteri/physiology ; *Probiotics/administration & dosage ; Uric Acid/metabolism/blood ; Humans ; Mice, Inbred C57BL ; Bacteria/classification/isolation & purification/genetics/metabolism ; Signal Transduction ; },
abstract = {BACKGROUND: Hyperuricemia, a major risk factor for gout and kidney disease, requires safe and effective dietary strategies beyond conventional pharmacotherapy. This study investigated the multi-target effects of the food-grade probiotic Limosilactobacillus reuteri RE225 on hyperuricemia. It was evaluated in vitro for xanthine oxidase (XOD) inhibition and nucleoside degradation, and in vivo in hyperuricemic mice gavaged daily with low or high doses of RE225 (1 × 10[6] or 1 × 10[9] CFU). Serum uric acid (UA), XOD activity, inflammatory cytokines, intestinal permeability markers - fluorescein isothiocyanate-dextran (FITC-dextran), lipopolysaccharide (LPS), and d-lactate - and renal TLR4/NF-κB signaling were quantified. Fecal metagenomics and Kyoto Encyclopedia of Genes and Genomes ortholog (KO) profiling were used to assess microbiota structure and function.

RESULTS: Limosilactobacillus reuteri RE225 dose-dependently inhibited XOD and degraded more than 50% of nucleosides in vitro. In vivo, RE225 reduced serum urate, restored intestinal barrier function, suppressed inflammation, and downregulated renal TLR4/NF-κB signaling. Metagenomic analysis showed that L. reuteri RE225 reversed UA-induced loss of microbial richness and evenness, enriched Faecalibaculum and Erysipelotrichaceae, and shifted functional profiles from proliferation- and inflammation-related modules (K02315, K02970, and K03496) toward carbohydrate utilization and genetic stability pathways (K01784 and K07491).

CONCLUSION: Limosilactobacillus reuteri RE225 shows promise as a dietary intervention for the management of hyperuricemia. © 2026 Society of Chemical Industry.},
}

Animals
*NF-kappa B/metabolism/genetics
*Xanthine Oxidase/metabolism/antagonists & inhibitors/genetics
*Toll-Like Receptor 4/genetics/metabolism
Mice
*Kidney/metabolism/drug effects
*Hyperuricemia/metabolism/microbiology/genetics/drug therapy
*Gastrointestinal Microbiome/drug effects
Male
*Limosilactobacillus reuteri/physiology
*Probiotics/administration & dosage
Uric Acid/metabolism/blood
Humans
Mice, Inbred C57BL
Bacteria/classification/isolation & purification/genetics/metabolism
Signal Transduction

@article {pmid42231497,
year = {2026},
author = {Vayena, G and Giangeri, G and Gaspari, M and Ghofrani-Isfahani, P and Tsapekos, P and Kougias, PG and Angelidaki, I},
title = {Ecological and metabolic restructuring of anaerobic microbiomes under sulfate stress via magnetite-enhanced cooperative networks.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42231497},
issn = {2049-2618},
mesh = {*Sulfates/metabolism ; *Ferrosoferric Oxide/metabolism/pharmacology ; Methane/metabolism/biosynthesis ; Anaerobiosis ; Bioreactors/microbiology ; Hydrogen Sulfide/metabolism ; Metagenomics/methods ; *Microbiota ; *Bacteria, Anaerobic/metabolism/genetics/classification ; *Bacteria/metabolism/genetics/classification ; Microbial Interactions ; },
abstract = {BACKGROUND: Anaerobic digestion systems with elevated sulfate often suffer reduced methane yields, challenged by the competition between sulfate-reducing bacteria and methanogens, and inhibited by hydrogen sulfide introduction. The present work explores the role of magnetite in improving anaerobic digestion performance under elevated sulfate conditions by chemically influencing the anaerobic system and reshaping microbial interaction patterns.

RESULTS: Magnetite addition mitigated hydrogen sulfide toxicity via precipitation and increased methane production by 19%. Genome-centric metagenomics revealed a notable proliferation of the methanogenic population in the magnetite-amended reactors, consistent with the elevated methane output in the presence of both magnetite and sulfate, without suppressing sulfate-reducing, homoacetogenic, or syntrophic acetate-oxidizing activity. Magnetite was associated with enhanced methanogenesis and a strengthened cooperative syntrophic network among the four microbial guilds, in line with more efficient carbon and electron flow despite sulfate stress. Community genome-scale metabolic modeling supported these trends, validating the feasibility of the proposed interaction network and indicating that interspecies metabolite transfer between partners is stoichiometrically feasible, supporting the observed community behavior.

CONCLUSIONS: This study demonstrates the role of magnetite not only as a hydrogen sulfide scavenger but also as a community modulator, promoting resilient direct electron transfer-based networks, ultimately unlocking higher-efficiency biogas production in sulfate-impacted digesters. Our findings support the concept that interactions between sulfate-reducers and hydrogenotrophic methanogens are not purely competitive, and that conductive materials such as magnetite can enhance their metabolic coupling even under sulfate stress. Video Abstract.},
}

*Sulfates/metabolism
*Ferrosoferric Oxide/metabolism/pharmacology
Methane/metabolism/biosynthesis
Anaerobiosis
Bioreactors/microbiology
Hydrogen Sulfide/metabolism
Metagenomics/methods
*Microbiota
*Bacteria, Anaerobic/metabolism/genetics/classification
*Bacteria/metabolism/genetics/classification
Microbial Interactions

@article {pmid42242448,
year = {2026},
author = {Ammar, M and Fang, Y and Saqib, M and Xiao, J and Sial, AU and Wu, Q and Mansoor, MK and Wu, X and Moaaz, M and Butt, MU and Hafeez, R and Iqbal, K and Zohaib, A and Shen, S and Deng, F},
title = {Metagenomic and serological evidence of emerging tick-borne viruses in livestock, humans, and rats in Pakistan.},
journal = {Virologica Sinica},
volume = {41},
number = {3},
pages = {523-531},
doi = {10.1016/j.virs.2026.06.001},
pmid = {42242448},
issn = {1995-820X},
mesh = {Animals ; Pakistan/epidemiology ; Humans ; Antibodies, Viral/blood ; *Tick-Borne Diseases/virology/epidemiology/veterinary ; Rats/virology ; *Livestock/virology ; Phylogeny ; *Ticks/virology ; Metagenomics ; *Viruses/genetics/classification/isolation & purification ; Virome ; *Communicable Diseases, Emerging/virology/veterinary/epidemiology ; },
abstract = {Tick-borne viruses (TBVs) pose significant emerging threats to public and veterinary health worldwide. In Pakistan, the potential threats posed by TBVs extend far beyond Crimean-Congo hemorrhagic fever virus (CCHFV), which causes outbreaks and severe hemorrhaging with a high fatality rate among humans each year. However, the full extent of the tick-borne virome remains largely unexplored. This study presents the metagenomic profiling of viruses in livestock-associated ticks from Pakistan. Eighty-seven ticks belonging to the genera Ixodes, Rhipicephalus, Haemaphysalis, and Hyalomma species from livestock in Punjab. These ticks were subsequently grouped into 11 pools for RNA sequencing. Our analysis revealed extensive viral diversity, identifying sequences related to 31 viruses spanning at least 11 families. New strains of Jingmen tick virus (JMTV), Brown dog tick phlebovirus 2 (BDTPV-2), and Liman tick virus (LMTV) were characterized, confirming their presence in the region. Serological surveys performed among 319 livestock, 253 humans, and 214 rats detected antibodies against these viruses, indicating host exposure. Notably, the presence of JMTV-neutralizing antibodies was confirmed in two livestock animals, one human, and one rat, providing evidence of productive infection. Our findings significantly expand the known diversity and distribution of TBVs in Pakistan, establish the preliminary baseline of the tick virome in the country, and provide serological evidence of cross-species exposure to emerging TBVs. This study highlights the underestimated risk of tick-borne viral zoonoses in Pakistan and underscores the urgent need for enhanced surveillance and risk assessment.},
}

Animals
Pakistan/epidemiology
Humans
Antibodies, Viral/blood
*Tick-Borne Diseases/virology/epidemiology/veterinary
Rats/virology
*Livestock/virology
Phylogeny
*Ticks/virology
Metagenomics
*Viruses/genetics/classification/isolation & purification
Virome
*Communicable Diseases, Emerging/virology/veterinary/epidemiology

@article {pmid42321844,
year = {2026},
author = {Li, Y and Chen, Q and Bin, X and Xu, S and Ma, H},
title = {Bronchoalveolar lavage microbiota signatures and stage-associated alterations in early-stage and advanced-stage non-small cell lung cancer: a pilot study.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42321844},
issn = {1479-5876},
support = {2023YXZX17//Tianjin Municipal Education Commission/ ; TJYXZDXK-3-032C//National Key Clinical Specialty Discipline Construction Program of China/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology/pathology/genetics/immunology ; *Lung Neoplasms/microbiology/pathology/genetics/immunology ; *Microbiota/genetics ; Neoplasm Staging ; Pilot Projects ; *Bronchoalveolar Lavage Fluid/microbiology ; Female ; Male ; ROC Curve ; Middle Aged ; Aged ; *Bronchoalveolar Lavage ; Bacteria/genetics ; },
abstract = {OBJECTIVES: The aims of this study were to characterize the microbial flora in the bronchoalveolar lavage fluid (BALF) of patients with early-stage (stage I, II, IIIA) and advanced-stage (stage IIIB, IIIC, IV) non-small cell lung cancer (NSCLC), and to explore the associations between microbial flora and lung cancer stage.

METHODS: We collected BALF from NSCLC patients (early-stage group 26 cases; advanced-stage group 31 cases). Absolute quantitative metagenomic sequencing was performed to identify differential taxa, genes, and enriched pathways. Flow cytometry was used to profile T cell subsets. We correlated the microbial species with immune cell and gene expression. Receiver operating characteristic (ROC) curve analysis was performed to assess the ability of differential taxa to distinguish advanced-stage from early-stage NSCLC.

RESULTS: Dokdonia (q = 0.040, LDA = 5.704) and Cocleimonas (q = 0.026, LDA = 5.329) were enriched in the early-stage group, whereas Barnesiella (q = 0.046, LDA = 4.784), Pedobacter (q = 0.040, LDA = 4.913) and unclassified Bacteroides (q = 0.046, LDA = 4.932) were significantly enriched in the advanced-stage group. The microbial genes gmhD (q < 0.001, LDA = 3.926), rfaD (q < 0.001, LDA = 3.918), nudF (q = 0.004, LDA = 4.283) and sfsA (q = 0.004, LDA = 3.915) were expressed remarkably in the advanced-stage group. The advanced-stage group exhibited altered T cell subset distributions, including a higher proportion of CD8⁺ T lymphocytes (q < 0.001), whereas it showed a lower proportion of CD4⁺ T cells and a decreased CD4/CD8 ratio (q < 0.001; q < 0.001). Bifidobacterium was negatively associated with the CD4/CD8 ratio (q = 0.015) and positively significant correlated with the genes which enriched in the advanced-stage group.

CONCLUSIONS: This study delineated the microbial structure and function of early-stage and advanced-stage of NSCLC. We identified discriminating taxa, genes, and pathways linked to cancer progression, characterized the T cell subset distributions in the advanced-stage of NSCLC. Bifidobacterium abundance was associated with altered T cell subset distributions and stage-related microbial genes, providing hypotheses for future mechanistic studies on microbiota-driven NSCLC progression.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/microbiology/pathology/genetics/immunology
*Lung Neoplasms/microbiology/pathology/genetics/immunology
*Microbiota/genetics
Neoplasm Staging
Pilot Projects
*Bronchoalveolar Lavage Fluid/microbiology
Female
Male
ROC Curve
Middle Aged
Aged
*Bronchoalveolar Lavage
Bacteria/genetics

@article {pmid42324270,
year = {2026},
author = {Ma, Y and Yang, M and Xu, A and Zhao, X and Dong, X and Li, W and Tu, H and Guo, Y and Song, Z and Wu, X},
title = {Characterization of gut microbiome signatures in metabolic dysfunction associated steatotic liver disease.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42324270},
issn = {2055-5008},
support = {K20230085//Healthy Zhejiang One Million People Cohort/ ; 2020E10004//Zhejiang Key Laboratory of Intelligent Preventive Medicine/ ; 2019R01007//the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang/ ; 2020C03002//Cancer Center, Zhejiang University and Key Research and Development Program of Zhejiang Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Cross-Sectional Studies ; *Fatty Liver/microbiology/metabolism ; Male ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Adult ; Metagenome ; Metabolic Networks and Pathways ; },
abstract = {This cross-sectional study compared the gut microbiota between metabolic dysfunction associated steatotic liver disease (MASLD) patients and healthy controls. A total of 1401 participants, including 392 MASLD patients and 1009 healthy controls, were enrolled from one project site of the Healthy Zhejiang One Million People Cohort (HOPE) between January 2022 and June 2023. Shotgun metagenomic sequencing was conducted to compare the composition and functional profiles of the gut microbiome between MASLD patients and healthy controls. Compared to the control group, MASLD patients exhibited significant alterations in both alpha and beta diversity, along with reduced connectivity and robustness of the gut microbial network. We identified significant changes in the abundance of 12 microbial strains between the two groups with two strains (t_SGB4749 and t_SGB4753) enriched and ten strains depleted in MASLD patients. In comparison to the control group, MASLD patients demonstrated distinct differences in the genomic potential related to increased glycolysis, decreased pyruvate metabolism, and elevated lipopolysaccharide (LPS) biosynthesis in both metagenomic functional profiling and single-strain genome analysis. These findings suggest that alterations in specific microbial strains and metabolic pathways may contribute to MASLD pathogenesis.},
}

Humans
*Gastrointestinal Microbiome
Metagenomics
Cross-Sectional Studies
*Fatty Liver/microbiology/metabolism
Male
Female
Middle Aged
*Bacteria/classification/genetics/isolation & purification/metabolism
Adult
Metagenome
Metabolic Networks and Pathways

@article {pmid42330834,
year = {2026},
author = {Cabrera, C and Carrión, N and Mateo, D and Heredia, L and Pino, M and Galvez, S and Forcadell-Ferreres, E and Vicens, P and Torrente, M},
title = {Shotgun metagenomic profiling of the gut microbiota in Parkinson's disease dementia and dementia with Lewy bodies.},
journal = {Parkinsonism & related disorders},
volume = {149},
number = {},
pages = {108400},
doi = {10.1016/j.parkreldis.2026.108400},
pmid = {42330834},
issn = {1873-5126},
mesh = {Humans ; *Parkinson Disease/microbiology/complications/physiopathology ; Female ; Male ; *Lewy Body Disease/microbiology/physiopathology ; Aged ; Cross-Sectional Studies ; Middle Aged ; *Gastrointestinal Microbiome/genetics/physiology ; Aged, 80 and over ; Case-Control Studies ; Metagenomics ; *Dementia/microbiology ; *Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Parkinson's disease (PD) and dementia with Lewy bodies (DLB) are related α-synucleinopathies that share Lewy pathology, but they differ clinically. Increasing evidence links gut microbiota (GMB) dysbiosis and microbially derived metabolites to Parkinsonian disorders yet reported associations remain heterogeneous across cohorts and the Lewy body dementia syndromes are comparatively under characterized. This study integrated clinical characterization and GMB profiling in Parkinson's disease dementia (PDD), DLB, and healthy controls (HC) to identify shared and syndrome specific features, and to relate these patterns to cognitive, neuropsychiatric, and functional outcomes.

METHODS: The present cross-sectional case-control study in Spain included 76 adults aged 60 to 85 years (HC = 38, PDD = 27, DLB = 11). Stool samples underwent shotgun metagenomic sequencing, with species-level taxonomic profiling using Kraken2. Community diversity was assessed using observed species and Chao1 richness, Shannon alpha diversity, and Bray-Curtis dissimilarity for beta diversity. LEfSe and multivariate linear modeling with MaAsLin2 were performed to identify GMB species associated with PDD and DLB and their clinical correlates.

RESULTS: PDD showed higher richness compared with HC. Shannon alpha diversity did not differ between groups. Bray-Curtis differed by separation of HC from both PDD and DLB, with no significant difference between Lewy body dementia syndromes. LEfSe identified 19 significantly differential taxa. Furthermore, several taxa showed significant multivariable associations with clinical outcomes.

CONCLUSIONS: PDD and DLB shared a broadly similar GMB alteration away from HC, with multivariable associations between several taxa and clinical outcomes. Longitudinal and functional studies are needed to clarify causality and biomarker potential.},
}

Humans
*Parkinson Disease/microbiology/complications/physiopathology
Female
Male
*Lewy Body Disease/microbiology/physiopathology
Aged
Cross-Sectional Studies
Middle Aged
*Gastrointestinal Microbiome/genetics/physiology
Aged, 80 and over
Case-Control Studies
Metagenomics
*Dementia/microbiology
*Dysbiosis/microbiology

@article {pmid42335476,
year = {2026},
author = {Valentino, V and De Filippis, F and Ercolini, D},
title = {Fermented foods: lessons learned from metagenomics.},
journal = {Current opinion in biotechnology},
volume = {100},
number = {},
pages = {103545},
doi = {10.1016/j.copbio.2026.103545},
pmid = {42335476},
issn = {1879-0429},
mesh = {*Metagenomics/methods ; *Fermented Foods/microbiology ; *Food Microbiology ; Fermentation ; Microbiota ; Multiomics ; Probiotics ; },
abstract = {Thanks to the standard microbiology protocols of isolation and culturing, hundreds of strains have been isolated from fermented foods throughout the last decades, and phenotypic traits linked with pro-technological properties and health claims have been investigated. However, culture-independent metagenomic analyses have revealed an unexpected microbial diversity in foods fermented spontaneously or by undefined starter cultures. Here, we report the most groundbreaking advancements in the understanding of fermented foods ecology by presenting case studies where metagenomics has been applied, contributing to identifying novel species in silico or to deciphering the microbiome structure associated with spontaneous fermentations. We also highlight the potential of metagenomics in supporting the identification of potential probiotics and discuss the future ahead, particularly focusing on the integration of multi-omics approaches.},
}

*Metagenomics/methods
*Fermented Foods/microbiology
*Food Microbiology
Fermentation
Microbiota
Multiomics
Probiotics

@article {pmid42413135,
year = {2026},
author = {Hernández-Velázquez, R and Bokulich, NA},
title = {Unlocking the biotechnological potential of traditional fermented food microbiomes.},
journal = {Current opinion in biotechnology},
volume = {100},
number = {},
pages = {103550},
doi = {10.1016/j.copbio.2026.103550},
pmid = {42413135},
issn = {1879-0429},
mesh = {*Biotechnology ; *Microbiota ; *Fermented Foods/microbiology ; Fermentation ; *Food Microbiology ; Multiomics ; Humans ; },
abstract = {Fermented foods are a globally important source of dietary microbes, cultural heritage, and functional diversity, yet current microbiome research captures only a narrow fraction of this richness. Public sequencing datasets are heavily skewed toward a limited set of regions and fermentation types, leaving vast areas of geographic, substrate, and process diversity underrepresented. This imbalance constrains the discovery of novel microbial species, enzymes, and biosynthetic capacities, and risks accelerating homogenization through standardized starter cultures. We argue that coordinated, ethically grounded global efforts integrating metagenomics, multi-omics, standardized metadata, and biobanking are urgently needed to document, preserve, and responsibly leverage fermented food microbial diversity for sustainable food systems and innovation.},
}

*Biotechnology
*Microbiota
*Fermented Foods/microbiology
Fermentation
*Food Microbiology
Multiomics
Humans

@article {pmid42442320,
year = {2026},
author = {Sabater, C and Calvete-Torre, I and Vázquez, X and Cobo-Díaz, JF and Álvarez-Ordoñez, A and Ruas-Madiedo, P and Ruiz, L and Margolles, A},
title = {Metagenomics to assess authenticity and traceability of Asturian Gamonéu PDO cheese: A multi-omic study.},
journal = {International journal of food microbiology},
volume = {460},
number = {},
pages = {111939},
doi = {10.1016/j.ijfoodmicro.2026.111939},
pmid = {42442320},
issn = {1879-3460},
mesh = {*Cheese/microbiology/analysis ; Spain ; *Metagenomics/methods ; Volatile Organic Compounds/analysis ; Food Microbiology ; *Bacteria/genetics/classification/isolation & purification ; Multiomics ; Machine Learning ; Microbiota ; },
abstract = {Cheese is one of the most widely consumed fermented foods in Europe. The Principality of Asturias (northern Spain) has a broad tradition in cheese making including four cheeses under Protected Designation of Origin (PDO) status (Cabrales, Gamonéu, Casín and Afuega'l Pitu). The added value of PDO food products increases the risk of fraudulently copied cheeses reaching the market. The aim of this work was to develop a novel microbiome-based method contributing to the assessment of the authenticity of Gamonéu PDO cheese. For this purpose, cheese metagenomes and volatile organic compounds (VOCs) profiles were integrated using machine learning (ML) algorithms. Computational models accurately discriminated between samples from 9 Gamonéu PDO cheese producers, as well as between cheeses ripened in different natural caves. Furthermore, they allowed distinguishing PDO and non-PDO Gamonéu-like cheeses produced in the same area. Potential microbial markers of the geographical origin of Gamonéu PDO cheese included Debaryomyces hansenii, Lacticaseibacillus paracasei and Penicillium roqueforti (more abundant in non-PDO cheeses), and Brachybacterium faecium (more abundant in PDO cheeses). Computational models presented in this work may contribute to improving existing traceability methods in the field of fermented foods and may be applied to a wide range of cheese varieties.},
}

*Cheese/microbiology/analysis
Spain
*Metagenomics/methods
Volatile Organic Compounds/analysis
Food Microbiology
*Bacteria/genetics/classification/isolation & purification
Multiomics
Machine Learning
Microbiota

@article {pmid42468189,
year = {2026},
author = {Wan, S and Huang, W and Zhang, Z and Liu, X and Dong, W and Chen, Y and Ke, L and Yang, Q and Chen, S and Hu, Y and Zhang, Y},
title = {Microbial succession and flavor-related metabolic potential during industrial eight-round mechanized stacking fermentation of Maotai-flavor Baijiu.},
journal = {International journal of food microbiology},
volume = {460},
number = {},
pages = {111975},
doi = {10.1016/j.ijfoodmicro.2026.111975},
pmid = {42468189},
issn = {1879-3460},
mesh = {Fermentation ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Flavoring Agents/metabolism ; Volatile Organic Compounds/analysis/metabolism ; Taste ; *Wine/microbiology/analysis ; Fungi/metabolism/genetics/classification/isolation & purification ; Gas Chromatography-Mass Spectrometry ; Microbiota ; Food Microbiology ; },
abstract = {Mechanized production of Maotai-flavor Baijiu (MFB) is increasingly adopted in the Baijiu industry; however, microbial succession and flavor-related metabolic potential throughout the complete eight-round mechanized stacking fermentation (SF) process remain insufficiently understood. In this study, microbial communities, functional genes, physicochemical properties, and volatile compounds during SF were investigated using metagenomic sequencing and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC/MS). A total of 168 volatile compounds were detected, of which 41 representative compounds were selected for further analysis. Among them, 15 differential volatiles were identified by PLS-DA, with furfural showing the highest abundance. Microbial profiling revealed pronounced community differentiation and continuous succession across fermentation rounds. Acidity, starch, and reducing sugars were significantly associated with microbial community variation, with acidity and starch exhibiting the strongest associations. In the initial round (R1), microbial communities were mainly derived from raw materials and Daqu. Bacterial communities shifted from lactic-acid-bacteria-enriched communities to those characterized by Kroppenstedtia and Bacillus, whereas fungal communities transitioned from yeast-enriched stages to mold-enriched and mold-yeast coexistence stages. Metagenome-inferred functional annotation, co-occurrence network, and correlation analyses suggested potential links between microbial succession and flavor-related metabolic pathways. Yeasts were mainly associated with ethanol- and organic-acid-related metabolism during the early stage, whereas Bacillus and Kroppenstedtia were linked to predicted starch-degradation and organic-acid-related pathways during the middle and late stages. Overall, this study provides a comprehensive characterization of microbial succession and metagenome-inferred flavor-related metabolic potential during mechanized SF and offers reference data for process monitoring and quality management in MFB production.},
}

Fermentation
*Bacteria/metabolism/classification/genetics/isolation & purification
*Flavoring Agents/metabolism
Volatile Organic Compounds/analysis/metabolism
Taste
*Wine/microbiology/analysis
Fungi/metabolism/genetics/classification/isolation & purification
Gas Chromatography-Mass Spectrometry
Microbiota
Food Microbiology

@article {pmid42476558,
year = {2026},
author = {D'Agostino, GD and Kim, CH and Park, J and Zhang, Y and Amer, B and Franzosa, EA and Bird, SS and Huttenhower, C and Huh, JR and Devlin, AS},
title = {Comparative Metabolomics Reveals the Production of Sulfated Metabolites by Human Gut Bacteria.},
journal = {Journal of the American Chemical Society},
volume = {148},
number = {30},
pages = {31759-31773},
doi = {10.1021/jacs.6c02487},
pmid = {42476558},
issn = {1520-5126},
support = {R01 DK140810//National Institutes of Health (NIH)/ ; R35 GM128618//National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Sulfates/metabolism/chemistry ; *Metabolomics ; *Gastrointestinal Microbiome ; Sulfotransferases/metabolism ; Phosphoadenosine Phosphosulfate/metabolism ; },
abstract = {The sulfated metabolome─the collection of sulfate-containing metabolites─is an emerging source of structurally unique bioactive compounds that influence metabolism, immune responses, and neurological function. Recent studies have shown that, in addition to host enzymes, gut bacteria also encode sulfotransferase enzymes (SULTs) that generate sulfated metabolites. However, the substrate scope of characterized gut bacterial SULTs remains narrow, and comprehensive discovery is limited by a lack of methods to detect and assign sulfated metabolites in complex samples. Here, we develop a comparative metabolomics workflow that leverages the universal SULT cofactor 3'-phosphoadenosine-5'-phosphosulfate (PAPS) to incorporate heavy (34S) or light (32S) sulfur into sulfated metabolites, enabling discovery of microbiome-dependent sulfated compounds. By applying this approach in both "bottom-up" bacterial culture and "top-down" in vivo studies, we find that gut bacteria sulfonate hydroxy fatty acids. We identify a gut commensal microbe, Eubacterium ramulus, that performs this transformation, as well as an enzyme in this bacterium that performs this sulfonation, ErSULT. Metagenomic analyses reveal that ErSULT is prevalent across diverse human gut microbiomes. Together, this workflow and its application demonstrate that sulfated metabolite production by gut bacteria is more widespread than previously appreciated and provide a platform for future studies investigating the biosynthesis and biological functions of microbiome-derived sulfated small molecules.},
}

Humans
*Sulfates/metabolism/chemistry
*Metabolomics
*Gastrointestinal Microbiome
Sulfotransferases/metabolism
Phosphoadenosine Phosphosulfate/metabolism

@article {pmid42508331,
year = {2026},
author = {Zhang, J and Cao, W and Xiong, W and Yao, Y and Jiang, D and Liang, W and Wang, L},
title = {Revealing the correlation between microbial community and flavor compounds in traditional Chinese sourdough by integrating flavoromics and metagenomics.},
journal = {International journal of food microbiology},
volume = {460},
number = {},
pages = {111927},
doi = {10.1016/j.ijfoodmicro.2026.111927},
pmid = {42508331},
issn = {1879-3460},
mesh = {Volatile Organic Compounds/analysis ; *Bread/microbiology/analysis ; Fermentation ; China ; Metagenomics ; Taste ; *Flavoring Agents/analysis/chemistry ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Saccharomyces cerevisiae/isolation & purification/genetics/metabolism ; Odorants/analysis ; },
abstract = {Traditional Chinese sourdough (CTS) is mainly used for the fermentation of steamed pastries, providing a unique natural fluffiness and distinctive flavor, and thus holds important culinary value. However, the microbial mechanisms underlying the diversity of its regional characteristic flavors remain poorly understood. In this study, we integrated metagenomic sequencing with multi-platform flavor profiling-including high-performance liquid chromatography (HPLC), electronic nose, gas chromatography-mass spectrometry (GC-MS), and gas chromatography-ion mobility spectrometry (GC-IMS)-to characterize the physicochemical properties, microbial composition, and flavor compounds of 10 CTS samples collected from five provinces across China. A total of 1231 genera and 3358 species were identified, with Fructilactobacillus sanfranciscensis, Saccharomyces cerevisiae and Lactiplantibacillus plantarum being the dominant species. Flavor profiling analysis revealed 109 volatile organic compounds (VOCs), of which 11 key aroma-active compounds (e.g., 1-nonanol, phenethyl alcohol) were identified based on odor activity values (OAV ≥ 1). Using orthogonal partial least squares (O2PLS) modeling, we established associations between 25 potential flavor-producing microorganisms and specific metabolites. Notably, S. cerevisiae exhibited a significant positive correlation with acetic acid, 1-nonanol and glutamic acid, while L. plantarum showed a strong positive correlation with phenethyl alcohol. This study reveals the correlation patterns between microbial communities and flavor compounds in CTS, offering foundational insights for starter culture design, flavor standardization, and industrial application of traditional fermented doughs.},
}

Volatile Organic Compounds/analysis
*Bread/microbiology/analysis
Fermentation
China
Metagenomics
Taste
*Flavoring Agents/analysis/chemistry
*Microbiota
*Bacteria/classification/genetics/isolation & purification/metabolism
Food Microbiology
Gas Chromatography-Mass Spectrometry
Saccharomyces cerevisiae/isolation & purification/genetics/metabolism
Odorants/analysis

@article {pmid42518807,
year = {2026},
author = {Hamiyeh, R and Salhab, Z and Bahmad, HF and Abou Fayad, AG and Abou-Kheir, W},
title = {Anticancer natural products from the Middle East and North Africa: biodiversity, mechanisms, and translational challenges.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1846357},
pmid = {42518807},
issn = {2234-943X},
abstract = {Cancer remains one of the leading causes of morbidity and mortality worldwide, imposing substantial clinical, societal, and economic burdens. Despite major advances in surgical oncology, systemic chemotherapy, radiation therapy, molecularly targeted therapeutics, and immune checkpoint inhibition, contemporary cancer treatment remains constrained by dose-limiting toxicities, intratumoral and intertumoral heterogeneity, and the inexorable emergence of multifaceted drug resistance mechanisms. These persistent therapeutic challenges have reinstated interest in natural products (NPs) as evolutionarily refined sources of anticancer agents characterized by structurally diverse molecular targets and pleiotropic mechanisms of action. Indeed, a substantial proportion of currently approved anticancer drugs are either directly derived from or structurally inspired by natural compounds. This comprehensive review examines the role of NPs as anticancer agents, with particular emphasis on bioactive compounds isolated from plants, fungi, marine organisms, and environmental bacteria indigenous to the Middle East and North Africa (MENA) region. We summarize exemplary MENA-derived NPs demonstrating cytotoxic, antiproliferative, pro-apoptotic, anti-angiogenic, anti-metastatic, and immunomodulatory activities across a wide range of preclinical cancer models. Mechanistically, these compounds converge on critical oncogenic signaling networks, including p53-caspase apoptotic cascades, NF-κB transcriptional inhibition, reactive oxygen species modulation, cell-cycle arrest, epigenetic reprogramming, and suppression of tumor invasion and chronic inflammation. In parallel, we highlight transformative technological innovations-including high-throughput phenotypic and biochemical screening platforms, metagenomics, genome mining algorithms, biosynthetic gene cluster activation, and synthetic biology approaches-that are fundamentally reshaping NP discovery and enabling access to previously cryptic or unculturable microbial biosynthetic pathways. These methodological advances, coupled with multi-omics integration, artificial intelligence-driven compound prediction, and heterologous expression systems, are accelerating the identification and characterization of structurally novel anticancer agents. Collectively, the evidence presented underscores the MENA region as a significantly underexplored yet exceptionally promising biodiverse reservoir of anticancer NPs with substantial therapeutic potential. Strategic harnessing of this biodiversity through interdisciplinary collaborative research, ethically governed bioprospecting frameworks, and translational development pipelines may yield structurally innovative, mechanistically distinct, and potentially safer therapeutic modalities to complement existing cancer treatments and address critical unmet clinical needs in precision oncology.},
}

@article {pmid42520232,
year = {2026},
author = {Bhuta, R and Kuntz, T and DeNardo, B and Morgan, X and Shapiro, J},
title = {Shotgun Metagenomics Identify Unique Changes of the Intestinal Microbiome in Pediatric Survivors of Acute Lymphoblastic Leukemia.},
journal = {Rhode Island medical journal (2013)},
volume = {109},
number = {8},
pages = {32-37},
pmid = {42520232},
issn = {2327-2228},
mesh = {Humans ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology/drug therapy ; Metagenomics ; Child ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Child, Preschool ; Adolescent ; Survivors ; *Dysbiosis/microbiology ; Feces/microbiology ; Shotgun Sequencing ; Case-Control Studies ; *Cancer Survivors ; },
abstract = {BACKGROUND: Intestinal microbiota plays an important role in human health and metabolism. Microbial dysbiosis has been observed in various chronic conditions, many of which are late effects of leukemia treatment. We previously observed significant differences in the gut microbiome of pediatric ALL survivors compared to healthy sibling controls. Shotgun metagenomic analyses were completed to better characterize the durability and metabolic implication of these changes.

PROCEDURE: Shotgun metagenomic sequencing was completed on DNA extracted from stool samples obtained from nine survivors of childhood acute lymphoblastic leukemia (ALL) and 10 healthy sibling controls.

RESULTS: Beta diversity (dissimilarity between samples) was significant with survivors' microbiomes becoming more similar to siblings further from treatment. The functional potential of gluconate-5-dehydrogenase enzyme (Ga5DH) decreased significantly with time from treatment. Relative abundance of Faecalibacterium prausnitzii was identified as the major contributor to differential Ga5DH expression within subjects.

CONCLUSIONS: Time from treatment has a significant effect on functional microbial recovery in ALL. Increased time from chemotherapy corresponds to microbiomes becoming more similar to sibling controls in select dyads. More significant differences were noted in patients closer to treatment. Additional, prospective studies will focus on deeper characterization of these findings and further investigate the functional role of Ga5DH in ALL survivors.},
}

Humans
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology/drug therapy
Metagenomics
Child
*Gastrointestinal Microbiome/genetics
Male
Female
Child, Preschool
Adolescent
Survivors
*Dysbiosis/microbiology
Feces/microbiology
Shotgun Sequencing
Case-Control Studies
*Cancer Survivors

@article {pmid42521068,
year = {2026},
author = {Pavon, JAR and Neves, NADS and Martins, AP and Pinho, JB and de Souza, VJ and Nunes, MRT and Slhessarenko, RD},
title = {RNA viruses in sylvatic mosquitoes and phlebotomine sand flies from Alto Pantanal, Mato Grosso, Brazil 2019.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108258},
doi = {10.1016/j.actatropica.2026.108258},
pmid = {42521068},
issn = {1873-6254},
abstract = {The Pantanal biome harbors exceptional biodiversity but has been increasingly impacted by climate change and human activities. This region is considered a high-risk zone for zoonotic spillover, making viral studies in sylvatic mosquitoes and other invertebrates indispensable, as these vectors are involved in the transmission of pathogens of public health concern. This study aimed to describe viral genomes identified in Aedes spp., Ochlerotatus sp., Mansonia sp., Phlebotomus sp., Psorophora spp., and Anopheles spp. dipterans collected in March and June 2019, in Pirizal and Porto São Luiz, Alto Pantanal, Mato Grosso State, Brazil. Diptera specimens were pooled by genera, and nucleic acids were extracted, followed by library preparation and sequencing on the Illumina NextSeq 500/550 platform. A total of 39 putative viral sequences were recovered, including 23 potentially novel viruses. Coding-complete genomes were identified from Virgaviridae (n=1), Rhabdoviridae (n=1), and Metaviridae (n=1), as well as seven coding-complete segments from Partitiviridae (n=4) and Solemoviridae (n=3). Additionally, 29 partial genomes were recovered from Partitiviridae (n=7), Metaviridae (n=6), Chuviridae (n=2), Sedoreoviridae (n=1), Nodaviridae (n=3), Tombusviridae (n=2), Phasmaviridae (n=2), Flaviviridae (n=3), Virgaviridae (n=1), and Solemoviridae (n=2). Viral characterization in Diptera specimens has gained increasing importance with the advancement of metagenomic approaches, which contribute to global One Health initiatives by providing data that may support the prediction and prevention of future viral spillover events.},
}

@article {pmid42521693,
year = {2026},
author = {Rodríguez-Ramos, JA and Zimmerman, AE and Wu, R and Bell, SL and Alfaro, TD and Reichart, NJ and Hofmockel, KS and Nelson, WC},
title = {Preparation method shapes the recovery and ecological interpretation of DNA and RNA soil viral communities.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42521693},
issn = {2041-1723},
support = {FWP 70880//DOE | SC | Biological and Environmental Research (BER)/ ; FWP 70880//DOE | SC | Biological and Environmental Research (BER)/ ; },
mesh = {*Soil Microbiology ; Metagenomics/methods ; *RNA, Viral/isolation & purification/genetics ; *RNA Viruses/genetics/isolation & purification ; *DNA, Viral/isolation & purification/genetics ; Soil/chemistry ; *DNA Viruses/genetics/isolation & purification ; Metagenome ; *Virome/genetics ; Genome, Viral ; Bacteria/genetics ; },
abstract = {Deciphering viral ecology in soils is challenging due to soil's high physicochemical and microbial community complexity. To enhance detection of DNA and RNA viruses, we applied different preparation methods to soils collected from a grassland field experiment. Analyses included metagenomics and metatranscriptomics of size-fractionated extracellular viruses, total soil metagenomics and metatranscriptomics, total soil metatranscriptomics with polyadenylation enrichment, and metagenomics of bacteria/archaea as well as eukaryote-enriched samples. DNA viromes outperformed total soil metagenomes in viral detection and quality. Contrastingly, RNA viromes and total soil metatranscriptomes performed similarly for viral recovery, though RNA viromes yielded higher-quality genomes. Together, our results highlight how different preparation methods can influence the recovery and quality of DNA and RNA vOTUs. Further, we demonstrate the power of different methods in identifying distinct viral communities with unique host predictions, which in turn can have significant implications for ecological investigations related to interkingdom interactions.},
}

*Soil Microbiology
Metagenomics/methods
*RNA, Viral/isolation & purification/genetics
*RNA Viruses/genetics/isolation & purification
*DNA, Viral/isolation & purification/genetics
Soil/chemistry
*DNA Viruses/genetics/isolation & purification
Metagenome
*Virome/genetics
Genome, Viral
Bacteria/genetics

@article {pmid42524914,
year = {2026},
author = {Calixto, SL and Macedo, ACLP and Aguiar, JAK},
title = {GUT MICROBIOTA ALTERATIONS IN RODENT MODELS OF CHOLESTASIS INDUCED BY BILE DUCT LIGATION: A SYSTEMATIC REVIEW.},
journal = {Arquivos de gastroenterologia},
volume = {63},
number = {},
pages = {e25159},
pmid = {42524914},
issn = {1678-4219},
mesh = {Animals ; *Cholestasis/microbiology ; *Gastrointestinal Microbiome/physiology ; Disease Models, Animal ; Ligation ; Bile Ducts/surgery ; Mice ; *Dysbiosis/microbiology ; Rats ; },
abstract = {BACKGROUND AND OBJECTIVE: Cholestatic liver diseases are a major public health issue, marked by impaired bile flow and significant disruptions in liver and systemic physiology. Growing evidence points to the gut microbiota as a key player in cholestasis pathogenesis through gut-liver axis interactions. This systematic review aimed to synthesize and evaluate current findings on intestinal microbiota changes in rodents (rats and mice) subjected to bile duct ligation (BDL)-induced cholestasis, focusing on microbial diversity, taxonomic shifts, and potential pathophysiological implications.

METHODS: A comprehensive literature search was conducted in PubMed, Scopus, and Embase for studies published from January 2020 to February 2025, following PRISMA guidelines. Eligible studies included original research using BDL in rodents without therapeutic intervention and reporting gut microbiota profiles. Data were qualitatively analyzed, emphasizing experimental conditions and microbiome outcomes.

RESULTS: Twenty-two studies met inclusion criteria. Most used 16S rRNA sequencing; two used shotgun metagenomics. BDL consistently induced gut dysbiosis, with reductions in alpha diversity (in most studies), altered beta diversity, and shifts in dominant phyla such as Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Verrucomicrobiota. At finer taxonomic levels, increases in Prevotella, Enterococcus, Escherichia coli, and Alistipes were common, while Lactobacillus and Ruminococcus often decreased. Elevated levels of Akkermansia muciniphila and Bifidobacterium pseudolongum may represent compensatory microbial responses.

CONCLUSION: Bile duct ligation (BDL)-induced cholestasis leads to complex changes in the microbiota that can worsen intestinal barrier integrity, increase bacterial translocation, and intensify liver inflammation. These findings reinforce the central role of the gut-liver axis and corroborate the potential of microbiota-targeted therapies in the management of cholestatic liver diseases. However, as most of the available evidence derives from experimental models, further well-designed clinical studies are needed to validate the safety, efficacy, and translational applicability of these strategies in human diseases.},
}

Animals
*Cholestasis/microbiology
*Gastrointestinal Microbiome/physiology
Disease Models, Animal
Ligation
Bile Ducts/surgery
Mice
*Dysbiosis/microbiology
Rats

@article {pmid42528818,
year = {2026},
author = {Chen, M and Wang, X and Peng, G and Jiang, L and Liang, H and Cui, P},
title = {Gut microbiota induces immune-related alterations in gene expression, RNA methylation, and metabolism in glioblastoma revealed by single-cell and spatial multi-omics.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1899954},
pmid = {42528818},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology/drug effects ; RNA Methylation ; *Brain Neoplasms/metabolism/genetics/immunology/microbiology ; Mice ; Multiomics ; *Glioblastoma/metabolism/genetics/immunology/microbiology ; Humans ; *Gene Expression Regulation, Neoplastic ; Epitranscriptome ; Single-Cell Analysis ; Spatial Transcriptomics ; Epigenesis, Genetic ; Tumor Microenvironment/immunology ; Single-Cell Gene Expression Analysis ; Gene Expression Profiling ; },
abstract = {Glioblastoma (GBM) is a highly malignant tumor with poor prognosis and limited effective treatment options. Emerging studies have suggested that gut microbiota may influence glioma progression through the gut-brain axis, though the precise mechanisms remain largely unclear. In this study, we employed a comprehensive multi-omics approach-encompassing single-cell transcriptomics, spatial transcriptomics, metagenomics, metabolomics, and m6A-seq-to investigate how antibiotic-induced gut microbiota disruption impacts glioma progression in a mouse model. Gene expression analysis revealed significant alterations in antibiotics-treated mice (ABX-treated mice), including reduced expression of Epha6 and upregulated expression of Tead1, key genes associated with glioma progression and immune modulation. Spatial transcriptomics and metabolomic profiling identified reduced methionine levels in gliomas of ABX-treated mice, linking gut-derived metabolite changes to epigenetic regulation via m6A methylation. Single-cell RNA sequencing further demonstrated an increased proportion of AC-like cells, disrupted intercellular communication, and aberrations in the EPHA and NRXN signaling pathways. These findings highlight the interplay between gut microbiota, immune signaling, and epigenetic modifications in shaping the glioma microenvironment. This study advances our understanding of the gut-brain axis in glioma biology and proposes the EPHA pathway as a promising biomarker for the immune-mediated modulation of tumor progression, thereby providing new insights into the role of the gut-brain axis in glioma regulation.},
}

Animals
*Gastrointestinal Microbiome/immunology/drug effects
RNA Methylation
*Brain Neoplasms/metabolism/genetics/immunology/microbiology
Mice
Multiomics
*Glioblastoma/metabolism/genetics/immunology/microbiology
Humans
*Gene Expression Regulation, Neoplastic
Epitranscriptome
Single-Cell Analysis
Spatial Transcriptomics
Epigenesis, Genetic
Tumor Microenvironment/immunology
Single-Cell Gene Expression Analysis
Gene Expression Profiling

@article {pmid42531517,
year = {2026},
author = {Cheng, C and Wang, L and Li, R and Lai, W and Sun, C and Cui, J and Zhu, B and Zhang, J},
title = {Association Characteristics and Potential Mechanisms of Aging, Gut Microbiota, and Hearing Loss.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70156},
pmid = {42531517},
issn = {1749-4877},
support = {32370536//National Natural Science Foundation of China/ ; QNTS202304//CIB Youth Exploration Project/ ; //Tianchi Talents Fund of Xinjiang/ ; },
abstract = {Age-related hearing loss (ARHL) is the leading sensory disability among the global elderly, yet its pathogenesis remains unclear. The "gut-ear axis" hypothesis offers a novel perspective. Using young, middle-aged, and aging C57BL/6 mice, we systematically investigated the interplay between aging, gut microbiota, and hearing loss through auditory function tests, cochlear histology, microbiome, and metabolome profiling. Results showed that aging induced a gradient hearing decline starting at high frequencies, progressing to severe pan-frequency loss in old age. Histology confirmed the degeneration of inner hair cells and synaptic connections, alongside hair cell loss in the basal cochlea. While gut microbiota α-diversity remained stable, β-diversity shifted significantly, marked by increased Bacteroidota and decreased Bacillota. Furthermore, 22 genera, 67 species, and 207 functional pathways were identified as being commonly associated with both aging and hearing loss. Metabolomic profiling further screened out 285 metabolites significantly associated with aging, 16 of which were also correlated with hearing loss. KEGG enrichment analysis suggested that chronic inflammation mediated by arachidonic acid metabolism, energy metabolic dysfunction regulated by the PPAR signaling pathway, and actin cytoskeleton homeostasis imbalance may represent a potential axis linking systemic metabolic dysregulation to cochlear‑specific damage. Moreover, these metabolites exhibited significant correlations with gut microbiota abundance. In conclusion, aging is associated with ARHL progression alongside gut microbiota remodeling and metabolic dysregulation. These findings supported a potential relationship between gut microbial-metabolic alterations and ARHL, which suggested that the gut microbiota may represent a candidate target for future mechanistic investigation.},
}

@article {pmid42531759,
year = {2026},
author = {Pacholak, A and Musielok, Ł and Smułek, W},
title = {Effect of pyrethrins and permethrin insecticides on soil bacterial biodiversity.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120564},
doi = {10.1016/j.ecoenv.2026.120564},
pmid = {42531759},
issn = {1090-2414},
abstract = {Soil microorganisms play a key role in maintaining ecosystem stability, yet they are frequently exposed to insecticides used in agriculture and pest control. This study investigated the effects of natural pyrethrins and synthetic permethrin on soil bacterial metabolic activity, functional diversity, community structure, and biodegradation potential. Soil samples collected from a long-term protected, non-agricultural forest area were incubated with commercial formulations containing pyrethrins (Afizol AE) or permethrin (Afanisep® 25 WP) for 7 and 15 days. Microbial metabolic activity was assessed using the Alamar Blue assay and Biolog EcoPlate™ system, while bacterial community composition was analyzed through 16S rRNA gene sequencing. Additionally, the degradation of insecticide active compounds was quantified using UHPLC-QTOF-MS. Permethrin-treated soils exhibited the highest and most sustained microbial metabolic activity, whereas pyrethrin-treated soils showed an initial stimulation followed by a decline over time. Functional diversity indices revealed that permethrin initially promoted metabolic diversity, but prolonged exposure led to a reduction in substrate utilization breadth. Metagenomic analysis demonstrated pronounced shifts in bacterial community composition under both treatments, with strong selection toward Firmicutes-dominated assemblages. Biodegradation assays confirmed substantial degradation of both pyrethrins and permethrin, although incomplete removal and partial accumulation of selected compounds were observed. The obtained results highlight that both natural and synthetic pyrethroids significantly alter soil bacterial communities, emphasizing the need to consider their short-term ecological effects on soil health.},
}

@article {pmid42533345,
year = {2026},
author = {Devasahayam, BRF and McNeil, T and Wubet, T and Schmutzer, T},
title = {Nanopore sequencing reveals coordinated host and microbiome responses across barley genotypes.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {},
pmid = {42533345},
issn = {1741-7007},
mesh = {*Hordeum/genetics/microbiology ; *Microbiota/genetics ; *Genotype ; Nanopore Sequencing ; Rhizosphere ; Plant Roots/microbiology/genetics ; Metagenome ; Metagenomics ; Transcriptome ; },
abstract = {BACKGROUND: Barley (Hordeum vulgare L.) provides a suitable model for studying domestication-driven plant-microbiome interactions. Although wild, landrace, and modern genotypes host distinct rhizosphere communities, the extent to which roots and microbes reciprocally influence each other remains unclear. Here, we applied an integrated multi-omics approach combining long-read metagenomics, root transcriptomics, and plant genomics to understand genotype-specific host-microbiome coordination.

RESULTS: Oxford Nanopore whole metagenome sequencing (WMS) revealed genotype-associated shifts in rhizosphere communities across seasons. Functional profiling showed a conserved metabolic backbone including amino acid metabolism, energy production, and secondary metabolite biosynthesis, alongside genotype-dependent variation in carbohydrate metabolism and transport-associated pathways. Genome-resolved analysis through metagenome-assembled genomes (MAGs) further detailed the taxonomic and functional architecture of key rhizosphere lineages. Root transcriptome profiling identified extensive differential expression associated with microbial perception, signaling, defense, and metabolic processes. Integration of host and microbiome data revealed coordinated molecular patterns, indicating that barley genotypes are associated with distinct microbial assemblages and corresponding transcriptional responses.

CONCLUSIONS: These findings indicate that domestication has shaped coordinated associations between barley genotypes and their rhizosphere microbiomes, reflected in both microbial community composition and host transcriptional regulation. This work provides new insights into the evolutionary tuning of plant-microbiome relationships and highlights opportunities for microbiome-informed strategies in barley improvement.},
}

*Hordeum/genetics/microbiology
*Microbiota/genetics
*Genotype
Nanopore Sequencing
Rhizosphere
Plant Roots/microbiology/genetics
Metagenome
Metagenomics
Transcriptome

@article {pmid42533554,
year = {2026},
author = {Yang, K and Yang, M and Yu, Q and Liong, MT and Chen, D and Cai, M},
title = {The Effect of a Probiotic on Gut Microbiota Stability and Systemic Well-Being during Short-Term Travel.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510037},
pmid = {42533554},
issn = {1738-8872},
mesh = {Humans ; *Probiotics/administration & dosage ; *Bifidobacterium/physiology ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; Adult ; *Travel ; Male ; China ; Female ; Feces/microbiology ; Young Adult ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Short-term travel, particularly to new environments, can disrupt gut microbiota homeostasis and induce a range of physical and psychological symptoms. While probiotics are proposed to mitigate these effects, evidence from well-controlled trials during domestic travel, especially along unique routes like China's Silk Road, remains limited. This study investigated the efficacy of a multi-strain Bifidobacterium probiotic in maintaining gut microbiota stability and alleviating travel-related symptoms. In a randomized, double-blind, placebo-controlled trial, 74 healthy adults traveling to Xinjiang were assigned to receive either a probiotic (n = 39; B. longum subsp. infantis M-63, B. breve M-16V, and B. longum BB536, 1.5 × 10[9] CFU/day) or a placebo (n = 35) for five days during travel. Gut microbiota was profiled via metagenomic sequencing (pre- and post-travel), and symptoms were recorded daily. Primary outcomes were changes in gut microbiota composition and function (KEGG pathways). Secondary outcomes included respiratory, gastrointestinal, and systemic symptom scores. Data were analyzed on an intention-to-treat basis. While alpha and beta diversity remained stable in both groups, the probiotic group exhibited a distinct post-travel microbiota enriched with beneficial taxa, including Bifidobacterium breve and Intestinibacillus at the genus level, and Lacticaseibacillus rhamnosus, Lacticaseibacillus paracasei, and other Lacticaseibacillus species. qPCR confirmed significant increases in administered strains B. longum subsp. infantis (p < 0.001) and B. breve (p < 0.001). KEGG analysis revealed that the probiotic group maintained a metabolically focused profile (e.g., peptidoglycan biosynthesis, histidine metabolism), whereas the placebo group showed increased abundance of microbial pathways associated with host disease-related signaling (e.g., Huntington disease, various cancers) and inflammatory signaling (e.g., PI3K-Akt signaling pathway). Symptomatically, the probiotic group demonstrated a significantly greater reduction than the placebo in irritability (-92% vs. -31%; p = 0.033) and fatigue (-24% vs. +43%; p = 0.024) post-travel, and reported less dizziness (-100% vs. -35%; p = 0.024). Supplementation with a multi-strain Bifidobacterium probiotic during short-term travel promoted the colonization of beneficial bacteria, stabilized gut microbial function against travel-induced dysregulation, and may contribute to supporting systemic well-being during travel.},
}

Humans
*Probiotics/administration & dosage
*Bifidobacterium/physiology
*Gastrointestinal Microbiome/drug effects
Double-Blind Method
Adult
*Travel
Male
China
Female
Feces/microbiology
Young Adult
Bacteria/classification/genetics/isolation & purification

@article {pmid42533584,
year = {2026},
author = {He, LW and Tang, RX and Liu, SY and Zhang, ZJ and Li, Y and Wang, XM and Yue, BS and Fan, ZX},
title = {Host phylogeny and diet shape gut microbiome and virome in wild small mammals of Gongga Mountain, China.},
journal = {Zoological research},
volume = {47},
number = {4},
pages = {1338-1358},
doi = {10.24272/j.issn.2095-8137.2025.448},
pmid = {42533584},
issn = {2095-8137},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Phylogeny ; *Virome ; *Diet/veterinary ; China ; *Rodentia ; *Mammals/virology ; },
abstract = {Gut microbiotas play pivotal roles in host adaptation, yet their composition and function in high-altitude small mammals remain poorly characterized. This study investigated how host phylogeny (order-level) and dietary habits shape the gut microbiome and virome of three mammalian orders (Eulipotyphla, Rodentia, Lagomorpha) in Gongga Mountain, a biodiversity hotspot on the Qinghai-Xizang Plateau. Metagenomic sequencing of 219 samples from 22 species revealed order-specific microbial signatures: Eulipotyphla (carnivorous) harbored higher abundances of potential pathogens (e.g., Helicobacter, Hafnia) and Retroviridae; Lagomorpha (herbivorous) was enriched in cellulolytic bacteria (e.g., Lachnospiraceae, Prevotella) and carbohydrate-active enzymes (CAZymes); Rodentia (omnivorous) showed intermediate traits. We reconstructed 1 385 high-quality metagenome-assembled genomes (MAGs), 1 328 representing novel species, and identified 749 viral operational taxonomic units (vOTUs), >80% being Caudoviricetes. Crucially, Retroviridae abundance in Eulipotyphla suggests zoonotic risk. Phage-host network analysis indicated Caudoviricetes regulates cellulolytic bacteria in Lagomorpha. Host phylogeny and diet jointly drive gut microbiome divergence in small mammals. We establish the first gut microbiome and virome resource of small mammals in the high-altitude area of Gongga Mountain, highlighting Eulipotyphla as a potential vector for zoonotic pathogens.},
}

Animals
*Gastrointestinal Microbiome
*Phylogeny
*Virome
*Diet/veterinary
China
*Rodentia
*Mammals/virology

@article {pmid42534899,
year = {2026},
author = {Guitart-Matas, J and Bravo, M and Tort-Miró, C and Giler-Baquerizo, N and Fraile, L and Caldas-Ramayo, Y and Ballester, M and Migura-Garcia, L},
title = {Dynamics of archaeal diversity and functionality in the piglet gut microbiome under common antimicrobial treatments.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1833734},
pmid = {42534899},
issn = {2235-2988},
mesh = {Animals ; *Archaea/classification/genetics/drug effects ; Swine ; Metagenomics ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Metagenome ; Weaning ; *Biodiversity ; *Anti-Infective Agents/administration & dosage/pharmacology ; Gene Expression Profiling ; Phylogeny ; Diarrhea/drug therapy/veterinary ; Anti-Bacterial Agents ; },
abstract = {INTRODUCTION: The gut microbiota comprises a diverse and dynamic community of microorganisms that collectively enhance host metabolism, physiology, and overall functionality. In this context, the swine archaeome remains largely underexplored despite growing evidence that archaea may greatly influence host health. Advances in high-throughput approaches provide new opportunities to reveal the dynamics and composition of archaea. Herein, we uncover the taxonomic and functional landscape of the piglet archaeome during the weaning transition under multiple experimental conditions, integrating shotgun metagenomic and metatranscriptomic analyses to elucidate its contribution to gut microbial ecology.

METHODS: The seven experimental conditions included four antibiotic treatments for post-weaning diarrhoea (trimethoprim/sulfamethoxazole, colistin, gentamicin, amoxicillin), an oral vaccine, acidifiers in drinking water, and a no-intervention group. A total of 280 faecal samples were collected longitudinally one day before weaning (ST1), three days (ST2), two weeks (ST3), and four weeks (ST4) after the start of the treatment. Treatment was initiated eleven days after arrival at the experimental farm following the onset of clinical signs. Shotgun metagenomics was used to assess archaeal taxonomic diversity and recover archaeal metagenome-assembled genomes (aMAGs), while metatranscriptomics was integrated to assess differentially expressed genes at ST1, ST2, and ST4.

RESULTS: The results revealed archaea as the second most abundant microorganism, exhibiting a longitudinal increase in diversity over the experimental time. The most predominant genus was Methanobrevibacter, including Methanobrevibacter smithii. Eleven high-quality aMAGs were recovered, belonging to the Methanobacteriota and Thermoplasmatota phyla. Genome-inferred functional analyses revealed that the predominant metabolic processes included the biosynthesis of nucleic acids, amino acids, organic anions, and vitamins. Additional functional traits suggested potential roles in the degradation of sugars, amino acids, and antibiotics were also observed. Moreover, significant differences were detected on the archaeal metatranscriptome between the experimental groups treated with antibiotics and the rest of the groups, underscoring their response to changes in microbial interactions, substrate availability and, in some cases, direct effect of the antimicrobials on metabolic pathways.

DISCUSSION: Altogether, this study highlights the biological significance of archaeal dynamics during initial life stages and demonstrates how combining metagenomics and metatranscriptomics uncovers their functional potential and the pathways actively expressed in the piglets' gut.},
}

Animals
*Archaea/classification/genetics/drug effects
Swine
Metagenomics
*Gastrointestinal Microbiome/drug effects
Feces/microbiology
Metagenome
Weaning
*Biodiversity
*Anti-Infective Agents/administration & dosage/pharmacology
Gene Expression Profiling
Phylogeny
Diarrhea/drug therapy/veterinary
Anti-Bacterial Agents

@article {pmid42538237,
year = {2026},
author = {Szentiványi, T and Vásárhelyi, Z and Garamszegi, LZ},
title = {Emerging methods in noninvasive parasite surveillance in wildlife disease ecology.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.07.006},
pmid = {42538237},
issn = {1471-5007},
abstract = {Noninvasive approaches are increasingly reshaping parasite and disease surveillance by reducing stress and harm to hosts while expanding opportunities for ecological and epidemiological research. In this opinion article, we discuss these emerging approaches, which rely on molecular, citizen-science, and computational methods, for monitoring parasites, vectors, and hosts. These tools can improve spatial and temporal coverage, support the surveillance of rare or threatened hosts and parasites, and contribute to the understanding of transmission pathways and disease dynamics. However, their reliability depends on careful validation, standardized protocols, and awareness of methodological limitations. While not direct substitutes for invasive methods, these approaches lift a considerable burden from wildlife. Integrating noninvasive approaches thus provides a strong basis for advancing disease ecology, wildlife health monitoring, and biodiversity conservation.},
}

@article {pmid42548466,
year = {2026},
author = {Yang, L and Tao, Y and He, Y and Liu, S and Gan, L and Dai, A and Ni, Q and Wang, Y and Li, F and Liu, Q and Hu, Y and Wang, Y and Lu, W},
title = {Metagenomic and metabolomic profiling in primary aldosteronism with coexisting obstructive sleep apnea.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1858100},
pmid = {42548466},
issn = {1664-2392},
mesh = {Humans ; *Sleep Apnea, Obstructive/metabolism/complications/microbiology/genetics ; Female ; *Hyperaldosteronism/metabolism/complications/genetics/microbiology ; Male ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; *Metabolome ; Adult ; Feces/microbiology ; Polysomnography ; },
abstract = {BACKGROUND: Primary aldosteronism (PA) frequently coexists with obstructive sleep apnea (OSA), and this comorbidity is associated with increased cardiometabolic risk. Although both PA and OSA have been individually linked to gut microbiome alterations, it remains unclear which layer of gut microbiome-associated variation best reflects clinical heterogeneity in PA with coexisting OSA.

METHODS: In this prospective observational study, we performed shotgun metagenomic sequencing and untargeted fecal metabolomic profiling in 29 adults with clinically confirmed PA, who were stratified according to OSA severity (G1-G4) based on overnight polysomnography. Microbial gene richness, taxonomic composition, functional potential based on KEGG annotation, and antibiotic resistance gene profiles were analyzed using standardized bioinformatic workflows. Metabolomic variation was assessed using multivariate analysis, pathway enrichment, and additional exploratory analyses incorporating apnea-hypopnea index (AHI) as a continuous variable. Multiple-testing correction was applied to metabolite-level comparisons.

RESULTS: Global gut microbial gene richness, alpha diversity, beta diversity, and broad functional profiles did not show strong group-level separation across OSA severity strata. Additional analyses using AHI as a continuous variable similarly showed no significant association between AHI and overall gene richness or alpha diversity indices. Nevertheless, selective genera showed exploratory associations with AHI, suggesting that localized taxonomic signals may occur despite relative stability of global community structure. Antibiotic resistance gene profiles showed marked inter-individual variability without clear group-level separation, although ARO richness showed an exploratory inverse association with AHI. In contrast, fecal metabolomic profiling revealed nominal phenotype-associated differences, including trehalose-related metabolites and FAHFA species that showed inverse exploratory associations with AHI. However, no individual metabolite remained significant after global Benjamini-Hochberg false discovery rate correction.

CONCLUSIONS: In PA with coexisting OSA, gut microbiome-associated heterogeneity appears to be more readily reflected by selected taxonomic and metabolic signals than by global microbial diversity or broad functional potential. However, given the small sample size, limited control of clinical and lifestyle confounders, and lack of metabolite-level significance after global FDR correction, these findings should be interpreted as exploratory and hypothesis-generating. Larger controlled cohorts incorporating PA subtype, medication exposure, dietary assessment, and longitudinal validation are needed.},
}

Humans
*Sleep Apnea, Obstructive/metabolism/complications/microbiology/genetics
Female
*Hyperaldosteronism/metabolism/complications/genetics/microbiology
Male
*Metagenomics/methods
*Metabolomics/methods
Prospective Studies
Middle Aged
*Gastrointestinal Microbiome/genetics
*Metabolome
Adult
Feces/microbiology
Polysomnography

@article {pmid42549419,
year = {2026},
author = {Li, X and Jiang, J and Li, X and Jian, G and Li, F},
title = {Effects of diarrhea and antibiotic-induced microbial elimination on dynamic changes in fecal microbial communities and antibiotic resistance of Hu sheep lambs (Ovis aries).},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21574},
pmid = {42549419},
issn = {2167-8359},
mesh = {Animals ; *Diarrhea/microbiology/veterinary/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Sheep/microbiology ; *Feces/microbiology ; *Sheep Diseases/microbiology/drug therapy ; *Gastrointestinal Microbiome/drug effects/genetics ; Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; *Drug Resistance, Microbial/genetics ; },
abstract = {BACKGROUND: As a highly reproductive meat sheep breed in China, Hu sheep is an important economic group in ruminant animal breeding. However, research on its intestinal microbiomes under the background of diarrhea and antibiotic treatment remains relatively limited.

METHODS: This study investigated the intestinal microbiota of Hu sheep lambs in the preliminary stage of diarrhea (group DM), the late recovery stage of diarrhea (group DL), and the healthy stage (group H). Diseased individuals (groups DM and DL) were treated with a combination of Shuanghuanglian, Cefazolin, Lincomycin, and Dexamethasone (0.2 mL dosage). To characterize the intestinal microbiota, fecal samples were collected from all groups, and metagenomic sequencing was performed. Using metagenomic binning tools and co-assembly methods, we reconstructed 482 high-quality non-redundant metagenome assembled genomes (MAGs).

RESULTS: Among these MAGs, 70% belong to the phyla Bacillota, Bacteroidota, and Pseudomonadota, highly consistent with the typical structure of intestinal microbiota in ruminants. Functional annotation revealed that the genes encoding carbohydrate-active enzymes (CAZymes) are more abundant in Bacillota and Bacteroidota, which supports the degradation and energy metabolism functions of Hu sheep on fibrous feed. During the preliminary stage of diarrhea, the virulence genes carried by symbiotic bacteria such as Lachnospiraceae, Acutalibacteraceae and Bacteroidaceae were enriched. Although diarrhea symptoms alleviated during the late recovery stage of diarrhea, the combined use of multiple antibiotics led to the continuous enrichment of antibiotic resistance genes (ARGs) related to lincosamides and cephalosporins. The average abundance of cephalosporin-related ARGs in group DL was significantly higher than that in group DM and H, indicating a risk of residual ARGs. Microbial diversity analysis showed that there was no significant overall difference in MAGs between group DM and H, but both groups showed significant differences compared to group DL, suggesting that antibiotic driven clearance of sensitive bacteria is the core driving force. Moreover, our study shows that the abundance of the zoonotic pathogens Barnesiella and Campylobacter significantly increased in the diarrhea group (p <  0.05), and they carry 567 and 382 virulence genes, respectively. Their pathogenicity is regulated by the dynamic changes in the host intestinal microbiota.

CONCLUSIONS: This study not only expands the genomic database of ruminant intestinal microorganisms but also provides a key theoretical basis for formulating intestinal microecological regulation strategies and optimizing diarrhea treatment regimens for Hu sheep.},
}

Animals
*Diarrhea/microbiology/veterinary/drug therapy
*Anti-Bacterial Agents/pharmacology/therapeutic use
Sheep/microbiology
*Feces/microbiology
*Sheep Diseases/microbiology/drug therapy
*Gastrointestinal Microbiome/drug effects/genetics
Bacteria/drug effects/genetics
*Drug Resistance, Bacterial/genetics
Metagenome
*Drug Resistance, Microbial/genetics

@article {pmid42551623,
year = {2026},
author = {Shahid, M and Raj, A and Shafi, Z and Ali, S},
title = {Nanopesticides-rhizo-microbiome interactions: Biochemical mechanisms, ecotoxicological effects and implications for pesticide fate and transformation.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110651},
doi = {10.1016/j.cbpc.2026.110651},
pmid = {42551623},
issn = {1532-0456},
abstract = {Nano-enabled pesticides (NanoPs) formulations have emerged as promising alternative to conventional pesticides by improving ingredient stability, delivery, and controlled release. However, their unique physicochemical properties also influence interactions with soil microorganisms, raising concerns regarding ecological safety and long-term impacts on soil ecosystem functions. This review has critically synthesized the current knowledge about NanoPs-microbiome interactions with a focus on biochemical mechanisms underlying microbial responses and implications for pesticide fate and transformation. We review how the properties of NPs (e.g., particle size, surface charge, coatings, dissolution, and eco-corona formation) influence mobility, bioavailability, and microbial exposure. Mechanistic evidence of oxidative stress, membrane damage, enzyme inhibition, metal-ion-mediated toxicity and quorum sensing interference is critically synthesized to elucidate biochemical basis of NanoPs-induced microbial responses. Recent advances in high throughput sequencing and multi-omics technologies are also used to assess changes in microbial diversity, community composition, functional redundancy, microbial interaction networks and ecosystem resilience. The review further compares conventional and nano-formulated pesticides, highlighting differences in microbial toxicity, degradation kinetics, transformation pathways, and metabolite profiles. Current challenges associated with environmental fate assessment, standardized ecotoxicological testing, and microbiome-informed risk evaluation are critically discussed. Emerging opportunities for integrating metagenomics, artificial intelligence, and predictive modelling into environmental risk assessment are also highlighted. Finally, we propose a future research framework centered on microbiome-informed safe-by-design NanoPs, standardized testing protocols, and long-term field validation to support development of environmentally responsible nano-enabled crop protection technologies while preserving soil biodiversity and ecosystem functions.},
}

@article {pmid42218533,
year = {2026},
author = {Kim, W and Kim, JE and Hong, YS and Hwang, DW and Kim, J and Lee, JS and Shin, JH and Kim, TW and Nagarkar, D and Byrd, A and Sung, CO and Kim, SY},
title = {Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42218533},
issn = {1756-994X},
support = {ASA-1 project//This work was supported by the imCORE Network on behalf of F. Hoffmann-La Roche (ASA-1 project)./ ; },
mesh = {Humans ; *Liver Neoplasms/secondary/drug therapy ; *Colorectal Neoplasms/pathology/drug therapy/microbiology ; Female ; Neoadjuvant Therapy ; Male ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Fluorouracil/therapeutic use ; Leucovorin/therapeutic use ; Middle Aged ; Tumor Microenvironment/drug effects ; Aged ; Treatment Outcome ; Bevacizumab/therapeutic use ; Adult ; *Microbiota ; Organoplatinum Compounds/therapeutic use ; },
abstract = {BACKGROUND: This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes.

METHODS: The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n = 60, CRLM treated with or without neoadjuvant chemotherapy) and prospectively registered cohort B (n = 20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was performed for stool samples from cohort B.

RESULTS: Durable disease control (PFS ≥ 24 months) was observed in 35% (7/20) of patients receiving ABFOLFOX. Analysis revealed a progressive increase in the immunogenic microenvironment within CRLM tissues upon the addition of therapeutic agents, specifically bevacizumab, and the most significant TE changes in CRLM were observed in those treated with ABFOLFOX in cohort B. The monocyte lineage was significantly associated with benefit from ABFOLFOX. Good responders exhibited improved immune response and notable activation of the SP140 transcription factor regulon. Moreover, microbiome analysis revealed that high abundance of Prevotella was positively correlated with good response and enhanced immune environment within the tumor. Causal mediation analysis suggested that the gut microbiome partially links the ABFOLFOX treatment response to the tumor microenvironment.

CONCLUSIONS: ABFOLFOX enhances the TE immune profile of CRLM, which is further augmented by the gut-liver axis characterized by Prevotella abundance, and can induce durable disease control in a subgroup of patients.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT03698461. May 08, 2019 (prospectively registered).},
}

Humans
*Liver Neoplasms/secondary/drug therapy
*Colorectal Neoplasms/pathology/drug therapy/microbiology
Female
Neoadjuvant Therapy
Male
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use
Fluorouracil/therapeutic use
Leucovorin/therapeutic use
Middle Aged
Tumor Microenvironment/drug effects
Aged
Treatment Outcome
Bevacizumab/therapeutic use
Adult
*Microbiota
Organoplatinum Compounds/therapeutic use

@article {pmid42364169,
year = {2026},
author = {Pan, P and Zhou, NY},
title = {Metabolic interactions enable aerobic degradation of the environmental pollutant BDE-47.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag163},
pmid = {42364169},
issn = {1751-7370},
support = {JYB2025XDXM906//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; 2024YFA0919000//National Key R&D Program of China/ ; },
mesh = {*Halogenated Diphenyl Ethers/metabolism ; Biodegradation, Environmental ; Aerobiosis ; *Environmental Pollutants/metabolism ; Metabolic Networks and Pathways ; Wastewater/microbiology ; Microbial Consortia ; },
abstract = {As a prevalent congener of polybrominated diphenyl ethers (PBDEs), 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) poses significant environmental and health risks due to its persistence and bioaccumulation. However, the limited understanding of the microbial degradation mechanism of BDE-47 has hindered the development of effective bioremediation strategies. Here, we decipher an aerobic catabolic pathway of BDE-47 mediated by metabolic relay within a synthetic consortium composed of two environmental isolates, Rhizorhabdus wittichii YL-JM2C and Cupriavidus necator JMP134. Bioaugmentation with this consortium achieved complete removal of BDE-47 in real wastewater samples. The molecular basis underlying this cooperative degradation was elucidated through the heterologous expression and functional characterization of key enzymes involved. Namely, the dioxygenase TcsAaAb from strain YL-JM2C catalyzed the initial conversion of BDE-47 into 2,4-dibromophenol (2,4-DBP) and 3,5-dibromocatechol (3,5-DBC). As a dead-end intermediate in strain YL-JM2C, the former (2,4-DBP) was subsequently transformed into the latter (3,5-DBC) by the hydroxylase TfdB from strain JMP134. The resulting 3,5-DBC was catabolized through the downstream ortho-cleavage pathway present in both strains. These key enzymes for BDE-47 degradation coexist across diverse environments, including soil, seawater, and marine sediments. Global marine metagenomic profiling revealed a significant enrichment of these catabolic signatures in the Mariana Trench, implying that microorganisms in the hadal zone possess the genetic potential for PBDE catabolism. This study unveils previously unrecognized aerobic catabolic mechanisms for BDE-47 within natural ecosystems, offering promising bioremediation strategies for PBDE-contaminated environments.},
}

*Halogenated Diphenyl Ethers/metabolism
Biodegradation, Environmental
Aerobiosis
*Environmental Pollutants/metabolism
Metabolic Networks and Pathways
Wastewater/microbiology
Microbial Consortia

@article {pmid42515825,
year = {2026},
author = {Kean, K and Mayne, RM and Reid, K and Secret, S and Singleton, BK and Rockett, R and Rajendra, P and Harvala, H and Breuer, J and Azim Ansari, M and Lythgoe, K and Simmonds, P and Golubchik, T},
title = {A Snapshot of the UK Blood Donor Plasma Virome: A Retrospective Cross-Sectional Cohort Study.},
journal = {Journal of medical virology},
volume = {98},
number = {8},
pages = {e71081},
pmid = {42515825},
issn = {1096-9071},
support = {NIHR203338//National Institute for Health and Care Research/ ; },
mesh = {Humans ; *Blood Donors ; *Virome ; Cross-Sectional Studies ; United Kingdom/epidemiology ; *Plasma/virology ; Retrospective Studies ; Female ; Male ; Viral Load ; Metagenomics ; Blood Donation ; Adult ; *Viruses/classification/isolation & purification/genetics ; Prevalence ; Sequence Analysis, DNA ; Phylogeny ; Middle Aged ; },
abstract = {Estimates of population prevalence and genetic diversity of bloodborne viruses in healthy humans are essential to support population-scale monitoring for transfusion transmission risk. In the UK and globally, blood donations are routinely screened for a limited number of high-consequence pathogens, but the full composition of the plasma virome remains to be characterized. Using a novel quantitative targeted metagenomics sequencing approach, we analyzed previously unscreened plasma donations collected by NHS Blood and Transplant in England for all major pathogenic and known commensal human bloodborne viruses, and quantified their viral burden. Here we show that in a representative sample of 5064 UK blood donors in pools of 24 collected over a 1-month period, the virome was dominated by a small number of largely persistent species, representing < 10% (10/106) of previously identified human bloodborne viruses. The principal genera of human anelloviruses (TTV, TTMV and TTMDV) were detected in 89% of pools, albeit at low read count, inconsistent with measured anellovirus viral loads. In contrast, human pegivirus type 1 (HPgV-1), had an estimated population prevalence of 3.7% (95% CI 3.0%-4.4%), with high read count and complete genome recovery in around one half of positive pools, consistent with high titer in plasma. Less common detections included one species of gemykibovirus in five separate plasma pools, one hepatitis C virus (genotype 1a), and polyomaviruses and herpesviruses with prevalences between 0.04% (parvovirus 4, BK polyomavirus) to 0.41% (human herpesvirus 6). Phylogenetic analyses revealed mixed TTV, TTMV, and TTMDV populations and almost exclusively genotype 2 HPgV-1, consistent with known genotype distributions in Europe. Our results provide a baseline for describing the healthy plasma virome in UK blood donors.},
}

Humans
*Blood Donors
*Virome
Cross-Sectional Studies
United Kingdom/epidemiology
*Plasma/virology
Retrospective Studies
Female
Male
Viral Load
Metagenomics
Blood Donation
Adult
*Viruses/classification/isolation & purification/genetics
Prevalence
Sequence Analysis, DNA
Phylogeny
Middle Aged

@article {pmid42516368,
year = {2026},
author = {Zhang, Y and Wang, S and Chang, S and Li, Y and Dang, Y and Wang, Z},
title = {Navigating the gut-metabolite-immune axis: enhancing efficacy and mitigating toxicity of immune checkpoint inhibitors.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1803970},
pmid = {42516368},
issn = {1664-3224},
mesh = {Humans ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; *Gastrointestinal Microbiome/immunology/drug effects ; Animals ; *Neoplasms/immunology/drug therapy/microbiology/metabolism ; Tumor Microenvironment/immunology/drug effects ; Fecal Microbiota Transplantation ; },
abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the oncological landscape by disrupting inhibitory pathways, notably programmed cell death protein-1/programmed death-ligand 1 (PD-1/PD-L1) and cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) pathways, thereby reinvigorating host antitumor immunity. Although these agents have emerged as frontline standard therapies for malignancies, their clinical utility remains limited. Interpatient therapeutic variability is inextricably linked to the composition and functional capacity of the gut microbiome. The underlying mechanisms appear to involve a complex dialogue between the microbiota and host immune system, where microbial metabolites serve as critical mediators in remodeling the tumor microenvironment. Despite these insights, progression in the field remains constrained due to heterogeneity in study cohorts and sample-processing methodologies, hindering the establishment of reproducible individualized predictive models and clinical intervention strategies. Consequently, there is an urgent need to systematically delineate the microbiome-metabolite-immune axis to optimize the balance between ICI efficacy and systemic toxicity. By synthesizing the latest evidence, this review aimed to highlight the pivotal roles of specific taxa, including Bacteroides, Bifidobacterium, and Akkermansia muciniphila, in ICI efficacy. These microbes and their metabolic byproducts potentiate therapeutic responses by enhancing dendritic cell cross-presentation and promoting CD[8+] T-cell infiltration, often via activation of the cyclic GMP-AMP synthase-stimulator of interferon genes or nucleotide-binding oligomerization domain-containing protein 2 signaling pathways. Furthermore, these microbial components demonstrate the ability to protect the heart and colon against inflammation and barrier disruption, thereby mitigating immune-related adverse events. Although the feasibility and safety of interventions such as fecal microbiota transplantation and supplementation with next-generation encapsulated probiotics, postbiotics, or dietary fiber have been demonstrated in preclinical and Phase I trials, substantial hurdles remain. Future progress requires large-scale, multicenter, standardized, longitudinal studies integrating metagenomics and metabolomics to construct robust cross-cancer and cross-population predictive models. Such rigorous validation would enable the development of precise microbial interventions that maximize therapeutic gains while minimizing the incidence of adverse reactions.},
}

Humans
*Immune Checkpoint Inhibitors/adverse effects/therapeutic use
*Gastrointestinal Microbiome/immunology/drug effects
Animals
*Neoplasms/immunology/drug therapy/microbiology/metabolism
Tumor Microenvironment/immunology/drug effects
Fecal Microbiota Transplantation

@article {pmid41387551,
year = {2026},
author = {Kelsey, C and Moulder, R and Yancey, H and Prescott, S and McCulloch, JA and Trinchieri, G and Dreisbach, C and Alhusen, J and Grossmann, T},
title = {Bidirectional relations between the maternal and infant gut microbiome and behavior.},
journal = {Pediatric research},
volume = {99},
number = {6},
pages = {2335-2344},
pmid = {41387551},
issn = {1530-0447},
support = {K99 HD115830/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; Female ; Infant ; *Gastrointestinal Microbiome ; *Infant Behavior ; *Mothers ; Adult ; Feces/microbiology ; Male ; Infant, Newborn ; *Mother-Child Relations ; Temperament ; Surveys and Questionnaires ; Metagenomics ; },
abstract = {BACKGROUND: An infant's mother is one of the first sources of neonatal microbial colonization, and infant-maternal dyad microbial variations have been linked to childhood behavioral traits and mental health outcomes. However, how the gut microbiome influences mental health, including potential bidirectional relations between mother and child, remains poorly understood.

METHOD: Using metagenomic sequencing and behavioral questionnaires, we examined within-person and between-person (mother-infant dyad) associations between the gut microbiota and behavior across the first year of postnatal life (N = 121 dyads; N = 514 stool samples).

RESULTS: There were rapid changes in taxa diversity and gut microbiota composition for infants, whereas the maternal microbiome remains relatively constant. Gut microbes and functional terms (e.g., antibiotic resistance genes and virulence factors) were associated with infant temperament but not maternal depression symptoms. Whereas maternal depression was not associated with any maternal taxa or functional terms.

CONCLUSIONS: Our findings provide evidence for complex within- and between-person relations between maternal and infant gut microbiomes and behavioral traits.

IMPACT: How the gut microbiome influences maternal mental health and infant behavior remains poorly understood. We measured mothers' and infants' gut microbiota composition and behavior across the first year of the infant's life. Individual taxa from the infant, but not the maternal, gut were associated with infant behavioral temperament. Our findings provide evidence for complex bidirectional gut-behavior associations between mothers and infants.},
}

Humans
Female
Infant
*Gastrointestinal Microbiome
*Infant Behavior
*Mothers
Adult
Feces/microbiology
Male
Infant, Newborn
*Mother-Child Relations
Temperament
Surveys and Questionnaires
Metagenomics

@article {pmid41934012,
year = {2026},
author = {Moraïs, S and Mizrahi, I},
title = {Micro-scale spatial metagenomics opens a new era in microbiome ecology.},
journal = {Trends in microbiology},
volume = {34},
number = {8},
pages = {820-827},
doi = {10.1016/j.tim.2026.03.005},
pmid = {41934012},
issn = {1878-4380},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; Microbial Interactions ; Ecosystem ; Ecology ; Bacteria/genetics ; },
abstract = {Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, genes, expression profiles, and interactions at scales and dimensions in which microbial life unfolds. In this opinion article, we synthesize recent findings and emerging approaches that enable the investigation of microbial interactions within their native 3D context. We propose conceptual frameworks for integrating spatial-functional information into comprehensive ecological maps, providing new avenues to interpret microbial interactions and to test ecological theory in situ. Together, these insights outline a new ecological paradigm for microbiome research and highlight how spatially resolved understanding can be harnessed to interpret and ultimately guide the modulation of microbial interactions and ecosystem function in natural settings.},
}

*Microbiota/genetics
*Metagenomics/methods
Microbial Interactions
Ecosystem
Ecology
Bacteria/genetics

@article {pmid41947478,
year = {2026},
author = {Yang, X and Zhu, C and Liu, B and Yang, P and Cao, Z and Liang, J and Hu, J and Yu, Q and Zhong, Y and Du, W and Chow, J and Yan, S and Liu, H and Li, L and Wang, T and Gu, Y and Ma, G},
title = {Astragaloside IV Exhibited Antidiabetic Effects by Improving Glucose Metabolism, Repairing Damaged Gut Barrier and Regulating Intestinal Microbiota.},
journal = {Phytotherapy research : PTR},
volume = {40},
number = {8},
pages = {5016-5029},
doi = {10.1002/ptr.70205},
pmid = {41947478},
issn = {1099-1573},
support = {81374051//National Natural Science Foundation of China/ ; 81873078//National Natural Science Foundation of China/ ; 82074109//National Natural Science Foundation of China/ ; 82374133//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Saponins/pharmacology ; Humans ; *Triterpenes/pharmacology ; Caco-2 Cells ; *Gastrointestinal Microbiome/drug effects ; *Hypoglycemic Agents/pharmacology ; Mice ; Intestinal Barrier Function/drug effects ; Male ; Diabetes Mellitus, Type 2/drug therapy/metabolism ; Fatty Acids, Volatile/metabolism ; *Glucose/metabolism ; Mice, Inbred C57BL ; Intestinal Mucosa/drug effects/metabolism ; Feces/chemistry ; Blood Glucose/metabolism/drug effects ; },
abstract = {Astragaloside IV (AS-IV), a main active ingredient derived from Astragali Radix, displays a favorable effect in treating type 2 diabetes mellitus (T2DM). This study was aimed to figure out its antidiabetic mechanisms. The db/db mice were treated with AS-IV, and the metabolism phenotype and epithelial barrier permeability were tested. Trans-epithelial resistance assay was performed in Caco-2 cells. Metagenomic sequencing was used to determine the gut microbiota composition and function. The content of short-chain fatty acid (SCFA) in feces was determined using Agilent 8890-5977B GC-MS. Despite increasing mice body weight, AS-IV significantly reduced hyperglycemia in the db/db mice, decreased the ratio of liver weight/body weight, alleviated hepatic total cholesterol and triglyceride levels. AS-IV reduced inflammation through suppressing pro-inflammatory genes (Il1b, Tnf, Ccl2) and elevating anti-inflammatory genes (Il10, Il4, Il13, Il33) in the colonic epithelium. AS-IV also reversed the increased intestinal permeability and decreased expression of tight junction (TJ) proteins Claudin-1, ZO-1 in the db/db mice and Claudin-1, Occludin in Caco-2 cells. Additionally, metagenomic sequencing showed AS-IV altered composition and function of gut microbiota. The 80 species of gut microbiota were markedly changed, e.g., boosting of Alistipes spp. and Prevotella copri, decreasing of relative abundance of Ruminococcus gnavus and Enterocloster bolteae. AS-IV upregulated the SCFA related pathway, increased the content of SCFA, upregulated the transcription levels of SCFA receptors (i.e., GPR41, GPR43 and GPR109a), thereby improved glucose metabolism in the db/db mice. These findings demonstrate that AS-IV exhibited favorable antidiabetic effects by improving glucose metabolism and altering intestinal microbiota symbiosis via repairing the damaged gut barrier. This study will provide valuable reference for the development of new antidiabetic drugs and medication of T2DM.},
}

Animals
*Saponins/pharmacology
Humans
*Triterpenes/pharmacology
Caco-2 Cells
*Gastrointestinal Microbiome/drug effects
*Hypoglycemic Agents/pharmacology
Mice
Intestinal Barrier Function/drug effects
Male
Diabetes Mellitus, Type 2/drug therapy/metabolism
Fatty Acids, Volatile/metabolism
*Glucose/metabolism
Mice, Inbred C57BL
Intestinal Mucosa/drug effects/metabolism
Feces/chemistry
Blood Glucose/metabolism/drug effects

@article {pmid42062664,
year = {2026},
author = {Kieliszek, M},
title = {Selenium: From Redox Signaling to Interactions with the Gut Microbiome.},
journal = {Biological trace element research},
volume = {204},
number = {9},
pages = {6552-6563},
pmid = {42062664},
issn = {1559-0720},
mesh = {*Selenium/metabolism ; Humans ; Oxidation-Reduction ; *Gastrointestinal Microbiome/physiology ; *Signal Transduction ; Animals ; Selenoproteins/metabolism ; Antioxidants/metabolism ; },
abstract = {Selenium is an element that plays a crucial role in the proper functioning of the body. It is a component of selenoproteins, which exhibit strong antioxidant properties. This allows it to neutralize reactive oxygen species and protect cells from oxidative stress. It also plays a crucial role in supporting the proper functioning of the immune system. In this context, particular importance is attributed to its influence on the Th1/Th2 immune response and the activity of T lymphocytes and NK cells. There is a mutual relationship between selenium and the intestinal microbiota. Microorganisms in the gastrointestinal tract participate in the accumulation, transformation, and differentiation of selenium's chemical forms. These processes influence selenium's bioavailability and its activity in the host organism. The development of metagenomic methods has enabled the identification of specific selenium-dependent metabolic pathways within the microbiome. This represents an important research direction in the development of this field of biotechnology. In turn, appropriate selenium levels and selenoprotein activity influence the composition of the intestinal microbiota and the metabolite profile it produces. It is worth emphasizing that in the context of the development of microbiome engineering, there are also emerging concepts of designing probiotics capable of controlled selenium biotransformation. The beneficial properties of selenium for organisms depend on its appropriate chemical form and dose. It is worth noting that selenium deficiency can impair the antioxidant system, leading to a redox imbalance. Such processes can weaken the integrity of the intestinal barrier, leading to the development of various gastrointestinal diseases. Therefore, the interaction with intestinal microflora is such a crucial element of selenium's action. Microorganisms inhabiting the digestive tract participate in the processes of accumulation and transformation of various chemical forms of this element. These biochemical properties of microorganisms are crucial for the bioavailability of selenium in the human body. Therefore, the appropriate form of selenium is crucial for the proper functioning of the intestinal barrier. This article discusses the importance of selenium in redox processes and in the function of the gut microbiota. It highlights the potential role of this element in the prevention and treatment of gastrointestinal diseases. Future research should focus on further understanding these interactions and developing targeted approaches that utilize selenium-dependent pathways to restore intestinal homeostasis.},
}

*Selenium/metabolism
Humans
Oxidation-Reduction
*Gastrointestinal Microbiome/physiology
*Signal Transduction
Animals
Selenoproteins/metabolism
Antioxidants/metabolism

@article {pmid42141123,
year = {2026},
author = {Han, S and Wu, Z and Wu, Y and Wang, Z and Qian, P and Chu, J and Li, J and Zhuang, J and Yang, X},
title = {Decoding the human gut bacterial plasmids in colorectal cancer.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {42141123},
issn = {2399-3642},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Plasmids/genetics ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics ; Metagenomics ; },
abstract = {Gut plasmids show heightened sensitivity to gut microenvironmental changes compared to their bacterial hosts. To explore their significance in colorectal cancer (CRC), we analyzed metagenomic data from 863 participants (312 CRC, 387 high-risk, 164 low-risk). Plasmid and bacterial profiles were characterized, along with trace elements and metabolites. Differential analysis, functional gene assessment (ARG, MGE, MRG, VFGB), random forest modeling, and structural equation modeling (SEM) were applied. In terms of overall abundance, plasmids in both the high-risk and CRC groups exhibited a decreasing trend. Gut plasmids significantly influenced the functional genes (ARG, MGE, MRG, VFGB) of their bacterial hosts. Six key bacterial hosts (Enterobacterales, Bucrkholderiales, Hyphomicrobiales, Lactobacillales, Bacteroidales, Campylobacterales) and 12 plasmid markers were identified. The plasmid-based model effectively predicted CRC risk. SEM revealed that trace elements (e.g., Ni), metabolites (e.g., 5-Hydroxytryptophol), and host bacteria (e.g., Campylobacterales, Enterobacterales) predominantly exerted negative effects on most plasmids, whereas Ni exhibited a positive influence on plasmids NZ_CP013564.1, NZ_CP024312.1, and NZ_CP48284.1. We characterized the composition of gut plasmids and their bacterial hosts, explored the impacts of gut plasmids on bacterial functionality, and mapped multi-omics interaction networks linking plasmids, hosts, and metabolic features.},
}

Humans
*Colorectal Neoplasms/microbiology/genetics
*Plasmids/genetics
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics
Metagenomics

@article {pmid42315843,
year = {2026},
author = {Hounmanou, YMG and Gussin, GM and Conlan, S and Singh, RD and Deming, C and Proctor, DM and Teixeira, M and Earl, AM and Worby, CJ and Kong, HH and Huang, SS and Segre, JA},
title = {Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42315843},
issn = {2041-1723},
support = {ZIA-HG200382-14//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; },
mesh = {Humans ; Nursing Home Residents ; *Nursing Homes ; Skin Microbiome ; *Skin/microbiology ; Escherichia coli/isolation & purification/genetics ; Female ; Male ; Drug Resistance, Multiple, Bacterial/genetics ; Metagenomics ; Aged ; Aged, 80 and over ; Methicillin-Resistant Staphylococcus aureus/isolation & purification/genetics ; Staphylococcus epidermidis/isolation & purification/genetics ; California ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Metagenome ; },
abstract = {Antimicrobial resistance (AMR) is a health threat disproportionately affecting nursing home (NH) residents. Surveillance and infection control in NHs are restricted to nares or perirectal cultures, overlooking skin colonization and multidrug-resistant organisms (MDROs) not recovered by selective media. Here, within the PROTECT trial NCT03118232, we show, that NH residents' skin serves as a reservoir of transmissible MDROs. We analyzed 207 groin and axilla swabs from 38 residents across 15 California NHs using metagenomics, culturing, and genome sequencing. Culture detected MDROs in 10 of 38 residents (26.3%), including 4 (10.5%) with ESBL-producing Escherichia coli sequence type (ST)131/ST648 and 7 (18.4%) with methicillin-resistant Staphylococcus aureus. Skin microbiome analysis by metagenome-assembled genomes identified broader MDRO colonization, including 27 (71.1%) with E. coli ST93, 14 (36.8%) with Staphylococcus epidermidis ST2, 16 (42.1%) with Proteus mirabilis, 7 (18.4%) with Providencia stuartii, 7 (18.4%) with Enterococcus faecalis, and 5 (13.2%) with Pseudomonas aeruginosa. Colonization persisted after bathing. Clonal E. coli ST93 was shared by 27 residents across 9 facilities, and 5 resident pairs carried clonally related strains of ≥2 MDRO species, suggesting polymicrobial transmission. We confirmed skin as a reservoir of MDROs, utilizing metagenomics to detect colonization and transmission pathways, supporting AMR surveillance in long-term care.},
}

Humans
Nursing Home Residents
*Nursing Homes
Skin Microbiome
*Skin/microbiology
Escherichia coli/isolation & purification/genetics
Female
Male
Drug Resistance, Multiple, Bacterial/genetics
Metagenomics
Aged
Aged, 80 and over
Methicillin-Resistant Staphylococcus aureus/isolation & purification/genetics
Staphylococcus epidermidis/isolation & purification/genetics
California
Anti-Bacterial Agents/pharmacology/therapeutic use
Metagenome

@article {pmid42398208,
year = {2026},
author = {Yi, Y and Li, D and Li, Y and Wang, H and Yang, D and Yang, S and Xing, S and Wei, S and Yang, J and Guo, H and Luo, Z},
title = {Abrus cantoniensis α-glucan-like polysaccharide alleviates influenza via gut microbial acetate to activate free fatty acid receptor 2/ mitochondrial antiviral signaling protein/interferon-beta pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {159},
number = {},
pages = {158533},
doi = {10.1016/j.phymed.2026.158533},
pmid = {42398208},
issn = {1618-095X},
mesh = {Animals ; *Polysaccharides/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Orthomyxoviridae Infections/drug therapy ; Signal Transduction/drug effects ; *Abrus/chemistry ; *Antiviral Agents/pharmacology ; Interferon-beta/metabolism ; Female ; Mice, Inbred BALB C ; Influenza A Virus, H1N1 Subtype/drug effects ; Dogs ; Male ; },
abstract = {BACKGROUND: The gut microbiota is critical for host defense against influenza. Polysaccharides are known for their microbiota-modulating and immunomodulatory activities; however, the anti-influenza efficacy of homogeneous Abrus cantoniensis polysaccharides (ACP) remains unexplored.

PURPOSE: The present study seeks to clarify the protective role of ACP in influenza and explore its underlying molecular mechanisms.

METHODS: Initially, crude polysaccharides were extracted via ethanol precipitation and subsequently purified by gel chromatography. Systematic structural characterization of ACP was then performed using carbohydrate chemistry techniques, including scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), ultraviolet (UV) spectroscopy, and nuclear magnetic resonance (NMR). The therapeutic efficacy of ACP was assessed by monitoring various indicators such as body weight, survival rate, viral load, and pulmonary pathological changes in mouse models. Furthermore, to elucidate the biological mechanism underlying ACP's anti-influenza activity via regulation of pulmonary interferon-beta (IFN-β) immune networks by intestinal acetate-producing microbiota, multi-omics analyses integrating metagenomics, metabolomics, gene knockout, immunofluorescence, and Western blot were conducted. Finally, the potential anti-influenza effects of ACP via the gut-lung axis were evaluated based on in vivo and in vitro detection of protein expression of IFN-β, free fatty acid receptor 2 (FFAR2), and mitochondrial antiviral signaling protein (MAVS), as well as antiviral interferon-stimulated genes (ISGs).

RESULTS: In this study, we purified a novel polysaccharide, ACP-A1, with a backbone of→4)-α-D-Glcp-(1→,→4)-β-D-Galp-(1→, and →4,6)-α-D-Glcp-(1→ linkages and α-D-Glcp-(1→ branches at O-6. In H1N1-infected mice, oral ACP-A1 alleviated weight loss, increased survival, and reduced lung inflammation and viral load. Metagenomic and targeted metabolomic analyses showed that ACP-A1 enriched Limosilactobacillus reuteri and elevated acetate levels. Fecal microbiota transplantation, FFAR2 inhibition, and MAVS knockout experiments demonstrated that ACP-A1 enhances the FFAR2/MAVS/IFN-β antiviral pathway via microbial-derived acetate.

CONCLUSION: Collectively, our findings elucidate that ACP mitigates influenza virus-induced lung dysfunction by promoting the proliferation of acetate-producing gut microbiota, particularly Limosilactobacillus reuteri, and activating the FFAR2/MAVS/IFN-β antiviral axis in pulmonary immune cells. These findings establish ACP-A1 as a natural polysaccharide regulating IFN-β homeostasis, highlighting its potential for influenza prevention.},
}

Animals
*Polysaccharides/pharmacology
Mice
*Gastrointestinal Microbiome/drug effects
*Orthomyxoviridae Infections/drug therapy
Signal Transduction/drug effects
*Abrus/chemistry
*Antiviral Agents/pharmacology
Interferon-beta/metabolism
Female
Mice, Inbred BALB C
Influenza A Virus, H1N1 Subtype/drug effects
Dogs
Male

@article {pmid42448967,
year = {2026},
author = {Sittipo, P and Park, JY and Tiffany, E and Oh, A and Moon, S and Lee, CH and Oh, JS and Kim, TY and Kweon, MN and Choi, J and Song, KH and Lee, DW and Nam, MH and Hong, SJ and Lee, EY and Jeon, SR and Song, HY and Kim, BS and Lee, YK},
title = {Gut microbiome modulation by Veillonella ratti induces resistance to EAE pathogenesis via microbe-derived metabolites.},
journal = {Experimental & molecular medicine},
volume = {58},
number = {7},
pages = {2339-2355},
pmid = {42448967},
issn = {2092-6413},
support = {2021M3A9I4027993//National Research Foundation of Korea (NRF)/ ; RS-2023-00219563//National Research Foundation of Korea (NRF)/ ; 2021M3A9I4023974//National Research Foundation of Korea (NRF)/ ; },
mesh = {Animals ; *Encephalomyelitis, Autoimmune, Experimental/metabolism/microbiology/etiology/pathology/immunology ; Humans ; Mice ; *Gastrointestinal Microbiome ; Female ; Disease Models, Animal ; Microglia/metabolism/immunology ; Phosphatidylethanolamines/metabolism ; Multiple Sclerosis ; },
abstract = {The progression of multiple sclerosis (MS) is potentially influenced by the microbiome. Elucidating host-microbiome interactions in MS may aid in developing microbiome-based applications; however, these interactions remain unclear. Here, we aimed to elucidate how Veillonella ratti MHL0042, isolated from human infant feces, modulates neuroinflammation and disease severity in experimental autoimmune encephalomyelitis, a murine MS model. Whole metagenomic sequencing revealed that V. ratti MHL0042 reshaped disrupted gut microbiota via microbial interactions throughout the intestinal tract. V. ratti MHL0042 administration significantly reduced central nervous system inflammation, notably decreasing CD4[+]IFN-γ[+] T cell populations and activated spinal cord microglia. Mechanistically, V. ratti MHL0042 depleted pldA-containing bacteria, involved in phosphatidylethanolamine metabolism, thus elevating dioleoyl phosphatidylethanolamine (DOPE) levels. Increased DOPE was not only detected in the intestinal tract but also extended systemically and reflected in the central nervous system. Exogenous DOPE administration recapitulated the attenuation of experimental autoimmune encephalomyelitis pathogenesis by suppressing microglial activation. These findings highlight the therapeutic applicability of the microbiome and underscore its potential in human disease treatment.},
}

Animals
*Encephalomyelitis, Autoimmune, Experimental/metabolism/microbiology/etiology/pathology/immunology
Humans
Mice
*Gastrointestinal Microbiome
Female
Disease Models, Animal
Microglia/metabolism/immunology
Phosphatidylethanolamines/metabolism
Multiple Sclerosis

@article {pmid42477864,
year = {2026},
author = {Lakamp, AD and Adams, S and Kuehn, LA and Snelling, WM and Wells, J and Hales, K and Neville, B and Fernando, SC and Spangler, ML},
title = {Influence of host genetics on the functional composition of the rumen metagenome in beef cattle.},
journal = {Journal of animal science},
volume = {104},
number = {},
pages = {},
doi = {10.1093/jas/skag224},
pmid = {42477864},
issn = {1525-3163},
support = {2022-33522-38219//USDA-National Institute of Food and Agriculture/ ; 2023-68015-40015//USDA-National Institute of Food and Agriculture/ ; 2024-33522-43699//USDA-National Institute of Food and Agriculture/ ; 2018-67015-27496//USDA-National Institute of Food and Agriculture/ ; },
mesh = {Animals ; *Rumen/microbiology ; Cattle/genetics/microbiology ; *Metagenome ; Diet/veterinary ; Genotype ; *Gastrointestinal Microbiome/genetics ; Male ; },
abstract = {Cattle rely on the microorganisms in their rumen to break down plant matter into useable nutrients. Studies have demonstrated that the rumen microbiome plays a critical role in economically important traits. One factor that impacts rumen microbial community assembly is the host genome. Previous studies have demonstrated host genetics affect rumen microbial community composition and the association of microbiome features with production traits. However, gaps exist relative to the underlying host genetic influence on functional features of the rumen metagenome. Here we elucidated the relationship between host genetics and functional composition of the rumen metagenome while identifying metagenomic features which may provide targets for genetic selection. Rumen samples were collected via esophageal tubing from 717 beef cattle on four diets and were subjected to shotgun sequencing from which open reading frames (ORFs) were predicted. Animal genotypes were generated from imputation based on low-pass sequencing and array data. The log-transformed relative abundance of 16,350 ORFs were used as phenotypes in linear mixed models with the random effect of host genotype. In this population of 717 animals, approximately 4% of the ORFs had heritability estimates larger than twice their standard error and more than 10% of the ORFs had estimates greater than 0.20. Functions of highly heritable ORFs included aromatic amino acid biosynthesis and genome regulation. Additionally, some ORFs were genetically correlated with production traits. Eleven host genes were associated with more than one ORF. The functionality of these candidate host genes can be generally classified as either immune-related, metabolism-related, or possibly involved in host-microbiome crosstalk. Host genetics influence the rumen microbiome function making genetic selection of the host an avenue to alter rumen microbiome functionality. Associations between host genes and rumen metagenome composition indicate multiple potential biological mechanisms underlie these associations. Moreover, a portion of the highly heritable ORFs are genetically correlated with feed efficiency traits making them potential selection targets to increase productivity. The functions of the candidate host genes show the rumen metagenome is influenced by multiple complex biological systems of the host.},
}

Animals
*Rumen/microbiology
Cattle/genetics/microbiology
*Metagenome
Diet/veterinary
Genotype
*Gastrointestinal Microbiome/genetics
Male

@article {pmid42489029,
year = {2026},
author = {Ma, R and Guo, G and Liu, C and Deng, P and Dong, X and Mu, L and Qu, Q and Hu, X},
title = {Microplastic Pollution Is Associated with Fragmentation and Environmental Sensitivity of Marine Planktonic Microbial Communities.},
journal = {Environmental science & technology},
volume = {60},
number = {30},
pages = {21051-21060},
doi = {10.1021/acs.est.6c06158},
pmid = {42489029},
issn = {1520-5851},
support = {2025D01E63//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 22576112//National Natural Science Foundation of China/ ; 25JCYBJC00100//Natural Science Foundation of Tianjin Municipality/ ; NA//Fundamental Research Funds for the Central Universities/ ; B17025//Higher Education Discipline Innovation Project/ ; 1102021600110070049//Central Public Research Institutes Basic Funds for Research and Development/ ; 25FV0CWZ02//Fujian Ocean Innovation Center/ ; },
mesh = {*Microplastics ; *Plankton ; *Microbiota ; },
abstract = {The effects of increasing marine microplastic (MP) pollution on the microbial community structure and function remain uncertain, particularly under natural conditions. Specifically, our study focuses on free-living marine microbial communities (0.8-5 μm) rather than plastisphere biofilms. Here, we systematically evaluated differences in microbial community responses to environmental gradients across MP concentration regimes on the basis of a response modulation analysis framework (RMAF). In this framework, co-occurrence network analysis, random forest modeling, and SHapley Additive exPlanations (SHAP) and partial dependence-based interpretation methods are integrated to quantify changes in microbial sensitivity and ecological interactions. Through the use of Tara Oceans metagenomic data, we analyzed seven functional gene categories and species diversity across MP concentration gradients. High-MP environments (with concentrations exceeding 5,500 items·km-2) were characterized by a notable decrease in nondominant taxa (from 17-21% to 6.53-9.45%) alongside increased dominance of abundant species. The functional profiles showed higher abundance levels of genes involved in carbon, nitrogen, and sulfur cycling. The results of network analysis indicated reduced connectivity and increased fragmentation, suggesting weakened ecological interactions and decreased system stability. Microbial communities in high-MP environments exhibited increased sensitivity to environmental drivers, characterized by response centralization and niche compression, suggesting a narrower range of environmental responses. MPs were associated with high microbial functional activity and potential indications of low ecosystem resilience.},
}

*Microplastics
*Plankton
*Microbiota

@article {pmid42515578,
year = {2026},
author = {Meyer, C and Jackson, VLN and de Haan, F and Bolhuis, H and Allen, MJ and Monier, A and Brussaard, CPD},
title = {Infection Dynamics and Coexistence of Two Novel Arctic Phytoplankton Viruses.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
pmid = {42515578},
issn = {1999-4915},
support = {na//University of Amsterdam/ ; na//Royal Netherlands Institute for Sea Research/ ; },
mesh = {Arctic Regions ; *Phytoplankton/virology ; Genome, Viral ; Phylogeny ; *Phycodnaviridae/genetics/classification/isolation & purification ; Host Specificity ; },
abstract = {Marine algal viruses exhibit a high level of diversity, and closely related viruses targeting the same algal host species can stably coexist. Here we report an example of a single virus-host system concealing hidden complexity. We discovered two double stranded (ds) DNA viruses infecting the Arctic picophytoplankter Micromonas polaris coexisting in culture for over a decade. Genomic sequencing of the lysate originally characterized as MpoV-44T revealed that it comprises two distinct prasinoviruses with ~203-204 kb genomes (MpoV-44T.A and MpoV-44T.B), of which conserved regions only accounted for 36% (the nucleotide level). The viruses were subsequently separated and compared at both genomic and phenotypic levels. In dual infection studies using a single host strain under nutrient-replete conditions, MpoV-44T.A outcompeted MpoV-44T.B. Yet MpoV-44T.B-like viruses were more abundant than MpoV-44T.A-like ones in natural Arctic metagenomes. This apparent paradox may be explained by differences in host strain specificity and/or possible resilience to nutrient stress by MpoV-44T.B, which we hypothesize based on genomic data. This work unveils hidden virus diversity, illustrating that the dynamics of viral coexistence are not always easily predictable, and underscores the importance of studying the underlying mechanisms at play.},
}

Arctic Regions
*Phytoplankton/virology
Genome, Viral
Phylogeny
*Phycodnaviridae/genetics/classification/isolation & purification
Host Specificity

@article {pmid42515587,
year = {2026},
author = {Yuan, L and Zhang, N and Yuan, M and Xu, J and Liu, Z and Li, Z},
title = {Novel Species Diversity in China's Northeastern Border Region.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
pmid = {42515587},
issn = {1999-4915},
support = {No. 2025ZD01900100//Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project/ ; },
mesh = {China/epidemiology ; Humans ; Animals ; Phylogeny ; *Viruses/classification/genetics/isolation & purification/pathogenicity ; *Biodiversity ; Metagenomics ; Genetic Variation ; *Virus Diseases/virology/epidemiology ; },
abstract = {The northeastern region of China is characterized by complex ecosystems, including forests and wetlands, and borders North Korea, Russia, and Mongolia. It serves not only as a natural reservoir for various microorganisms but also as a critical geographical and ecological hub for cross-border exchanges in Northeast Asia. Based on metagenomics and meta-transcriptomics investigations, this study systematically reviews the current research status of novel pathogens in the northeastern border region of China. It systematically organizes the newly discovered species, their classifications, and geographical distributions, with a focus on analyzing novel viruses that have potential pathogenicity to humans. The novel viruses identified in the northeastern border region belong to 11 viral families, including 9 from the Nairoviridae, 4 from the Rhabdoviridae, 3 each from the Astroviridae, Picornaviridae, and Parvoviridae, and 1-2 from other viral families, indicating a broad diversity of newly discovered viruses. These novel viruses are found in a wide range of hosts, including humans, ticks, minks, Marmota sibirica, and Myodes rufocanus, underscoring the significant public health risks these viruses pose. Geographically, the novel viruses discovered in the northeastern border region show a clustering pattern, with new species primarily concentrated in areas bordering Russia and North Korea. This highlights the unique role of the region as a hotspot for cross-border pathogen transmission and risk. The findings provide a systematic scientific reference for understanding the spectrum of unknown novel pathogens and their geographical distribution in the northeastern border region, assessing the risk of emerging infectious diseases, and optimizing active surveillance systems.},
}

China/epidemiology
Humans
Animals
Phylogeny
*Viruses/classification/genetics/isolation & purification/pathogenicity
*Biodiversity
Metagenomics
Genetic Variation
*Virus Diseases/virology/epidemiology

@article {pmid42515641,
year = {2026},
author = {Liu, W and Wang, Y and Ma, J and Liang, X and Yang, L},
title = {Composting Restructures Chicken Manure Viral Communities and Attenuates Virus-Associated Antibiotic Resistance Signals: Paired Metagenome and Virome Analyses.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
pmid = {42515641},
issn = {1999-4915},
support = {42407182//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Manure/virology/microbiology ; *Metagenome ; Chickens/virology ; *Composting ; *Drug Resistance, Microbial/genetics ; *Virome ; *Viruses/genetics/classification/isolation & purification/drug effects ; Metagenomics ; Genome, Viral ; },
abstract = {Composting is widely used to reduce biological risks during manure recycling, but changes in viral communities and virus-associated antibiotic resistance genes (ARGs) remain poorly resolved. This study aimed to assess changes in DNA viral communities, eukaryotic viral protein signals, virus-associated ARGs, and predicted virus-host linkages during chicken manure composting using paired analyses of total-community metagenomes and viral-particle-enriched viromes. Both approaches recovered viral assemblages dominated by Uroviricota and lytic viruses but produced distinct profiles. Viromes yielded more taxonomically assigned viral operational taxonomic units and a higher proportion of relatively complete viral genomes, whereas metagenomes produced a larger predicted virus-host network. Composting restructured viral communities, reducing manure-associated genera and enriching stage-specific groups. Eukaryotic viral protein signals declined during composting. Virus-associated ARGs accounted for 24.83-38.76% of ARG abundance in metagenomes and 5.38-45.09% in viromes, with lower abundance and richness in viromes. Selected virus-associated ARGs showed transient early enrichment, particularly in the virome. By maturity, both overall virus-associated ARG signals and higher-risk ARG signals had declined. Predicted virus-host associations included bacterial groups containing potential opportunistic pathogens. These results show that composting restructures viral communities and attenuates virus-associated ARG signals, while metagenomes and viromes provide complementary but non-interchangeable views of viral ecology and ARG risk.},
}

Animals
*Manure/virology/microbiology
*Metagenome
Chickens/virology
*Composting
*Drug Resistance, Microbial/genetics
*Virome
*Viruses/genetics/classification/isolation & purification/drug effects
Metagenomics
Genome, Viral

@article {pmid42264152,
year = {2026},
author = {Gibbons, JA and Nelson, RM and Dabrowski, CN and Narkhede, A and Szalacha, LA and Kneusel, ML and Maru, JS and Huszar, MR and Hoang, LK and Schiavo, V and Eddins, AC and Georgieff, MK and Neu, J and Donovan, SM and Groer, MW and Ho, TT},
title = {Enteral iron dose effect on iron storage, intestinal barrier, and gut microbiome in preterm infants: a randomized clinical trial.},
journal = {The American journal of clinical nutrition},
volume = {124},
number = {2},
pages = {101389},
pmid = {42264152},
issn = {1938-3207},
support = {K23 HL150300/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; Female ; Double-Blind Method ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome/drug effects ; Male ; *Iron/administration & dosage/metabolism ; Intestinal Barrier Function/drug effects ; Feces/microbiology ; Dietary Supplements ; Enteral Nutrition ; *Intestines/drug effects/microbiology ; *Iron, Dietary/administration & dosage ; },
abstract = {BACKGROUND: Preterm infants routinely receive enteral iron supplementation to support growth, replace phlebotomy losses, and prevent iron deficiency. However, concerns regarding potential harms, including those on the gut microbiome, have contributed to recommendations for lower dosing.

OBJECTIVES: This study aimed to compare the effects of 2 enteral iron doses on gut health in very-low-birth-weight preterm infants. We hypothesized that higher iron dose would increase abundances of pathogenic bacteria, intestinal inflammation, and barrier dysfunction.

METHODS: This randomized, double-blind clinical trial assigned preterm infants born <1500 g to receive either the recommended dose, 2 mg/kg/d, or a higher dose of 6 mg/kg/d of total enteral iron. The primary outcome was the fecal microbiome after 2 wk on iron, assessed by metagenomic sequencing. Secondary outcomes included biomarkers of intestinal inflammation and barrier function (fecal calprotectin, urinary claudin-3, and urinary intestinal fatty acid-binding protein). Iron status, adverse events, and auditory brainstem response latencies at 36 wk postmenstrual age were also evaluated.

RESULTS: Among 151 randomly assigned infants who received study iron (77 low dose; 74 high dose), bacterial diversity, individual taxa, virulence potential, bacterial overgrowth, and iron-related functional genes were not significantly different between the treatment groups. In the subgroup analysis of singletons, treatment groups demonstrated significant differences in temporal shifts in overall bacterial community structure. Infants receiving 2 mg/kg/d had higher posttreatment urinary claudin-3 concentrations, indicating possible differences in intestinal permeability, and a higher prevalence of iron deficiency than those receiving 6 mg/kg/d. Other biomarkers, clinical outcomes, adverse events, and auditory latencies did not differ between groups.

CONCLUSIONS: Enteral iron supplementation at 6 mg/kg/d is associated with improved iron status and lower intestinal barrier dysfunction, without evidence of harms on gut microbiome compared with the recommended 2 mg/kg/d dose. These findings do not support concerns regarding gut microbiome disruption as a justification for lower iron dosing in preterm infants. This trial was registered at clinicaltrials.gov as NCT04497012.},
}

Humans
Female
Double-Blind Method
*Infant, Premature
Infant, Newborn
*Gastrointestinal Microbiome/drug effects
Male
*Iron/administration & dosage/metabolism
Intestinal Barrier Function/drug effects
Feces/microbiology
Dietary Supplements
Enteral Nutrition
*Intestines/drug effects/microbiology
*Iron, Dietary/administration & dosage

@article {pmid42300105,
year = {2026},
author = {Wilson, SMG and Oliver, A and Alkan, Z and Patil, BS and Kable, ME and Lemay, DG},
title = {Association between dietary polyphenol intake and polyphenol-utilizing bacteria in healthy adults.},
journal = {Food & function},
volume = {17},
number = {15},
pages = {6868-6881},
doi = {10.1039/d6fo00158k},
pmid = {42300105},
issn = {2042-650X},
mesh = {Humans ; *Polyphenols/metabolism ; Female ; Adult ; Male ; Feces/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Cross-Sectional Studies ; Middle Aged ; *Gastrointestinal Microbiome ; Diet ; Young Adult ; },
abstract = {Dietary polyphenols are bioactive compounds with a bidirectional impact on the gut microbiome; they shape the microbial community and are transformed through bacterial metabolism. However, there are limited studies pairing metagenomic and dietary data to investigate the relationship between polyphenol intake and the taxonomic and functional profiles of the human gut microbiome. We examined if dietary polyphenol intake associates with microbial composition and polyphenol utilization capacity. Healthy adults participated in a cross-sectional study balanced for age, sex, and BMI. Polyphenol intake was previously estimated by mapping multiple 24 h dietary recalls to the Food Database (FooDB). We coupled intake with microbial taxonomic and functional profiles from shotgun-sequenced fecal metagenomes (n = 313). Microbial reads were mapped to dbPUP, a database with 60 experimentally characterized, gut-associated polyphenol utilization proteins (PUPs). We assessed the relationship of polyphenol intake on microbial diversity, abundance of microbes with PUP genes, PUP gene counts, and select lipopolysaccharide (LPS) producers, accounting for age, sex, BMI, fiber intake, and diet quality. Specific polyphenols associated with an increased abundance of nine PUP-containing genera. We found 117 associations between polyphenol intake and microbial PUP genes, with 85 associations involving hydrolysis PUPs. Diversity in polyphenol intake was positively associated with diversity in PUP genes but not with microbial diversity. Lastly, we detected a positive relationship between intake of olive-related polyphenol classes and abundance of order Bacteroidales, a producer of immunoinhibitory LPS. Dietary polyphenol intake may influence the gut microbiome's capacity for polyphenol utilization, particularly its hydrolytic activity, without impacting taxonomic diversity or composition.},
}

Humans
*Polyphenols/metabolism
Female
Adult
Male
Feces/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Cross-Sectional Studies
Middle Aged
*Gastrointestinal Microbiome
Diet
Young Adult

@article {pmid41148302,
year = {2026},
author = {Hirayama, M and Maeda, T and Kashihara, K and Tsuboi, Y and Ito, M and Nishiwaki, H and Ohno, K and Ueyama, J},
title = {Linking diet, gut microbiota, and metabolites to Parkinson's disease risk: a shotgun metagenomic comparison of Japanese and Taiwanese cohorts.},
journal = {Journal of neural transmission (Vienna, Austria : 1996)},
volume = {133},
number = {7},
pages = {1357-1368},
pmid = {41148302},
issn = {1435-1463},
support = {24K10657//Japan Society for the Promotion of Science/ ; 23H02794//Japan Society for the Promotion of Science/ ; 2022G025//Smoking Research Foundation/ ; },
mesh = {Humans ; *Parkinson Disease/metabolism/microbiology/epidemiology ; *Gastrointestinal Microbiome/genetics/physiology ; Taiwan/epidemiology ; Male ; Female ; *Diet ; Japan/epidemiology ; Metagenomics ; Aged ; Middle Aged ; Cohort Studies ; East Asian People ; },
abstract = {Emerging evidence suggests that gut microbiota and its metabolites play pivotal roles in the pathogenesis of Parkinson's disease (PD). However, cross-national differences in diet and microbial composition may account for the striking variability in PD prevalence worldwide. To address this, we performed a comparative shotgun metagenomic analysis between Japanese and Taiwanese individuals, two genetically similar East Asian populations with distinct dietary habits and differing PD incidence rates. Our analysis revealed marked differences in dietary intake: Taiwanese individuals consumed higher amounts of animal fats and tropical fruits, whereas the Japanese diet was characterized by greater intake of seafood, root vegetables, and traditional fermented foods such as natto. These dietary patterns were reflected in gut microbiota profiles. Japanese individuals exhibited a higher abundance of Blautia, Faecalibacterium, and Bifidobacterium, while Taiwanese samples were enriched in Bacteroides and Alistipes. Functionally, genes involved in short-chain fatty acid (SCFA), vitamin, and polyamine biosynthesis were significantly reduced in PD patients and in the Taiwanese cohort. Metabolomic analyses corroborated these findings, showing decreased levels of SCFAs, polyamines, and key vitamins such as nicotinate and pantothenate in PD patients. Notably, Blautia abundance correlated positively with a broad range of beneficial metabolites, highlighting its potential role as a central modulator of host-microbe metabolic interactions. Our findings suggest that traditional Japanese dietary practices may shape a gut microbial environment that confers resistance to PD, underscoring the need for future interventional studies targeting diet-microbiota interactions in PD prevention and treatment.},
}

Humans
*Parkinson Disease/metabolism/microbiology/epidemiology
*Gastrointestinal Microbiome/genetics/physiology
Taiwan/epidemiology
Male
Female
*Diet
Japan/epidemiology
Metagenomics
Aged
Middle Aged
Cohort Studies
East Asian People

@article {pmid42167986,
year = {2026},
author = {Thomas, J and Ananthanarayanan, V and Padmanabhan, S},
title = {Metagenomic analysis of oral microbiome around zinc oxide nanoparticle-coated mini-implants: A split-mouth trial.},
journal = {Journal of the World federation of orthodontists},
volume = {15},
number = {4},
pages = {299-309},
doi = {10.1016/j.ejwf.2026.03.003},
pmid = {42167986},
issn = {2212-4438},
mesh = {Humans ; *Zinc Oxide ; *Dental Implants/microbiology ; *Microbiota/genetics ; *Orthodontic Anchorage Procedures/instrumentation ; Female ; *Mouth/microbiology ; Metagenomics ; Male ; *Nanoparticles ; *Coated Materials, Biocompatible ; Adult ; Gingival Crevicular Fluid/microbiology ; },
abstract = {BACKGROUND: This study aimed to evaluate the changes in the oral microbiome surrounding zinc oxide nanoparticle (NP)-coated orthodontic mini-implants using whole-genome metagenomic sequencing and to compare the microbial colonization and clinical stability with uncoated orthodontic mini-implants.

METHODS: A randomized split-mouth trial was conducted on 12 orthodontic patients requiring bilateral skeletal anchorage in the maxillary arch. Each patient received one zinc oxide NP-coated mini-implant and one uncoated implant. The implants were coated using radiofrequency magnetron sputtering. Peri mini-implant crevicular fluid samples were collected at 1 week (T1), 4 weeks (T2), and 3 months (T3) postinsertion, and the pooled sample at each time point was subjected to whole-genome shotgun metagenomic sequencing. Taxonomic and functional profiles were analyzed using Kraken and MEGAN6, with diversity indices calculated via the VEGAN R package. Stability was assessed using a 4-point semiquantitative mobility scoring.

RESULTS: Alpha diversity indices (Shannon and Chao1) showed no comparable differences between coated and uncoated mini-implants at any time point. Descriptive analysis of pooled metagenomic samples showed lower relative abundance or absence of peri‑implant pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Parvimonas micra, around coated implants. Functional gene analysis revealed reduced expression of bacterial motility, chemotaxis, and ribosomal pathways in the coated group. All mini-implants remained clinically successful during follow-up. Mobility scores were significantly lower at 1 month (P = 0.04), but not at 3 months (P = 0.102).

CONCLUSIONS: Within the constraints of pooled metagenomic analysis, zinc oxide NP-coated mini-implants were associated with a lower relative abundance of selected peri‑implant pathogens and differences in functional pathway profiles compared with uncoated implants. Overall microbial diversity did not differ significantly between groups. Both implant types remained clinically stable, although coated implants showed reduced early mobility at 1 month. These findings should be interpreted as exploratory, and further validation through patient-level metagenomic studies is warranted.},
}

Humans
*Zinc Oxide
*Dental Implants/microbiology
*Microbiota/genetics
*Orthodontic Anchorage Procedures/instrumentation
Female
*Mouth/microbiology
Metagenomics
Male
*Nanoparticles
*Coated Materials, Biocompatible
Adult
Gingival Crevicular Fluid/microbiology

@article {pmid42343457,
year = {2026},
author = {Wang, C and Li, S and Liu, Y and Zhao, X and Wang, F and You, Y and Zhao, X},
title = {Temporal dynamics of rhizosphere microbiome assembly and carbon-phosphorus coupling in poplar-medicinal plant intercropping systems.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42343457},
issn = {2049-2618},
mesh = {*Populus/microbiology/growth & development/metabolism ; *Rhizosphere ; *Microbiota ; *Carbon/metabolism ; Soil Microbiology ; *Phosphorus/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics ; Plant Roots/microbiology ; Soil/chemistry ; },
abstract = {BACKGROUND: Intercropping can reshape the rhizosphere microbiome, but how specific companion plants influence nutrient cycling and host growth remains unclear. We proposed that intercropping poplar with medicinal plants creates distinct rhizosphere niches that select for microbial communities with distinct functional potential, thereby improving tree nutrition.

RESULTS: Intercropping significantly promoted poplar growth, with increases in diameter at breast height (DBH) of 15.33%, 14.3%, and 15.23% in systems with Anemarrhena asphodeloides, Belamcanda chinensis, and Saposhnikovia divaricata, respectively. Intercropping did not change microbial alpha diversity but led to plant-specific shifts in beta diversity with clear seasonal dynamics. Metagenomic analyses revealed corresponding shifts in the functional potential of microbial communities related to carbon (C) and phosphorus (P) cycling, including genes such as frdC, aldB, ppk2, and phnH. Intercropping, particularly with S. divaricata, was associated with an increased genetic potential for microbial C metabolism and​ a heightened potential for P solubilization. These co-occurring shifts in genetic potential were correlated with greater P accumulation in poplar leaves. Network analysis showed distinct temporal microbial co-occurrence patterns across intercropping treatments, with A. asphodeloides supporting the most interconnected community linked to P mobilization. Three bacterial genera (Priestia, Pseudomonas, Acinetobacter) were strongly associated with key soil nutrient pools. Re-inoculation experiments confirmed their functional roles: Priestia sp. increased N and P retention in the rhizosphere; Pseudomonas sp. promoted plant growth, suggesting a role in​ stimulating plant secondary metabolism; and Acinetobacter sp. enhanced organic C mineralization.

CONCLUSIONS: Intercropping with specific medicinal plants structures the rhizosphere microbiome through niche differentiation. This restructuring leads to distinct patterns of microbial functional potential, centered on C and P metabolism, which correlate with improved poplar nutrient acquisition and growth. Our findings, integrating metagenomic inference with experimental validation, provide a framework for selecting companion plants to steer the rhizosphere microbiome toward beneficial functional outcomes in agroforestry systems. Video Abstract.},
}

*Populus/microbiology/growth & development/metabolism
*Rhizosphere
*Microbiota
*Carbon/metabolism
Soil Microbiology
*Phosphorus/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenomics
Plant Roots/microbiology
Soil/chemistry

@article {pmid42505983,
year = {2026},
author = {Li, D and Wu, X and Yuan, F and Zhou, F and Cai, B and Wei, K and Huang, W},
title = {Microbial Community Differentiation and Predicted Chemical-Defense-Related Functional Potential Across Distinct Microhabitats of Cultured Hemicentrotus pulcherrimus.},
journal = {Marine drugs},
volume = {24},
number = {7},
pages = {},
pmid = {42505983},
issn = {1660-3397},
support = {2025Y01//Ningde Normal University/ ; },
mesh = {Animals ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Sea Urchins/microbiology ; Aquaculture ; Quorum Sensing ; Ecosystem ; },
abstract = {Sea urchins harbor diverse microbial communities that may contribute to host-associated ecological interactions, microbial competition, and chemical defense. However, the compartment-specific organization of sea urchin-associated microbiota and their predicted chemical-defense-related functional potential remain poorly understood under aquaculture conditions. In this study, 16S rRNA gene amplicon sequencing was used to characterize microbial communities in rearing water, coelomic fluid, intestine, stomach contents, and surface mucus of Hemicentrotus pulcherrimus (H. pulcherrimus). KEGG Orthology (KO)-based functional prediction was further performed to evaluate predicted chemical-defense-related functional potential, including predicted chemical-defense-related pathways, siderophore-related functions, quorum sensing-related functions, and bacterial competition- and secretion system-related functions. Rarefaction curves and Coverage values indicated sufficient sequencing depth. Alpha diversity and Nonmetric multidimensional scaling (NMDS) analyses revealed clear microbial differentiation among the five sample types, with rearing water showing higher microbial richness. Taxonomic analysis identified Pseudomonadota, Bacteroidota, Campylobacterota, Bacillota, Planctomycetota, and Spirochaetota as dominant phyla, with several discriminative taxa across compartments. KO prediction showed that total predicted abundance of predicted chemical-defense-related KOs differed significantly among sample types. Among host-associated compartments, surface mucus showed relatively higher predicted siderophore-related KO potential, whereas stomach contents showed higher predicted quorum sensing-related KO potential among host-associated compartments. These findings suggest compartment-specific microbial communities and predicted chemical-defense-related functional potential in cultured H. pulcherrimus under aquaculture conditions. Because these functions were inferred from 16S-based KO prediction, they should be interpreted as preliminary hypotheses for future metagenomic, metabolomic, and culture-dependent validation.},
}

Animals
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Sea Urchins/microbiology
Aquaculture
Quorum Sensing
Ecosystem

@article {pmid42509522,
year = {2026},
author = {Chen, PY and Hsu, TW and Chiang, TY and Huang, CL},
title = {Comparative analysis of root microbiomes in four Swertia species from Taiwan.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
pmid = {42509522},
issn = {1618-0860},
support = {NSTC 103-2621-B-006-002-//National Science and Technology Council/ ; },
abstract = {Swertia (Gentianaceae) comprises four species endemic to Taiwan that possess significant medicinal potential. While root microbiomes are known to promote plant adaptation, the microbial ecology of Taiwanese Swertia remains largely unexplored. We investigated the rhizosphere and root endosphere microbiomes of these species using 16S rRNA gene sequencing and predictive functional profiling, integrated with host phylogenetic data. Our results revealed that rhizosphere bacterial communities were significantly more diverse than those in the root endosphere. PERMANOVA indicated that host species and plant compartment significantly influenced bacterial communities, but the high residual variance suggests that much of the community variation remains unexplained by the variables measured in this study. Phylogenetic analysis indicated that the root endosphere is more strongly influenced by host phylogeny, with closely related species harboring more similar communities. Functional profiling further demonstrated that the rhizosphere is predicted to be enriched in pathways related to nitrogen fixation and organic matter degradation, whereas the endosphere harbors bacterial taxa potentially associated with pathogen suppression. These findings underscore the multifaceted roles of the root microbiome in supporting the development, stress adaptation, and ecosystem sustainability of Swertia species in Taiwan's unique altitudinal gradients.},
}

@article {pmid42511774,
year = {2026},
author = {Nappo, A and Abbasi, AM and Berno, G and Rueca, M and Smoquina, F and Gruber, CEM and Fabeni, L and Spezia, PG and Carletti, F and Pietrucci, D and Petricciuolo, M and Carnevali, A and Sanna, N and Talarico, C and Federici, E and Chillemi, G and Maggi, F},
title = {Comparative Analysis of Viral Communities in Hospital, University and Urban Wastewater by Shotgun Metagenomic Sequencing.},
journal = {International journal of molecular sciences},
volume = {27},
number = {14},
pages = {},
pmid = {42511774},
issn = {1422-0067},
support = {CUP F53C24001620001//European Union Next-GenerationEU/ ; Ricerca Corrente-Linea 1 on emerging and re-emerging infections//Ministry of Health/ ; },
mesh = {*Wastewater/virology ; *Metagenomics/methods ; Humans ; Shotgun Sequencing ; *Viruses/genetics/classification/isolation & purification ; Universities ; Hospitals ; *Virome ; Metagenome ; Phylogeny ; },
abstract = {Wastewater-based surveillance has emerged as a powerful approach for population-level monitoring of pathogen circulation in a timely and non-invasive manner. In this study, shotgun metagenomic sequencing was applied to wastewater samples collected from a hospital (HP), a university campus (UN), and a wastewater treatment plant (WTP). Viral sequences were taxonomically classified using Kraken2. Specifically, HP samples showed the highest viral richness, followed by WTP and UN samples (HP vs. UN, p = 0.0003; WTP vs. UN, p = 0.0018). Using Jaccard distance, significant differences were observed between WTP and UN (R[2] = 0.181, p < 0.001), WTP and HP (R[2] = 0.159, p < 0.001), and UN and HP (R[2] = 0.223, p < 0.001), and similarly, for Sørensen-Dice dissimilarity: WTP vs. UN (R[2] = 0.238, p < 0.001), WTP vs. HP (R[2] = 0.212, p < 0.001), and UN vs. HP (R[2] = 0.307, p < 0.001). Human-associated viral families were detected across all sources, predominantly Poxviridae, Orthoherpesviridae, Polyomaviridae and Circoviridae. Furthermore, the taxonomic composition of indirectly associated viruses, mainly Anelloviridae and Crassvirales, was examined. Overall, these findings support the potential of wastewater metagenomics as a reliable tool for monitoring viral diversity within environmental and public health contexts, although further research is needed to establish its operational utility for routine surveillance applications within a One Health framework.},
}

*Wastewater/virology
*Metagenomics/methods
Humans
Shotgun Sequencing
*Viruses/genetics/classification/isolation & purification
Universities
Hospitals
*Virome
Metagenome
Phylogeny

@article {pmid42515020,
year = {2026},
author = {Dalle Carbonare, L and Vareschi, A and Dervishi, K and Deiana, M and Locatelli, E and Minoia, A and Piritore, FC and Ruggiero, A and Barbu, IC and Zipeto, D and Piubelli, C and Valenti, MT},
title = {High-Touch, High-Risk: An Exploratory Microbiome Analysis of Hospital Wheelchairs.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {42515020},
issn = {2076-0817},
support = {FUR LDC//University of Verona/ ; FUR MTV//University of Verona/ ; Fondi Ricerca Corrente" - L3P6//Ministry of Health/ ; },
mesh = {Humans ; *Microbiota ; *Wheelchairs/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Equipment Contamination ; Pilot Projects ; DNA, Bacterial/genetics ; },
abstract = {In this exploratory pilot study, quantitative analyses were performed on seven leather wheelchairs and the protective barrier was evaluated on three leather wheelchairs, while shotgun metagenomic sequencing (Illumina and Oxford Nanopore) was conducted on pooled samples obtained from seven leather and three fabric wheelchairs to characterize microbial DNA recovered from wheelchair surfaces under routine clinical conditions. Microbial DNA and biomass were detected on all sampled surfaces, with median DNA concentrations of approximately 0.015 ng/µL, median cell counts of approximately 4.8 × 10[5] cells/mL, and median OD600 values of approximately 0.038, although variability among wheelchairs was observed. NGS analysis revealed heterogeneous microbial communities composed mainly of taxa associated with human skin microbiota and environmental sources. Opportunistic taxa including Escherichia coli, Staphylococcus haemolyticus, Achromobacter xylosoxidans, and Clostridioides difficile DNA were detected. Differences in microbial composition were observed between the pooled fabric and leather samples, with fabric samples characterized by the dominance of specific taxa and leather samples exhibiting a more heterogeneous microbial profile. In addition, median DNA concentration, cell counts, and OD600 values were reduced by approximately 98-100% on the protective barrier compared with uncovered wheelchair surfaces, with statistically significant differences between conditions. Overall, these findings suggest that hospital wheelchairs may harbor measurable levels of microbial biomass and microbial DNA despite routine sanitation procedures. Lower contamination levels were observed on the protective barrier under the conditions tested. Due to the exploratory nature of the study, the small sample size, and the use of pooled samples for metagenomic analyses, these observations should be interpreted with caution and require confirmation in larger studies.},
}

Humans
*Microbiota
*Wheelchairs/microbiology
*Bacteria/classification/genetics/isolation & purification
Equipment Contamination
Pilot Projects
DNA, Bacterial/genetics

@article {pmid42515556,
year = {2026},
author = {Martino, F and Panmei, K and Duchen, D and Thomas, DL and Kandathil, AJ and Clipman, SJ},
title = {Read-Level Error Characterization of Rolling-Circle Amplification-Based Nanopore Sequencing of the Circular DNA Virome.},
journal = {Viruses},
volume = {18},
number = {7},
pages = {},
doi = {10.3390/v18070704},
pmid = {42515556},
issn = {1999-4915},
support = {1DP2DA056130-01/NH/NIH HHS/United States ; R01DA058567/NH/NIH HHS/United States ; },
mesh = {*DNA, Circular/genetics ; *Nanopore Sequencing/methods ; *DNA, Viral/genetics ; *Nucleic Acid Amplification Techniques/methods ; *Virome/genetics ; Metagenomics/methods ; Genome, Viral ; Anelloviridae/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; },
abstract = {Oxford Nanopore technology enables cost-effective, portable, long-read analyses of pathogen genomes. Accurate detection and interpretation of small circular viral genomes, including Anelloviridae, remain challenging due to limited base-level error quantification in rolling-circle amplification (RCA)-derived datasets. Here, we characterized read-level sequencing error profiles using M13mp18, a 7.2 kb circular phage genome, subjected to 1X and 3X shearing during library preparation. M13mp18 DNA was serially diluted into pooled anellovirus-positive plasma DNA extracts. Using custom error-analysis pipelines, we quantified mismatch, insertion, and deletion rates and evaluated consensus reconstruction accuracy across simulated sequencing depths. Since metagenomic viromes contain mixtures of related genomes and uneven coverage across taxa, depth-normalized subsampling was used to assess the precision of read-level error estimates under heterogeneous coverage. Across four benchmarked datasets, per-base error rates ranged from 0.018 to 0.022 errors per aligned base. Complete M13mp18 reference reconstruction was achieved at input levels ≥ 4.6 log10 copies, and consensus sequences reached 100% identity at depths ≥ 15X when sufficient reads were available. Below 4.6 log10 input copies, recovery was inconsistent. These findings provide a controlled empirical characterization of read-level error behavior in RCA-derived nanopore sequencing and support the interpretation of circular DNA virome data generated in complex metagenomic backgrounds.},
}

*DNA, Circular/genetics
*Nanopore Sequencing/methods
*DNA, Viral/genetics
*Nucleic Acid Amplification Techniques/methods
*Virome/genetics
Metagenomics/methods
Genome, Viral
Anelloviridae/genetics
Sequence Analysis, DNA
High-Throughput Nucleotide Sequencing

@article {pmid41308739,
year = {2026},
author = {Zhang, Y and Liu, J and Zhang, X and Cheng, S and Liu, S and Huang, A and Yu, Y and Liu, J and Chen, H and Shang, D and Yin, P and Ma, S},
title = {Rhein alleviates acute pancreatitis by inhibiting TMAO-mediated inflammatory signaling pathways and reducing acinar cell injury.},
journal = {Journal of advanced research},
volume = {86},
number = {},
pages = {1035-1047},
doi = {10.1016/j.jare.2025.11.056},
pmid = {41308739},
issn = {2090-1224},
mesh = {Animals ; *Anthraquinones/pharmacology ; *Pancreatitis/drug therapy/metabolism/pathology/chemically induced ; Mice ; *Signal Transduction/drug effects ; *Acinar Cells/drug effects/metabolism/pathology ; *Methylamines/metabolism ; Male ; Gastrointestinal Microbiome/drug effects ; Inflammation/metabolism/drug therapy ; Mice, Inbred C57BL ; Fecal Microbiota Transplantation ; Disease Models, Animal ; NF-kappa B/metabolism ; Acute Disease ; },
abstract = {INTRODUCTION: Acute pancreatitis (AP) represents a significant global health challenge. Despite recent advances in medical treatment, the development of novel therapeutic strategies remains crucial.

OBJECTIVES: Rhein, a natural compound of the Chinese herb Rheum, shows promise in the treatment of AP. However, the exact mechanism underlying its therapeutic effect is still not fully understood.

METHODS: To investigate the association between the rhein-related gut microbiota and AP, we conducted antibiotic-mediated microbiota depletion experiments, fecal microbiota transplantation (FMT), and in vitro bacterial culture experiments. Concurrently, we performed 16S rRNA gene sequencing, metagenomic sequencing, and liquid chromatography‒mass spectrometry (LC‒MS) analyses on mouse fecal samples to characterize alterations in the microbiota and metabolome. Transcriptomic studies were also performed to elucidate the mechanisms underlying acinar cell inflammation.

RESULTS: Rhein alleviated AP by modulating the gut microbiota, as demonstrated by changes in the gut microbiota composition and improvements in AP after FMT in rhein-treated mice compared with those in cerulein-induced AP mice. Specifically, rhein is concentrated mainly in the stomach and intestines, where it exerts anti-inflammatory effects on acinar cells by antagonizing the TLR4/NF-κB/NLRP3 signaling pathway activated by trimethylamine-N-oxide (TMAO). This mechanism is associated with lipid peroxidation and necrosis mediated by oxidative stress. Clinically, disease severity in patients with AP is positively correlated with serum TMAO concentration.

CONCLUSION: Rhein alleviates AP by modulating the intestinal microbiota to reduce TMAO production, thereby suppressing TMAO-induced activation of the TLR4/NF-κB/NLRP3 signaling pathway and inhibiting acinar cell inflammation.},
}

Animals
*Anthraquinones/pharmacology
*Pancreatitis/drug therapy/metabolism/pathology/chemically induced
Mice
*Signal Transduction/drug effects
*Acinar Cells/drug effects/metabolism/pathology
*Methylamines/metabolism
Male
Gastrointestinal Microbiome/drug effects
Inflammation/metabolism/drug therapy
Mice, Inbred C57BL
Fecal Microbiota Transplantation
Disease Models, Animal
NF-kappa B/metabolism
Acute Disease

@article {pmid42049592,
year = {2026},
author = {Pailhoriès, H and Velo-Suarez, L and Moalic, Y and Alcoforado-Diniz, J and Gouriou, S and Bessou, A and Cambau, E and Burgel, PR and Herrmann, JL and Héry-Arnaud, G and , },
title = {A disrupted microbial network and an ecological shift towards anaerobes in NTM-infected cystic fibrosis patients.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {25},
number = {4},
pages = {655-663},
doi = {10.1016/j.jcf.2026.04.005},
pmid = {42049592},
issn = {1873-5010},
mesh = {Humans ; *Cystic Fibrosis/microbiology/complications/physiopathology ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Sputum/microbiology ; Male ; Microbiota ; Female ; *Bacteria, Anaerobic/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Cystic Fibrosis Transmembrane Conductance Regulator/genetics ; },
abstract = {Nontuberculous mycobacteria (NTM) are increasingly recognized as opportunistic pathogens in people with cystic fibrosis (pwCF), but the ecological factors shaping their presence remain poorly understood. This study characterized the airway microbiota associated with NTM-positive culture using 16S rRNA gene sequencing of sputum from 108 pwCF (36 NTM-positive and 72 NTM-negative), matched by age, sex at birth, and CFTR genotype. Analyses integrated diversity metrics, differential-abundance modeling, multivariate regression, and microbial network inference, while accounting for Pseudomonas aeruginosa colonization. NTM-positive individuals exhibited slightly higher α-diversity and enrichment in strictly anaerobic taxa such as Alloprevotella tannerae, Stomatobaculum spp., and Prevotella nanceiensis, alongside reduced network connectivity. P. aeruginosa remained the dominant ecological driver, strongly reducing community diversity and structure. Partial Least Squares regression revealed that CFTR modulators (lumacaftor/ivacaftor) use and lung function (FEV1%) were associated with distinct, commensal-enriched communities. In contrast, NTM status was associated with a distinct axis, indicating an independent ecological niche. Overall, NTM-positive cultures were associated with an anaerobe-enriched but less structured microbiota, likely reflecting localized hypoxia and biofilm-associated microenvironments rather than a direct effect of disease severity or modulator therapy. These findings highlight the role of airway microecology in NTM presence and provide a framework for understanding host-microbe interactions in chronic CF airway infections.},
}

Humans
*Cystic Fibrosis/microbiology/complications/physiopathology
*Mycobacterium Infections, Nontuberculous/microbiology/diagnosis
Sputum/microbiology
Male
Microbiota
Female
*Bacteria, Anaerobic/isolation & purification
RNA, Ribosomal, 16S/genetics
Cystic Fibrosis Transmembrane Conductance Regulator/genetics

@article {pmid42173938,
year = {2026},
author = {van Beek, N and Bargheet, A and Jian, C and Noordzij, HT and Ponsero, A and Pettersen, VK and Korpela, KE},
title = {Metagenomic survey of pathogen prevalence in the infant gut.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42173938},
issn = {2045-2322},
support = {101039583//ERC Starting Grant/ ; },
mesh = {Humans ; *Metagenomics/methods ; Female ; Prevalence ; Infant ; *Gastrointestinal Microbiome/genetics ; Breast Feeding ; Anti-Bacterial Agents/therapeutic use ; *Metagenome ; Infant, Newborn ; Male ; *Opportunistic Infections/microbiology/epidemiology ; *Bacteria/genetics/classification/isolation & purification ; },
abstract = {The human microbiota impacts our health and well-being from infancy throughout our lives. Besides mutualistic and commensal strains, it also contains opportunistic pathogens. Infants may be especially vulnerable to opportunistic pathogen colonisation due to their immature immune systems and low microbial diversity.The study aims to examine associations between opportunistic pathogen prevalence and factors such as breastfeeding, antibiotic use, birth-mode, and the presence of other bacterial taxa. This study analysed 3981 publicly available shotgun metagenomes collected from 1275 infants and 415 mothers across ten countries to identify species that may be considered opportunistic pathogens in the infant gut. The prevalence of C. difficile was decreased in breastfed infants and in those carrying Faecalibacterium and Dorea spp. S. aureus carriage was negatively associated with antibiotic use and positively with skin contact and breastfeeding. K. pneumoniae was acquired later in life and was more prevalent in premature infants, and less commonplace in vaginal deliveries without antibiotics. Our findings indicate that opportunistic pathogen prevalence in the infant gut is influenced by medical and caregiving practices and may be modifiable through targeted interventions. Reducing the spread of these opportunistic pathogens could contribute to global efforts against early life infections.},
}

Humans
*Metagenomics/methods
Female
Prevalence
Infant
*Gastrointestinal Microbiome/genetics
Breast Feeding
Anti-Bacterial Agents/therapeutic use
*Metagenome
Infant, Newborn
Male
*Opportunistic Infections/microbiology/epidemiology
*Bacteria/genetics/classification/isolation & purification

@article {pmid42174021,
year = {2026},
author = {Min, U and Kim, J and Kim, J and Jin, H and Oh, H and Ahn, S and Shin, H and Lee, W},
title = {Spicy food intake and dietary factors shape the gut microbiome and metabolism of mucin and short-chain fatty acids in healthy adults.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42174021},
issn = {2045-2322},
mesh = {Humans ; *Mucins/metabolism ; *Fatty Acids, Volatile/metabolism ; Female ; Male ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Alcohol Drinking ; *Diet ; *Eating ; },
abstract = {Whether spicy food intake independently modulates mucin metabolism and short-chain fatty acid (SCFA) production or depends on co-ingested factors such as alcohol remains poorly understood. Herein, shotgun metagenomics characterized gut microbial composition, functional pathways, and their relationship with spicy food intake, alcohol consumption, and intestinal fatty acid-binding protein (I-FABP) and liver fatty acid-binding protein (L-FABP) levels in 229 healthy Korean adults. Alcohol intake was positively correlated with urinary I-FABP levels indicating mild epithelial stress, whereas spicy food intake was not associated with either FABP biomarker. Consumption of highly spicy foods resulted in increased abundance of SCFA-producing and mucin-metabolizing taxa, along with mucin degradation and SCFA production. Individuals with high alcohol intake showed stronger enrichment of mucin-degrading taxa with reduced SCFA flux and increased abundance of Proteobacteria and Fusobacteria. The cross-classified dietary groups exhibited distinct mucin and SCFA activity patterns. The Drink-High-Spicy-High (DHSH) group displayed elevated mucin turnover and SCFA production with dysbiosis. These findings suggest that spicy food may modulate mucus layer metabolism in a context-dependent manner, whereas alcohol more consistently perturbs mucin-SCFA networks and epithelial integrity.},
}

Humans
*Mucins/metabolism
*Fatty Acids, Volatile/metabolism
Female
Male
*Gastrointestinal Microbiome
Adult
Middle Aged
Alcohol Drinking
*Diet
*Eating

@article {pmid42186028,
year = {2026},
author = {Larroya, A and Romera-Giner, S and Tolosa-Enguís, V and Rodríguez-Ruano, SM and Andrés-García, S and Soro-Conde, I and Codoñer, P and Sanz, Y},
title = {Gut microbiota and western dietary patterns associated with behavioral problems in children and adolescents: a cross-sectional study.},
journal = {Nutrition journal},
volume = {25},
number = {1},
pages = {},
pmid = {42186028},
issn = {1475-2891},
mesh = {Humans ; Cross-Sectional Studies ; Child ; Adolescent ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; *Diet, Western/adverse effects ; Child, Preschool ; Feces/microbiology ; Feeding Behavior ; *Problem Behavior ; },
abstract = {BACKGROUND: Childhood and adolescence are crucial periods for brain development, during which multiple environmental factors, including gut microbiota and dietary habits, play important roles. However, the combined impact of those factors on neurodevelopment and mental disease risk remains largely unexplored. Here, we aimed to investigate the relationships between gut microbiota and diet and their role in classifying behavioral problems that may precede mental disorders in children and adolescents.

METHODS: We performed a cross-sectional study, including data from 335 subjects, including 202 children (5-10 years) and 133 adolescents (11-17 years). Gut microbiota was analysed in stools by shotgun metagenomics. Dietary habits, lifestyle factors and emotional and behavioral difficulties were screened using validated questionnaires. Penalized Logistic Regression models were trained to classify individuals into Healthy and Behavioral Problem groups based on microbial diversity, differential abundance of bacterial species, dietary patterns, and food and nutrient intakes. Mediation analyses were applied to assess whether gut microbiota mediates the effect of diet on behavioral problems.

RESULTS: A Western diet characterized by poor adherence to dietary recommendations was consistently associated with behavioral problems in all age groups. Individuals with behavioral problems exhibited distinct gut microbiota profiles characterized by lower levels of short-chain fatty acid-producing bacteria (particularly butyrate-producing species) and higher levels of potential pathogens (e.g., Campylobacter coli and Lautropia mirabilis), linked to poor dietary choices. Furthermore, we evidenced the mediation role of the gut microbiota in the association between dietary patterns and food groups and behavioral problems. In adolescents, L. mirabilis was identified as a mediator of the relationship between a Western diet and behavioral problems, while Anaerostipes rhamnosivorans mediated the relationship between fish consumption and behavioral problems. Gut microbiota data enhanced the classification accuracy of logistic regression models for identifying individuals with behavioral problems over models based solely on dietary data.

CONCLUSION: Integrating dietary habits and gut microbiota data enables more accurate stratification of children and adolescents at risk for behavioral problems. Our findings may help to refine dietary interventions targeting the gut microbiota to improve mental health outcomes in these vulnerable populations.},
}

Humans
Cross-Sectional Studies
Child
Adolescent
Female
Male
*Gastrointestinal Microbiome/physiology
*Diet, Western/adverse effects
Child, Preschool
Feces/microbiology
Feeding Behavior
*Problem Behavior

@article {pmid42286003,
year = {2026},
author = {Hensen, ADO and Harmanus, C and Verbeek-Menken, PH and Koopman, JPR and Lamers, OAC and Roozen, GVT and Janse, JJ and Balke-Buijs, M and van der Stoep, MYEC and Meij, P and van Amerongen-Westra, IM and Schipper, P and Crul, C and Pattacini, L and Rox, K and Farowski, F and Tsakmaklis, A and Vehreschild, MJGT and Kuijper, EJ and Smits, WK and Roestenberg, M},
title = {Experimental human colonisation with non-toxigenic Clostridioides difficile: a placebo-controlled randomised clinical trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42286003},
issn = {2041-1723},
support = {101007799//Innovative Medicines Initiative (IMI)/ ; },
mesh = {Humans ; *Clostridioides difficile/drug effects/genetics/physiology ; Adult ; Female ; Vancomycin/administration & dosage/pharmacology/therapeutic use ; Male ; Middle Aged ; Anti-Bacterial Agents/administration & dosage/therapeutic use ; Adolescent ; Young Adult ; *Clostridium Infections/microbiology/drug therapy ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Clostridioides difficile infections remain a major global healthcare burden, underscoring the need for novel therapies. Human colonisation models provide mechanistic insight into C. difficile colonisation and facilitate identification of novel intervention targets. We conducted a placebo-controlled, randomised clinical trial (NCT05693077) administering non-toxigenic C. difficile (NTCD) capsules to healthy participants to assess safety and colonisation as primary endpoints, and microbiota susceptibility as a secondary endpoint. A total of 69 healthy participants (18-45 years), not previously colonised with C. difficile and without recent antibiotic use, were enrolled following a health assessment. NTCD capsules administered for five consecutive days at low or high dose, was safe with no dose-response relationship in colonisation outcomes. Vancomycin pretreatment induced colonisation success: with 5% colonisation without, 32% after one day, and 84% after five days vancomycin pretreatment. Some participants that cleared vancomycin rapidly acquired non-challenge C. difficile strains prior to NTCD challenge. Microbiota profiling (using shotgun metagenomics) revealed reduced α-diversity and pronounced community restructuring. These findings highlight the impact of antibiotic-mediated microbiota disruption, the widespread environmental presence of C. difficile, and the feasibility of meaningful microbiota assessment in small-scale intervention trials, thereby providing a robust tool to investigate this globally impactful infection.},
}

Humans
*Clostridioides difficile/drug effects/genetics/physiology
Adult
Female
Vancomycin/administration & dosage/pharmacology/therapeutic use
Male
Middle Aged
Anti-Bacterial Agents/administration & dosage/therapeutic use
Adolescent
Young Adult
*Clostridium Infections/microbiology/drug therapy
Feces/microbiology
Gastrointestinal Microbiome/drug effects

@article {pmid42384485,
year = {2026},
author = {Crouch, AL and Rambeau, M and Li-Pook-Than, J and Snyder, MP and Henderson, JA and Yracheta, JM and Anderson, MZ},
title = {The gut microbiome of a Northern Plains tribe is in transition between global Indigenous and industrialized populations.},
journal = {Cell reports},
volume = {45},
number = {7},
pages = {116334},
doi = {10.1016/j.celrep.2025.116334},
pmid = {42384485},
issn = {2211-1247},
mesh = {Humans ; *Indians, North American ; Bacteria/genetics/classification ; Archaea/genetics/classification ; Metagenome ; Metagenomics ; *Gastrointestinal Microbiome/genetics ; Microbiota ; },
abstract = {The human gut is shaped by environmental factors, producing distinct microbial communities. Indigenous individuals practicing traditional lifestyles often harbor more diverse microbiota, with taxa often absent in industrialized people. However, little engagement has occurred with American Indian communities in North America who experienced forced relocation and dietary programs during colonization. Here, shotgun metagenomics profiled the gut microbiome of people from a Northern Plains tribe (NPT) reservation in comparison to 12 global populations engaged in traditional, agrarian, or industrialized lifestyles. Analysis of the 532 samples revealed that the NPT microbiota exhibited greater bacterial and archaeal diversity than industrialized populations but reduced diversity compared to global traditional and agrarian populations. Relative to the general United States population, NPT microbiomes encoded more virulence factor and microbial defense genes and fewer CAZyme-encoding genes. These findings suggest that the NPT gut microbiome is in transition between lifestyles associated with global Indigenous and industrialized populations.},
}

Humans
*Indians, North American
Bacteria/genetics/classification
Archaea/genetics/classification
Metagenome
Metagenomics
*Gastrointestinal Microbiome/genetics
Microbiota

@article {pmid42429485,
year = {2026},
author = {Tian, B and Liu, Y and Su, KJ and Jiang, LD and Lin, X and Qiu, C and Luo, Z and Tian, Q and Shen, J and Shen, H and Zhang, LS and Xiao, HM and Deng, HW},
title = {Multi-omics analysis identify novel microbiome-metabolome signatures associated with obesity.},
journal = {Journal of applied microbiology},
volume = {137},
number = {7},
pages = {},
doi = {10.1093/jambio/lxag172},
pmid = {42429485},
issn = {1365-2672},
support = {2016YFC1201805//National Key R&D Program of China/ ; 2017YFC1001100//National Key R&D Program of China/ ; 201604020007//Science and Technology Program of Guangzhou, China/ ; 81770878//National Natural Science Foundation of China/ ; },
mesh = {*Obesity/microbiology/metabolism/blood ; Humans ; Multiomics ; Male ; *Metabolome ; Metabolomics ; Body Mass Index ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; Fatty Acids, Volatile/metabolism ; Cohort Studies ; },
abstract = {AIMS: Explore the potential microbiome and serum metabolome factors and their interactions associated with obesity.

METHODS AND RESULTS: We performed a systematic multi-omics analysis using paired metagenomic and metabolomic profiles-including untargeted serum metabolomics, lipidomics, and short-chain fatty acids (SCFAs)-with body mass index (BMI) from a cohort of 495 US men. Single omics analysis identified 52 gut bacteria species and 31 serum metabolites for potential associations with BMI. Among the identified bacteria, Collinsella stercoris (C. stercoris) (Coef.=-0.147, P = 0.015) was negatively associated, whereas Bacteroides fragilis (B. fragilis) (Coef.=0.294, P = 1.22E-04) and Veillonella dispar (V. dispar) (Coef.=0.135, P = 0.001) were positively associated, these results were further validated by an independent Chinese cohort. Several of the identified metabolites, including gamma-glutamylglycine (Coef.=-0.713, P = 4.53E-06), asparagine (Coef.=-0.629, P = 3.53E-05), glycine (Coef.=-0.952, P = 5.28E-09), and serotonin (Coef.=0.566, P = 1.78E-04) were associated with these significant bacteria (P < 0.05).

CONCLUSION: This multi-omics study identifies key gut bacteria and serum metabolites that interact to associate with host obesity, providing systemic insight into microbiome-host metabolic interactions.},
}

*Obesity/microbiology/metabolism/blood
Humans
Multiomics
Male
*Metabolome
Metabolomics
Body Mass Index
*Microbiota
*Bacteria/classification/genetics/isolation & purification/metabolism
*Gastrointestinal Microbiome
Metagenomics
Fatty Acids, Volatile/metabolism
Cohort Studies

@article {pmid42495540,
year = {2026},
author = {Chen, Y and Lai, Y and Liu, Z and Zhang, K and Zheng, J and Lu, S and Huang, Z},
title = {The adaptation of the gut microbiome to social environmental changes in an Asian langur.},
journal = {iScience},
volume = {29},
number = {8},
pages = {116779},
pmid = {42495540},
issn = {2589-0042},
abstract = {Social environments profoundly impact social animals' gut microbiome. Understanding such effects is critical for evaluating population fitness and conservation. Employing 16S rRNA and metagenomic sequencing, we investigated the gut microbiome of the endangered white-headed langur (Trachypithecus leucocephalus) to clarify its potential adaptive strategies to social environmental changes. Distinct differences were observed among social groups: the all-male group was enriched in Bacillota and showed stronger cellulose degradation potential, which might be associated with greater cellulose intake and higher cortisol and T3 levels; mixed-sex group was enriched in Actinomycetota, Pseudomonadota, and non-carbohydrate metabolism genes, possibly due to more young leaves consumption and reproductive needs. Alpha male replacement also shaped gut microbiome: the third alpha male period had highest Bacteroidota and lowest metabolic genes abundance, potentially related to improved food quality during this period. These preliminary findings highlight gut microbial adaptation to social environments in the studied population, providing implications for the conservation of this endangered species.},
}

@article {pmid42499546,
year = {2026},
author = {Jiang, Z and Li, L and Long, Q and Guo, W and Wang, M and Li, X and Li, J and Yi, Y},
title = {Cross-sectional gut microbiota and serum metabolite differences across clinically defined groups in colorectal cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1815707},
pmid = {42499546},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/blood/microbiology/pathology ; Cross-Sectional Studies ; Female ; Feces/microbiology ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Aged ; Metabolomics ; *Serum/chemistry ; *Metabolome ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Colorectal cancer (CRC) is a prevalent malignancy associated with alterations in the gut microbiota and host metabolic profiles. This cross-sectional study aimed to characterize gut microbiota and serum metabolite differences among healthy controls (HC), patients with non-metastatic colorectal cancer (CRC-nm), and patients with metastatic colorectal cancer (CRC-m). Stool metagenomic sequencing and untargeted serum metabolomics were performed in 107 participants, followed by exploratory differential analyses and internally cross-validated modeling to identify candidate microbial and metabolic features and evaluate their discriminatory performance. Differential analyses identified two CRC-m-enriched species-level features (Enterocloster clostridioformis and Lactobacillus crispatus) and two CRC-m-depleted features (Megamonas rupellensis and Phocaeicola plebeius) across comparisons with both CRC-nm and HC groups. Metabolomic analysis identified eight pathway-mapped metabolites, mainly involved in amino acid-related metabolic pathways. In modeling analyses, metabolite-only models provided the primary discriminatory signal, whereas adding bacterial features did not improve predictive performance. Integrated microbiota-metabolite models showed lower internal performance than metabolite-only models in some comparisons, including CRC-m versus CRC-nm. Overall, these findings suggest that observed discriminatory performance was primarily driven by serum metabolite features rather than additional bacterial features, and highlight candidate microbial and metabolic markers for future validation. Because all CRC-m cases were stage IV and all CRC-nm cases were stages I-III, these results should be interpreted as exploratory cross-sectional group differences that may reflect disease stage, tumor burden, or broader progression-related changes rather than metastasis-specific biology.},
}

Humans
*Colorectal Neoplasms/blood/microbiology/pathology
Cross-Sectional Studies
Female
Feces/microbiology
*Gastrointestinal Microbiome
Male
Middle Aged
Aged
Metabolomics
*Serum/chemistry
*Metabolome
Metagenomics
Bacteria/classification/genetics/isolation & purification

@article {pmid42502975,
year = {2026},
author = {Taldaev, A and Smutin, D and Danilov, L and Kashchenko, G and Ryabova, A and Adonin, L},
title = {Brain Transcriptomic Reprogramming and Comb-Associated Microbiome Variation During the Larva-To-Pupa Transition in Apis Mellifera.},
journal = {Archives of insect biochemistry and physiology},
volume = {122},
number = {4},
pages = {e70196},
pmid = {42502975},
issn = {1520-6327},
support = {25-26-00381//Russian Science Foundation/ ; },
mesh = {Animals ; Bees/microbiology/growth & development/genetics/metabolism ; *Brain/metabolism/growth & development ; Larva/growth & development/microbiology/genetics/metabolism ; *Transcriptome ; *Microbiota ; Pupa/growth & development/microbiology/genetics/metabolism ; Metamorphosis, Biological ; },
abstract = {The larva-to-pupa transition in honey bees (Apis mellifera) involves extensive neural remodeling, yet the molecular dynamics of brain development and their relationship with the surrounding microbial environment remain poorly characterized. This study integrated brain transcriptomic profiling with comb-associated metagenomic analysis to characterize stage-specific molecular signatures during metamorphosis. RNA sequencing of larval and pupal brains was combined with honeycomb shotgun metagenomics from the same sample. Brain transcriptomes exhibited marked stage-specific divergence. Pupae displayed downregulation of transcriptional regulators, ecdysone and insulin signaling, and growth-related pathways, alongside upregulation of cuticular proteins, glutathione metabolism, and odorant-binding proteins. Notably, numerous poorly annotated, lineage-specific loci showed extreme stage-specific regulation. In contrast, comb-associated microbial communities remained globally stable across developmental stages, though supervised ordination identified stage-discriminatory taxa, including core symbionts and opportunistic pathogens. Integrative network analysis revealed significant correlations between comb potential bee pathogens' abundances and brain transcripts involved in translation, stress response, and metabolic regulation. Our data suggest that honey bee neural maturation is primarily driven by intrinsic transcriptional reprogramming, while structured variation in the external microbial milieu correlates with host neural gene expression. Honeycomb microbiome shift should be the consequence of the environmental conditions changes and host developmental shifts. Their roles in that process, as well as the brood immune system-comb microbiome interactions, may be part of future research.},
}

Animals
Bees/microbiology/growth & development/genetics/metabolism
*Brain/metabolism/growth & development
Larva/growth & development/microbiology/genetics/metabolism
*Transcriptome
*Microbiota
Pupa/growth & development/microbiology/genetics/metabolism
Metamorphosis, Biological

@article {pmid41506580,
year = {2026},
author = {Nichols, S and Estandía, A and Young, CM and Knowles, LS and Palinauskas, V and Okamura, B and Clegg, SM},
title = {Host whole genome sequence data represent an untapped resource for characterising affiliated parasite diversity.},
journal = {International journal for parasitology},
volume = {56},
number = {8},
pages = {104768},
doi = {10.1016/j.ijpara.2025.104768},
pmid = {41506580},
issn = {1879-0135},
mesh = {Animals ; *Whole Genome Sequencing ; *Parasites/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; DNA Barcoding, Taxonomic ; Genetic Variation ; RNA, Ribosomal, 18S/genetics ; Multiplex Polymerase Chain Reaction ; *Biodiversity ; Shotgun Sequencing ; },
abstract = {Parasites are ubiquitous and exert varied ecological and evolutionary pressures on their hosts. Yet, characterising parasite diversity and distributions can be challenging and costly. Leveraging existing data to identify parasites is thus an attractive alternative. High-throughput sequencing (HTS) can generate whole genome sequence (WGS) data which are increasingly freely available in public repositories and represent an untapped resource for characterising parasites affiliated with hosts. In this study, we examine WGS data generated for the silvereye (Zosterops lateralis), to identify endogenous eukaryotic parasites that were inadvertently captured during host sequencing. We compared detection of parasite genera by this approach with detection via 18S metabarcoding. Mining WGS data for parasite DNA revealed the broadest range of genera. Results were verified by traditional microscopy of blood slides and conducting a targeted multiplex Polymerase Chain Reaction (PCR) for haemosporidian parasites. Detection of haemosporidians was largely consistent across microscopy, multiplex PCR and WGS data while 18S metabarcoding entirely failed to detect this group of parasites. Our results demonstrate that existing WGS datasets can be used to estimate endoparasite diversity and provide greater insights on diversity than metabarcoding whilst also avoiding the costs and challenges of direct sampling. We provide a framework outlining opportunities and constraints to consider when mining WGS data to identify parasite sequences. The framework particularly stresses the influences of sequencing depth, database completeness, and methodological biases. Our findings demonstrate how repurposing existing WGS data can provide a cost-effective and informative means of unravelling complex host-parasite interactions in future disease ecology studies.},
}

Animals
*Whole Genome Sequencing
*Parasites/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing
DNA Barcoding, Taxonomic
Genetic Variation
RNA, Ribosomal, 18S/genetics
Multiplex Polymerase Chain Reaction
*Biodiversity
Shotgun Sequencing

@article {pmid42154370,
year = {2026},
author = {Benekos, K and Katsanos, A and Laspas, P and Panos, GD and Vagiakis, I and Fousekis, FS and Luca, R and Zhou, B and Kostoulas, C and Georgiou, I and Katsanos, KH and Skondra, D and Konstas, AG},
title = {An Update and Overview of the Ocular and Extraocular Microbiome and Its Impact on Ophthalmic Care.},
journal = {Advances in therapy},
volume = {43},
number = {8},
pages = {3247-3280},
pmid = {42154370},
issn = {1865-8652},
mesh = {Humans ; *Eye Diseases/microbiology/therapy ; *Microbiota/physiology ; Probiotics/therapeutic use ; *Eye/microbiology ; Prebiotics ; },
abstract = {The microbiome has been described as the last human "organ" and is currently the topic of great research interest worldwide. The application of culture-independent methods, like 16S ribosomal next-generation sequencing, has offered researchers the opportunity to identify bacterial populations that were impossible to detect previously using conventional culture methods. Further standardization of these new approaches to characterizing the microbiome is desirable. The present review discusses the mounting evidence suggesting that alterations in the microbiome and microbial metabolites, such as short-chain fatty acids in the gut, mouth, and ocular surface, may play a key role in the pathogenesis of ocular pathologies such as ocular surface disease, glaucoma, uveitis, age-related macular degeneration, and diabetic retinopathy. Clarifying the probable role of the microbiome in ocular diseases would not only offer valuable insights into pathogenesis but could also enable the development of novel therapeutic approaches. As yet, microbial-based therapeutic applications in ophthalmology are limited. Nevertheless, recently emerging strategies utilizing probiotics and prebiotics, or even fecal transplantation to regulate microbiome composition, offer promising research avenues for developing future innovative therapies for ocular diseases. Further studies employing standardized methodological protocols are needed to ensure the reproducibility of results and to eventually unlock the precise links between the microbiome and the eye.},
}

Humans
*Eye Diseases/microbiology/therapy
*Microbiota/physiology
Probiotics/therapeutic use
*Eye/microbiology
Prebiotics

@article {pmid42251689,
year = {2026},
author = {Tao, M and Zhang, Z and Dai, L and Zeng, Y and Zhang, X},
title = {Metagenomic insights into potential horizontal transfer of resistance/virulence genes in gut microbiota from patients with Crohn disease.},
journal = {Inflammatory bowel diseases},
volume = {32},
number = {8},
pages = {1532-1546},
doi = {10.1093/ibd/izag090},
pmid = {42251689},
issn = {1536-4844},
support = {2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; 32101368//National Natural Science Foundation of China/ ; 1053320242393//Fundamental Research Funds for the Central Universities of Central South University/ ; },
mesh = {Humans ; *Crohn Disease/microbiology/genetics ; *Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Virulence/genetics ; Female ; Male ; Case-Control Studies ; Adult ; *Virulence Factors/genetics ; Metagenome ; },
abstract = {BACKGROUND: Unraveling the potential horizontal transfer of resistance genes/virulence genes (RGs/VGs) in gut microbiota from patients with Crohn disease (CD) is an interesting but poorly characterized issue.

METHODS: Quantitative assessment was performed to estimate the relative abundance and diversity of RGs/VGs/mobile genetic elements (MGEs). Differential analysis was applied to identify the CD-specific enriched genetic subtypes. A species-RGs/VGs/MGEs association network was constructed to explore possible co-occurrence patterns of these genetic elements across potential microbial hosts. Integrated with topological metrics and Zi-Pi computational modeling, co-occurrence network analysis was conducted to characterize potential associations among RGs, VGs, and MGEs.

RESULTS: Comparative metagenomic analyses indicated that the microbiome in group CD exhibited significantly higher relative abundance of RGs compared to that in healthy controls (HC; P = .040), with 131 specific RG/VG subtypes (eg, acrA/T6SS) exhibiting marked enrichment (P < .05). The co-occurrence network revealed intensified interconnectivity between RGs/VGs and MGEs in group CD, in which MGEs accounted for 71% of network nodes (vs 60.80% in HC), and 99.14% of the edges were positively correlated (vs 93.60% in HC). Network topology and Zi-Pi analysis further suggested reduced modularity (0.709 vs 0.979 in HC) and enhanced intergene connectivity (average degree: 12.288 vs 2.156; average weighted degree: 23.359 vs 3.688 in HC). There were no network hubs (0 vs 5 in HC) but abundant modular hubs (60 vs 25 in HC), peripheral nodes (2317 vs 1549 in HC), and connectors (61 vs 36 in HC), which may reflect conditions favorable for enhanced gene transfer potential. Cross-species transfer events were predicted across clinical-environmental-commensal boundaries, exemplified by tet(M) dissemination between Clostridioides difficile and Bacteroides sp., probably implying progressive erosion of ecological barriers.

CONCLUSIONS: Collectively, we inferred that the gut microbiome of CD patients might represent a high-risk reservoir for the horizontal transfer of pathogenic determinants, which may pose a potential threat for public health and biosecurity.},
}

Humans
*Crohn Disease/microbiology/genetics
*Gene Transfer, Horizontal
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Virulence/genetics
Female
Male
Case-Control Studies
Adult
*Virulence Factors/genetics
Metagenome

@article {pmid42390233,
year = {2026},
author = {Peng, Y and Liu, Q and Lin, X and Xing, F and Li, S and Liu, X and Han, Y and Chen, Y and Dong, X},
title = {Salinity-driven microbial adaptation of hydrocarbon-degrading communities in coastal sediments.},
journal = {mSphere},
volume = {11},
number = {7},
pages = {e0036926},
pmid = {42390233},
issn = {2379-5042},
mesh = {*Geologic Sediments/microbiology ; *Salinity ; *Hydrocarbons/metabolism ; *Bacteria/genetics/metabolism/classification ; Metagenomics ; *Adaptation, Physiological ; *Microbiota/genetics ; Biodegradation, Environmental ; Phylogeny ; Genome, Bacterial ; },
abstract = {Salinity is a major abiotic driver of microbial diversity and metabolic function in coastal ecosystems. While its broad ecological impacts are well established, its role in shaping hydrocarbon-degrading communities and their adaptive mechanisms remains poorly understood. Here, we integrated gene- and genome-resolved metagenomics to investigate how salinity regulates the diversity, ecological interactions, and evolutionary dynamics of aerobic hydrocarbon-degrading microbes in Zhenhai Bay sediments (0.17-28.54 practical salinity units [PSU]). Across the natural salinity gradient, 10 types of hydrocarbon-degrading genes and 30 bacterial genomes spanning four phyla were identified, revealing extensive metabolic potential for the aerobic degradation of both aliphatic and aromatic hydrocarbons. The functional diversity and relative abundance of these genes increased significantly with salinity, accompanied by strong correlations with organic carbon parameters and nitrogen availability. Co-occurrence network analyses showed that hydrocarbon degraders, particularly Gammaproteobacteria, acted as key taxa maintaining community stability under saline conditions. Comparative genomics revealed that these bacteria possess multiple halotolerance strategies, including compatible solute biosynthesis and ion transport, supported by diverse energy-generating pathways. Frequent horizontal gene transfer and duplication of alkane monooxygenases (alkB and cyp153) expanded substrate ranges and enhanced functional diversity in hydrocarbon oxidation, highlighting salinity-driven evolutionary innovation. Together, these findings demonstrate that salinity governs the structure, metabolism, and evolution of hydrocarbon-degrading microbes, promoting microbial adaptation and functional diversification in coastal sediments.IMPORTANCESalinity is a defining feature of coastal ecosystems and a major regulator of microbial processes that support carbon cycling and pollutant degradation. This study highlights that salinity plays a central role in structuring hydrocarbon-degrading microbial communities and shaping their functional capacities and evolutionary trajectories in coastal sediments. By integrating osmoadaptation, metabolic potential, and community organization, our work shows that hydrocarbon degraders function as key links between environmental conditions and ecological processes. Salinity-driven shifts in microbial networks and metabolic strategies illustrate how environmental gradients can foster resilience and stability in highly dynamic coastal systems. Beyond advancing understanding of microbial responses, this study has potential implications for the rational design of bioremediation strategies targeting hydrocarbon pollutants in saline and estuarine environments.},
}

*Geologic Sediments/microbiology
*Salinity
*Hydrocarbons/metabolism
*Bacteria/genetics/metabolism/classification
Metagenomics
*Adaptation, Physiological
*Microbiota/genetics
Biodegradation, Environmental
Phylogeny
Genome, Bacterial

@article {pmid42402030,
year = {2026},
author = {Qi, K and Zhang, S and Su, X and Chen, J and Huang, S and Chen, Y and Li, W and Ni, G and Duo, J and Yang, S and Shen, Q and Wang, X and Liu, Y and Wu, P and Yang, H and Ji, L and Wang, X and Zhang, W},
title = {Comparative analysis of gut viromes in four penguin species reveals diverse novel viruses and host-associated differences.},
journal = {mSphere},
volume = {11},
number = {7},
pages = {e0084825},
pmid = {42402030},
issn = {2379-5042},
support = {2023YFD1801300//National Key Research and Development Program of China/ ; No. 82341106//National Natural Science Foundation of China/ ; 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; },
mesh = {Animals ; *Spheniscidae/virology/classification ; *Virome ; Phylogeny ; Metagenomics ; Parvoviridae/genetics/classification/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; Cloaca/virology ; Microviridae/genetics/classification/isolation & purification ; Caliciviridae/genetics/classification/isolation & purification ; Anelloviridae/genetics/classification/isolation & purification ; Circoviridae/genetics/classification ; Genome, Viral ; *Gastrointestinal Microbiome ; },
abstract = {Penguins, as distinctive marine birds, play important roles in polar and sub-Antarctic ecosystems, yet the diversity and species-specific distribution of their gut viromes remain insufficiently understood. Here, we used viral metagenomics to characterize the cloacal viromes of four penguin species-Spheniscus humboldti (S. humboldti), Pygoscelis papua (P. papua), Pygoscelis adeliae (P. adeliae), and Aptenodytes forsteri (A. forsteri)-collected at Chimelong Ocean Kingdom. A total of 219 viral sequences representing potentially novel lineages were identified, with more than 94% sharing <80% amino acid similarity with previously known viruses. These sequences were assigned to several viral families, including Parvoviridae, Caliciviridae, Anelloviridae, Circoviridae, and Microviridae, among others. Marked interspecies differences in virome composition were observed: Parvoviridae dominated in S. humboldti, Microviridae were enriched in P. papua, Caliciviridae accounted for a substantial proportion in A. forsteri, and P. adeliae displayed the greatest overall virome diversity. Multiple-virus co-detections, particularly involving Parvoviridae, were frequent in S. humboldti. Phylogenetic analyses showed that many penguin-associated viruses clustered with viruses infecting other avian and fish hosts, suggesting possible dietary or environmental origins of some detected viral sequences. These findings expand current knowledge of penguin gut virome diversity and host-associated differences and provide a valuable foundation for evaluating the ecological roles, health implications, and transmission risks of penguin-associated viruses.IMPORTANCEThis study uncovers significant diversity in the gut viromes of four penguin species, revealing over 219 viral sequences representing potentially novel lineages, many of which showed host-associated distribution patterns. Using viral metagenomics, we identified notable interspecies differences, with Parvoviridae predominating in Spheniscus humboldti and Microviridae being enriched in Pygoscelis papua. These findings highlight the complexity of viral community structures in penguins, including frequent viral co-detections, which could impact host health and ecological adaptation. Additionally, novel bacteriophage communities were identified, emphasizing their potential role in shaping the gut microbiome and influencing viral dynamics. This work provides new insights into viral diversity in wildlife and lays the groundwork for future studies on viral transmission risks and ecological conservation.},
}

Animals
*Spheniscidae/virology/classification
*Virome
Phylogeny
Metagenomics
Parvoviridae/genetics/classification/isolation & purification
*Viruses/classification/genetics/isolation & purification
Cloaca/virology
Microviridae/genetics/classification/isolation & purification
Caliciviridae/genetics/classification/isolation & purification
Anelloviridae/genetics/classification/isolation & purification
Circoviridae/genetics/classification
Genome, Viral
*Gastrointestinal Microbiome

@article {pmid42405768,
year = {2026},
author = {Berryhill, BA and Gil-Gil, T and Burke, KB and Fontaine, J and Brink, CE and Harvill, MG and Goldberg, DA and Navas, JN and May, KL and Grabowicz, M and Konstantinidis, KT and Levin, BR and Woodworth, MH},
title = {Enteric populations of Escherichia coli are likely to be resistant to phages due to O antigen expression.},
journal = {mSphere},
volume = {11},
number = {7},
pages = {e0038626},
pmid = {42405768},
issn = {2379-5042},
support = {K23AI144036//National Institute of Allergy and Infectious Diseases/ ; K23 AI144036/AI/NIAID NIH HHS/United States ; U54CK000601/CC/CDC HHS/United States ; Research Scholar Award//Southern Society for Clinical Investigation/ ; R35GM156739/GM/NIGMS NIH HHS/United States ; AI175048//National Institute of Allergy and Infectious Diseases/ ; R35GM136407/GM/NIGMS NIH HHS/United States ; },
mesh = {*Escherichia coli/virology/genetics ; Humans ; *O Antigens/genetics ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Bacteriophages/physiology ; *Coliphages/physiology ; Fecal Microbiota Transplantation ; Models, Theoretical ; },
abstract = {Metagenomic data provide evidence that bacteriophage (phage) abound in the enteric microbiomes of humans. However, the contribution of these viruses in shaping the bacterial composition of the gut microbiome and how these phages are maintained remain unclear. We performed experiments with 756 combinations of 54 Escherichia coli and nine phage isolates from four fecal microbiota transplantation (FMT) doses and five laboratory phages as samples of non-dysbiotic human enteric microbiota. We also developed a mathematical model of the population and evolutionary dynamics of bacteria and phage. Our experiments predict that as a consequence of the production of the O antigen, most of the E. coli in the human enteric microbiome will be resistant to infections with the array of co-occurring phages. Our modeling suggests that phages are maintained in these enteric communities due to the high rates of transition between the O antigen-resistant and -sensitive states. Based on our observations and predictions from this theory, we postulate that the phage found in the human gut are likely to play a little role in shaping the strain composition of E. coli of healthy individuals. Although we only investigated E. coli, the mechanism of resistance described here is shared among most of the gram-negative bacteria. Evidence is provided that, as a consequence of O antigen-mediated resistance, the genetically diverse array of bacteriophage in the gut microbiome of humans plays little or no role in determining the densities and distribution of the genetically diverse strain E. coli in this habitat. Our mathematical model predicts and our experiments support the hypothesis that the phage present in the gut microbiome are maintained by replication on the minority of sensitive bacteria generated by the leakiness of O antigen-mediated resistance.IMPORTANCEBacteriophages (phages) are abundant in the human gut, yet whether these viruses shape the bacterial communities living there remains unresolved. Using Escherichia coli and phages isolated from the stool of healthy fecal microbiota transplantation (FMT) donors, together with a mathematical model, we show that the vast majority of gut E. coli are resistant to co-occurring phages because they express the O antigen, a surface structure that masks the receptors phages use to attach. Despite this widespread resistance, phages persist by replicating on a small, continually regenerated subpopulation of sensitive cells, a phenomenon we term leaky resistance. These findings suggest that phages play a little role in determining which E. coli strains dominate the healthy human gut. Because the O antigen is broadly expressed across gram-negative bacteria, this mechanism likely extends well beyond E. coli and helps explain why isolating therapeutic phages against many pathogens is difficult.},
}

*Escherichia coli/virology/genetics
Humans
*O Antigens/genetics
*Gastrointestinal Microbiome
Feces/microbiology
*Bacteriophages/physiology
*Coliphages/physiology
Fecal Microbiota Transplantation
Models, Theoretical

@article {pmid42419222,
year = {2026},
author = {Liang, Y and Gao, H and Chen, F and Sun, J and Sun, G and Wang, Z and Li, Y and Liu, H and Geng, M and Li, J and Zhang, Y},
title = {Bilateral intranigral α-synuclein seeding in A53T transgenic mice drives early Parkinsonism and concurrent gut dysbiosis.},
journal = {Biochemical and biophysical research communications},
volume = {830},
number = {},
pages = {154244},
doi = {10.1016/j.bbrc.2026.154244},
pmid = {42419222},
issn = {1090-2104},
mesh = {Animals ; *alpha-Synuclein/metabolism/administration & dosage/genetics ; Mice, Transgenic ; *Dysbiosis/pathology ; Male ; Mice ; Gastrointestinal Microbiome ; Substantia Nigra/metabolism/pathology ; *Parkinsonian Disorders/pathology/genetics/metabolism ; Disease Models, Animal ; Female ; },
abstract = {Heterozygous A53T α-synuclein transgenic mice (M83 line) typically exhibit late-onset Parkinson's disease (PD) symptoms. This study established an accelerated PD model via bilateral intranigral injection of α-synuclein preformed fibrils (PFF) to characterize central and peripheral pathologies. Three-month-old heterozygous A53T mice received bilateral substantia nigra injections of α-synuclein PFF or PBS. Motor function was assessed monthly. Following the onset of motor deficits, the substantia nigra was harvested for immunohistochemistry and colons were harvested for H&E, transcriptomic analysis and western blotting, while gut microbiota composition was assessed using metagenomic sequencing. Three months post-injection, PFF-treated mice exhibited significant motor deficits, dopaminergic neuron loss, and nigral α-synuclein aggregation, with no sex differences. Peripherally, mice displayed increased α-synuclein in colon, impaired gut motility, reduced Occludin expression indicating barrier damage, and colonic inflammation. Metagenomics identified gut dysbiosis characterized by a skewed Bacillota/Bacteroidota ratio, Lactobacillus depletion, and enrichment of inflammation-associated taxa. Bilateral intranigral α-synuclein PFF injection in A53T mice successfully induces an early-onset, progressive PD phenotype encompassing motor impairments, nigrostriatal neurodegeneration. Crucially, the model recapitulates key peripheral manifestations, including gastrointestinal dysfunction and microbial dysbiosis. These findings provide compelling evidence for a descending brain-to-gut pathological axis where central α-synuclein pathology drives distal gut alterations. This optimized model offers a valuable platform for investigating multi-system PD progression and bidirectional brain-gut communication mechanisms.},
}

Animals
*alpha-Synuclein/metabolism/administration & dosage/genetics
Mice, Transgenic
*Dysbiosis/pathology
Male
Mice
Gastrointestinal Microbiome
Substantia Nigra/metabolism/pathology
*Parkinsonian Disorders/pathology/genetics/metabolism
Disease Models, Animal
Female

@article {pmid42429456,
year = {2026},
author = {Flamholz, ZN and Mulay, SA and Leshyk, V and Caporaso, JG and Eisen, JA and Kelly, L and Lloyd, KG and Osburn, MR and Podar, M and Roux, S and Regberg, SAB and Ruff, SE and Tierney, B and Tighe, S and Trembath-Reichert, E and Venkateswaran, K and Woyke, T and Locken, KM and Sapers, HM and Whiteson, K},
title = {Exploring life's hidden majority: microbial dark matter symposium highlights.},
journal = {mSphere},
volume = {11},
number = {7},
pages = {e0058725},
pmid = {42429456},
issn = {2379-5042},
mesh = {Metagenomics ; *Microbiota ; Bacteria/genetics/classification ; Computational Biology ; Ecosystem ; },
abstract = {The Microbial Dark Matter Symposium held on August 28-29, 2025, in Laguna Beach, Orange County, CA, convened a multidisciplinary group of scientists to address the vast unknowns in microbial life-from uncultured taxa and uncharacterized proteins to elusive viruses and spacefaring microbes. Set against a scenic coastal backdrop, the symposium highlighted advances in single-cell genomics, proximity ligation sequencing, and artificial intelligence-ready bioinformatics, while also probing the limits of microbial persistence, metabolism, and ecological distribution. Sessions explored microbial dark matter from multiple dimensions: cultivability, where new strategies are enabling recovery of elusive microbes; functional ambiguity, where metagenomic dark zones are illuminated by computational annotation; and genomic representation, where single-cell methods bridge gaps left by shotgun community sequencing. Researchers shared breakthroughs in identifying atmospheric microbiomes, "dark oxygen" production in groundwater ecosystems, and microbial survival on the International Space Station. The symposium emphasized integration of methods, disciplines, and ecosystems, advancing a collective push to illuminate the microbial dark matter on Earth and beyond. By highlighting emerging tools, pressing questions, and cross-domain insights, the symposium underscored the need for collaborative, open, and adaptive approaches to study the microbial unknown. The meeting marks a pivotal moment in microbiology, where cultivating knowledge of the uncultivated promises transformative understanding of life, everywhere.},
}

Metagenomics
*Microbiota
Bacteria/genetics/classification
Computational Biology
Ecosystem

@article {pmid42429609,
year = {2026},
author = {Robertson, CM and Mercado-Evans, V and Larson, AB and Branthoover, H and Ottinger, S and Mejia, ME and Hameed, ZA and Gonzalez, LA and Serchejian, C and Ogilvie, L and Zulk, JJ and Patras, KA},
title = {Type 2 diabetes mellitus exacerbates vaginal group B Streptococcus colonization via impaired mucosal cytokine response.},
journal = {mSphere},
volume = {11},
number = {7},
pages = {e0002726},
pmid = {42429609},
issn = {2379-5042},
support = {DK138748/DK/NIDDK NIH HHS/United States ; AI167547//National Institute of Allergy and Infectious Diseases/ ; HD117458//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; HD111236//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; AI167538//National Institute of Allergy and Infectious Diseases/ ; DK136201/DK/NIDDK NIH HHS/United States ; DK128053/DK/NIDDK NIH HHS/United States ; AI173448//National Institute of Allergy and Infectious Diseases/ ; NGP10103//Burroughs Wellcome Fund/ ; },
mesh = {Animals ; Female ; *Vagina/microbiology/immunology ; *Cytokines/immunology ; Mice ; *Streptococcus agalactiae/growth & development/immunology ; *Streptococcal Infections/immunology/microbiology ; *Diabetes Mellitus, Type 2/immunology/complications/microbiology ; *Mucous Membrane/immunology/microbiology ; Mice, Inbred C57BL ; *Immunity, Mucosal ; Microbiota ; Disease Models, Animal ; },
abstract = {Type 2 diabetes mellitus (T2D) is a metabolic disorder that confers increased risk of microbial infections, including those caused by the opportunistic pathogen group B Streptococcus (GBS). Asymptomatic GBS vaginal carriage is a notable reservoir for infection, but the impact of T2D on the vaginal mucosa and GBS colonization is not fully understood. We employed a diet-induced mouse model of T2D to investigate the impact of diabetes on glucose availability, vaginal microbiome composition, and vaginal cytokines at baseline and in response to GBS. We observed enhanced susceptibility of diabetic mice to GBS vaginal colonization and reproductive tract dissemination. Despite experiencing hyperglycemia, diabetic mice did not exhibit elevated glucose in the reproductive tract. Regarding the vaginal microbiota, diabetic mice had minimal compositional differences, with decreased Mammaliicoccus being the only significant taxonomic variance. Vaginal cytokine profiling revealed consistently depressed cytokines in diabetic mice, beginning with KC at baseline and expanding to eight pro-inflammatory cytokines post-GBS infection. Diabetic mice exhibited decreased proportions of uterine neutrophils and, following GBS exposure, also displayed an expanded vaginal γδ T cell compartment compared with controls. Pairing cytokine observations with GBS colonization revealed a correlation between delayed vaginal IL-1α induction and persistent vaginal GBS, suggesting that vaginal cytokine deficiency may contribute to diabetic GBS phenotypes. Intravaginal supplementation with rIL-1α resolved GBS burden differences between diabetic mice and controls, confirming that deficient vaginal cytokines contribute to diabetic GBS vaginal persistence. These findings advance our understanding of diabetic vaginal mucosal susceptibility to pathogens and support the potential for immunological intervention.IMPORTANCEPeople with T2D are more susceptible to microbial infections, but there is limited understanding of the mechanisms that drive this vulnerability. One possibility is that T2D enhances the colonization of opportunistic pathogens, like GBS, in mucosal reservoirs as a precursor to infection. In this study, we used a diabetic mouse model to test whether diabetes alters the vaginal mucosa to promote GBS colonization. We found that increased vaginal GBS colonization in diabetic mice was not linked to tissue glucose availability or changes in the vaginal microbiome but instead was associated with impaired vaginal immune responses. These findings provide a foundation for translational approaches to reduce GBS persistence and dissemination in at-risk individuals.},
}

Animals
Female
*Vagina/microbiology/immunology
*Cytokines/immunology
Mice
*Streptococcus agalactiae/growth & development/immunology
*Streptococcal Infections/immunology/microbiology
*Diabetes Mellitus, Type 2/immunology/complications/microbiology
*Mucous Membrane/immunology/microbiology
Mice, Inbred C57BL
*Immunity, Mucosal
Microbiota
Disease Models, Animal

@article {pmid42480452,
year = {2026},
author = {Shan, X and Shi, L and Zhu, T and Liang, X and Yang, J and Zhou, G and He, L and Mei, B and Wang, S and Li, F},
title = {Microbial tryptophan-IPA axis mediates 6:2 chlorinated polyfluorinated ether sulfonate (6:2Cl-PFESA)-induced gut-brain dysfunction and neurobehavioral impairments.},
journal = {Environment international},
volume = {214},
number = {},
pages = {110422},
doi = {10.1016/j.envint.2026.110422},
pmid = {42480452},
issn = {1873-6750},
mesh = {Animals ; Mice ; Male ; Mice, Inbred C57BL ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Fluorocarbons/toxicity ; *Alkanesulfonic Acids/toxicity ; *Indoles/metabolism ; *Brain/drug effects ; Intestinal Barrier Function ; },
abstract = {Chlorinated polyfluoroalkyl ether sulfonic acids (Cl-PFESAs) are widely used substitutes for perfluorooctane sulfonate (PFOS) and are increasingly detected in environmental and human matrices, yet their neurobehavioral risks during early life remain poorly defined. Here, male C57BL/6J mice were orally exposed to F-53B (6:2Cl-PFESA; 0.1 or 1 mg/kg/day) during juvenility for four weeks. F-53B selectively impaired recognition memory and social novelty preference, whereas locomotor activity, anxiety-like behavior, and Y-maze working memory were largely preserved. Mechanistically, F-53B compromised intestinal barrier integrity, as evidenced by reduced occludin expression and disrupted ZO-1 continuity, accompanied by elevated circulating lipopolysaccharide (LPS) and a systemic pro-inflammatory cytokine shift. In parallel, the hippocampus exhibited microglial activation, enhanced inflammatory signaling, and reduced PSD95 expression, consistent with neuroinflammatory stress and synaptic vulnerability. Shotgun metagenomics revealed pronounced microbiome restructuring and network rewiring, while widely targeted metabolomics converged on a marked disruption of tryptophan metabolism, characterized by depletion of microbiota-derived indole metabolites, including indole-3-propionic acid (IPA), together with altered serotonin-related signatures. Notably, oral IPA supplementation rescued behavioral deficits and attenuated gut-brain inflammatory alterations, restoring intestinal aryl hydrocarbon receptor (AhR) nuclear translocation, reducing LPS and cytokine levels, and ameliorating hippocampal inflammatory phenotypes. Collectively, these findings provide mechanistic evidence that a microbiota-tryptophan metabolite-gut barrier-inflammation axis links exposure to substitute PFAS with selective neurobehavioral dysfunction, highlighting microbiota-derived metabolites as potential modulators of PFAS-associated neurotoxicity.},
}

Animals
Mice
Male
Mice, Inbred C57BL
*Tryptophan/metabolism
*Gastrointestinal Microbiome/drug effects
*Fluorocarbons/toxicity
*Alkanesulfonic Acids/toxicity
*Indoles/metabolism
*Brain/drug effects
Intestinal Barrier Function

@article {pmid42485562,
year = {2026},
author = {Dalal, R and Barot, J and Binsuwaidan, R and Alshammari, N and Adnan, M and Patel, M and Patel, K},
title = {Substrate-Driven Microbiome Assembly in Water Hyacinth Vermicompost: Combined 16S rRNA and Shotgun Metagenomics for Sustainable Agriculture.},
journal = {Journal of basic microbiology},
volume = {66},
number = {7},
pages = {e70185},
pmid = {42485562},
issn = {1521-4028},
support = {PNURSP2026R304//Princess Nourah bint Abdulrahman University/ ; },
mesh = {RNA, Ribosomal, 16S/genetics ; *Eichhornia/microbiology ; Metagenomics ; Biomass ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Microbiota/genetics ; Animals ; *Soil Microbiology ; Archaea/classification/genetics/isolation & purification/metabolism ; Composting ; Agriculture ; Fungi/classification/genetics/isolation & purification/metabolism ; Shotgun Sequencing ; Phylogeny ; },
abstract = {Substrate composition is a primary determinant of microbial succession and functional dynamics in vermicomposting systems. However, comparative insights into how biomass pre-treatment influences microbial architecture and how different sequencing approaches capture these changes remain limited. In this study, evaluation was carried out on microbial community structure and metabolic potential in vermicompost derived from three forms of Eichhornia crassipes (water hyacinth) biomass, burnt biomass (BB), composted biomass (CB) and dry biomass (DB) using both 16S rRNA gene amplicon sequencing and shotgun metagenomics. All treatments were dominated by bacterial communities (> 97%), with Proteobacteria (Pseudomonadota), Firmicutes (Bacillota), Actinobacteria and Bacteroidota representing core phyla across substrates. However, metagenomics revealed broader domain-level coverage, detecting Archaea and Fungi that were underrepresented in 16S datasets. Substrate-specific signatures were evident such as, composted biomass exhibited enrichment of lignin degradation and carbon cycling pathways; dry biomass showed methanogenesis, fermentation and phosphate solubilization signatures; and burnt biomass was associated with nitrogen fixation and sulphur metabolism. Shannon diversity was highest in composted biomass (H' = 5.21), reflecting enhanced niche diversification during substrate maturation. Comparative analysis demonstrated that 16S rRNA sequencing effectively captured dominant bacterial structure, whereas shotgun metagenomics provided superior taxonomic resolution and direct functional inference, particularly for low-abundance and non-bacterial taxa. Notably, functional differentiation among treatments was more pronounced than broad taxonomic shifts, indicating that biomass pre-treatment exerts stronger influence on ecological function than on core community composition. These findings demonstrate that integrating taxonomic and functional metagenomics enables substrate-specific optimization of vermicompost formulations and provides a framework for designing microbiome-informed strategies for sustainable agriculture and invasive biomass valorization.},
}

RNA, Ribosomal, 16S/genetics
*Eichhornia/microbiology
Metagenomics
Biomass
*Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota/genetics
Animals
*Soil Microbiology
Archaea/classification/genetics/isolation & purification/metabolism
Composting
Agriculture
Fungi/classification/genetics/isolation & purification/metabolism
Shotgun Sequencing
Phylogeny

@article {pmid42486576,
year = {2026},
author = {Venugopal, DC and Srinivas, KS},
title = {Challenges and future directions in head and neck microbiome research.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {189-227},
doi = {10.1016/bs.ai.2026.03.010},
pmid = {42486576},
issn = {1557-8445},
mesh = {Humans ; *Head and Neck Neoplasms/microbiology/therapy/immunology ; *Microbiota/immunology ; Animals ; *Dysbiosis/microbiology/immunology/therapy ; Fecal Microbiota Transplantation ; Metabolomics ; Metagenomics ; Probiotics/therapeutic use ; },
abstract = {The microbial imbalance in head and neck cancer (HNC) is a promising area of research for developing targeted therapies. Maintenance of microbial diversity and balance through prebiotics, probiotics and faecal microbial transplantation (FMT) holds a potential approach in reestablishing the gut health. Preclinical studies and early clinical trials have shown positive results in restoring the favourable microbial environment, thereby minimizing the inflammation and maximizing the positive immune response. However, the link between microbial flora associated with oral dysbiosis, the associated biomarkers and HNC tumorigenesis needs to be further explored. Future research focusses on developing standardised strategies for maintaining the microbial environment, to serve as an adjunct to the standard treatment protocols for HNC. Biomarkers predicting immune response, synthetic genetically engineered beneficial bacteria, integration of metagenomics, metabolomics and meta transcriptomics for intra-tumoral microbial evaluation are the focus areas of emerging research.},
}

Humans
*Head and Neck Neoplasms/microbiology/therapy/immunology
*Microbiota/immunology
Animals
*Dysbiosis/microbiology/immunology/therapy
Fecal Microbiota Transplantation
Metabolomics
Metagenomics
Probiotics/therapeutic use

@article {pmid42486580,
year = {2026},
author = {Perera, ML and Perera, IR},
title = {Microbiome based diagnostic approaches.},
journal = {Advances in immunology},
volume = {170},
number = {},
pages = {93-125},
doi = {10.1016/bs.ai.2026.03.004},
pmid = {42486580},
issn = {1557-8445},
mesh = {Humans ; *Microbiota/immunology ; *Head and Neck Neoplasms/diagnosis/microbiology ; Dysbiosis ; Animals ; Early Detection of Cancer ; },
abstract = {Cancers of the Head and Neck (HNC) ranks seventh most abundant cancer category according to global incidence. thus posing a pertinent health hallenge. Shift in the homeostatic relationship of head and neck microbiome, causes microbial metabolic dysbiosis. Consequently, there is an increase in the pathobiome and pathogenic functions potentiating initiation and progression of carcinogenesis. Infection, inflammation and immune mediation trigger the pathogenic mechanisms. Accordingly, periodontitis perpetrated by unsatisfactory oral hygiene is connected to initiation and progression of HNC supported by substantial evidence. Further, mechanistic evidence is emerging on pathogenesis of bacteria-mediated carcinogenesis via toxins, carcinogenic metabolites and inflammatory cytokines with a view to possible treatments to halt progression of cancers. Advancements in surgical management techniques and adjuvant radiotherapy treatment, chemotherapy and emerging therapies such as immunotherapy, have not significantly increased overall disease free survival rates of most of HNCs. Early detection of cancers therefore, facilitates favorable outcomes such as better survival rates. Nevertheless, traditional invasive diagnostic approaches such as tissue biopsy gives rise to pain and discomfort to the patient In contrast, microbiome based diagnostic approaches, underpinned by salivary and mouth rinse microbiome analyses offers promising non-invasive, screening tools for early detection of HNC. This is augmented by advances in next generation sequencing, third generation sequencing, bioinformatics and machine learning technologies. Current developments in metagenomics, transcriptomics along with metabolomics enhanced harnessing the immense potential saliva possesses as a valuable screening and diagnostic tool, not only for cancer detection but for a range of diseases such as gastrointestinal diseases, autoimmune and metabolic disorders. Microbiome signatures in risk assessment of HNC is emerging as a new dimension in personalized risk assessment, risk stratification and care based pathways. Salivary microbiome analyses provides a promising approach for risk stratification, early stratification, through to assessment of prognosis, treatment success and survival of HNC patients suggested by accumulating evidence. Against this backdrop, we aim to provide an overview of microbiome based diagnostic approaches exploring new dimensions of detection and identification of HNC specific microbial biomarkers, microbial signatures, screening tools, primary diagnostic biomarkers, prognostic markers and interpersonal microbiome in the arena of personalized medicine.},
}

Humans
*Microbiota/immunology
*Head and Neck Neoplasms/diagnosis/microbiology
Dysbiosis
Animals
Early Detection of Cancer

@article {pmid42487113,
year = {2026},
author = {Ma, Y and Sun, J and Guo, C and Cao, J and Zhang, L and Zhu, F and Yu, X and Yang, L and Fang, J},
title = {Exploring brain-gut interaction mechanisms in Transcutaneous auricular Vagus Nerve stimulation for Major Depressive Disorder.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {},
pmid = {42487113},
issn = {1471-244X},
support = {82474663//National Natural Science Foundation of China/ ; HLCMHPP2023072//High Level Chinese Medical Hospital Promotion Projec/ ; },
mesh = {Humans ; Magnetic Resonance Imaging ; *Major Depressive Disorder/therapy/physiopathology/diagnostic imaging ; Female ; *Vagus Nerve Stimulation/methods ; Male ; Adult ; *Transcutaneous Electric Nerve Stimulation/methods ; *Brain/physiopathology/diagnostic imaging ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Brain-Gut Axis/physiology ; Treatment Outcome ; },
abstract = {BACKGROUND: The gut microbiota is intricately implicated in the pathogenesis of Major Depressive Disorder (MDD), with the vagus nerve serving as a key regulatory bridge. Transcutaneous Auricular Vagus Nerve Stimulation (taVNS) has emerged as a promising non-invasive therapeutic strategy for MDD by modulating the gut-brain axis, yet the precise brain-gut interaction mechanisms underlying its antidepressant effects remain poorly characterized. This study is a registered clinical trial (ChiCTR2200059591; Registered 4 May 2022; https://www.chictr.org.cn).

OBJECTIVE/HYPOTHESIS: This study aimed to verify the clinical efficacy of taVNS for MDD and elucidate the underlying brain-gut crosstalk mechanisms, by integrating comprehensive clinical assessments, resting-state functional magnetic resonance imaging (rs-fMRI) neuroimaging data and gut metagenomic profiling.

METHODS: Ninety-five patients diagnosed with MDD were randomly allocated at a 1:1 ratio to either the active taVNS group (auricular concha stimulation) or the sham taVNS group (superior concha of mid-helix stimulation). Eighty patients (40 per group) completed the entire intervention course and were included in the final statistical analysis. All participants underwent 30-minute stimulation twice daily (4/20 Hz, 3-8 mA) for 8 consecutive weeks (5 days per week). Standardized clinical assessments were administered at baseline and post-intervention, including the 17-item Hamilton Depression Rating Scale (HAMD-17), 14-item Hamilton Anxiety Rating Scale (HAMA-14), and Gastrointestinal Symptom Rating Scale (GSRS). Rs-fMRI was performed to quantify core neural activity metrics, including amplitude of low-frequency fluctuation (ALFF), fractional ALFF (fALFF), regional homogeneity (ReHo), and degree centrality (DC); fecal samples were collected for high-throughput metagenomic analysis. Spearman correlation analysis and mediation analysis were further conducted to dissect the interactive relationships between brain neural activity and gut microbiota.

RESULTS: The active taVNS group achieved significantly superior clinical efficacy relative to the sham group, with a HAMD-17 response rate of 62.50% and remission rate of 35.00%, versus 30.00% and 2.50% in the sham group (all P < 0.05). Rs-fMRI analyses revealed significant group×time interaction effects on neural activity: decreased ALFF in the right calcarine sulcus; altered fALFF in the right inferior temporal gyrus, left cuneus, right superior frontal gyrus (SFG) and right angular gyrus; reduced ReHo in the right calcarine sulcus and bilateral insula; and increased DC in the right caudate nucleus and left anterior cingulate gyrus. Gut microbiota profiling identified anaerobic butyrate-producing bacteria and Faecalibacterium prausnitzii as potential biomarkers linked to taVNS therapeutic effects. HAMD-17 scores were negatively correlated with Faecalibacterium prausnitzii abundance (r=-0.566, P < 0.01) and positively correlated with anaerobic butyrate-producing bacteria abundance (r = 0.406, P < 0.01). Mediation analysis suggested that fALFF values in the right SFG may indirectly modulate depressive symptoms via regulating Faecalibacterium prausnitzii abundance (indirect effect 95% CI: 0.3039-2.4466), with a significant partial mediation effect observed, though future studies controlling for dietary and other confounding variables are needed to confirm this relationship.

CONCLUSION: taVNS effectively alleviates depressive symptoms in MDD patients via dual complementary pathways: directly modulating neural activity in the right SFG to regulate depression-related brain function, and indirectly maintaining gut microbiota homeostasis by enriching beneficial taxa such as Faecalibacterium prausnitzii. These findings provide novel mechanistic insights into the brain-gut interaction underlying the antidepressant effects of taVNS, laying a theoretical foundation for its clinical application in MDD management.},
}

Humans
Magnetic Resonance Imaging
*Major Depressive Disorder/therapy/physiopathology/diagnostic imaging
Female
*Vagus Nerve Stimulation/methods
Male
Adult
*Transcutaneous Electric Nerve Stimulation/methods
*Brain/physiopathology/diagnostic imaging
*Gastrointestinal Microbiome/physiology
Middle Aged
*Brain-Gut Axis/physiology
Treatment Outcome

@article {pmid42487569,
year = {2026},
author = {Allen, XJ and Cowger, C and Brown-Guedira, G and Hawkes, CV},
title = {Mycobiome Simplification in Wheat Is Associated With the Pathogen Parastagonospora nodorum.},
journal = {Molecular ecology},
volume = {35},
number = {14},
pages = {e70485},
pmid = {42487569},
issn = {1365-294X},
support = {NNF19SA0059348//Novo Nordisk Fonden/ ; 7005451//U.S. Department of Agriculture (HATCH Project)/ ; },
mesh = {*Triticum/microbiology/genetics ; *Ascomycota/pathogenicity/genetics ; *Plant Diseases/microbiology/genetics ; *Mycobiome/genetics ; Host-Pathogen Interactions/genetics ; North Carolina ; Plant Leaves/microbiology ; Metagenomics ; },
abstract = {Plant mycobiomes are essential to plant health, yet their assembly under biotic stressors such as pathogen infection remains poorly understood. Plant pathogens can influence microbial community composition through direct antagonism and suppression of host immune responses, potentially altering mycobiome composition in ways that could affect plant performance. We investigated how the wheat (Triticum aestivum L.) foliar mycobiome was associated with inoculation with the fungal pathogen Parastagonospora nodorum (Berk.) Quaedvlieg, Verkley & Crous, which can cause substantial loss of yield and grain density throughout its range. To address this, we studied inoculation effects in four wheat cultivars planted in a randomized block design at two North Carolina field sites. We used ITS amplicon metagenomics to characterize wheat mycobiome richness, composition, and structure. We found that P. nodorum inoculation reduced fungal richness by up to 38.5%. We also found simplified foliar fungal networks for plants inoculated with P. nodorum, with up to 13.1% fewer taxa present and up to 41.2% fewer associations among those taxa. As part of these changes, increasing P. nodorum absolute abundance was correlated with increasing proportional representation of pathogens in wheat leaves due to loss of non-pathogenic taxa. Fewer fungal taxa and reduced network connectivity were particularly evident in reportedly susceptible cultivars and at one of the two sites where conditions favoured pathogen success. Based on these results, we suggest that pathogen infection plays a significant role in mycobiome assembly and has implications for disease management and mycobiome-based interventions in agricultural systems.},
}

*Triticum/microbiology/genetics
*Ascomycota/pathogenicity/genetics
*Plant Diseases/microbiology/genetics
*Mycobiome/genetics
Host-Pathogen Interactions/genetics
North Carolina
Plant Leaves/microbiology
Metagenomics

@article {pmid42489979,
year = {2026},
author = {Zhao, Z and Zhao, Y and Sun, Y and Bao, Y and Feng, J and Jiang, T and Lin, A},
title = {Metagenomic screening of antimicrobial peptide candidates and isolation of two active peptides from bat gut bacteria.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {8},
pages = {},
pmid = {42489979},
issn = {1573-0972},
support = {32430066, 32271558, 32571749//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Antimicrobial Peptides/pharmacology/isolation & purification/genetics/chemistry ; Microbial Sensitivity Tests ; Metagenomics/methods ; *Chiroptera/microbiology ; Anti-Bacterial Agents/pharmacology/isolation & purification ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/drug effects ; Bacteriocins/pharmacology/isolation & purification/genetics ; Amino Acid Sequence ; Tandem Mass Spectrometry ; Metagenome ; },
abstract = {Bacterial antibiotic resistance has intensified the need to identify new antimicrobial molecules from underexplored microbial systems. Wild mammalian gut microbiota may harbor antimicrobial peptide (AMP) candidates and candidate bacteriocins, but these systems remain poorly investigated as sources for antimicrobial discovery. Here, we used parallel metagenomic and culture-dependent approaches to explore candidate AMP sequences and candidate bacteriocins from the gut bacteria of the Asian particolored bat Vespertilio sinensis. Machine-learning screening of 553,401 short non-redundant ORF protein sequences identified 12,907 candidate AMP sequences. Of these, 31 were prioritized after in silico safety and structural filtering. In parallel, culture-dependent screening yielded two antagonistic bacterial isolates, CQJ and LYS. Activity-guided purification followed by LC-MS/MS identified two active peptides, CQJ01 and LYS01, with no exact matches in public databases. Both peptides exhibited broad in vitro antibacterial activity against 16 pathogenic strains, with minimum inhibitory concentration (MIC) values as low as 8 µg/mL against selected Gram-positive and Gram-negative bacteria. CQJ01 retained activity across pH 2-9 and after heat treatment up to 80 °C, whereas LYS01 retained activity from - 20 °C to 100 °C. Both peptides remained active after catalase, trypsin, papain, and proteinase K treatments but were sensitive to pepsin. They showed low hemolytic activity and limited cytotoxicity in preliminary assays. These findings support bat gut bacteria as an underexplored source of AMP candidates and candidate bacteriocins.},
}

Animals
*Antimicrobial Peptides/pharmacology/isolation & purification/genetics/chemistry
Microbial Sensitivity Tests
Metagenomics/methods
*Chiroptera/microbiology
Anti-Bacterial Agents/pharmacology/isolation & purification
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/drug effects
Bacteriocins/pharmacology/isolation & purification/genetics
Amino Acid Sequence
Tandem Mass Spectrometry
Metagenome

@article {pmid42491728,
year = {2026},
author = {Suzuki, D and Yang, J and Obana, N and Yachida, S and Shiba, S and Mizutani, S and Takamaru, H and Saito, Y and Fukuda, S and Yamada, T},
title = {Clinical strains isolated from early-stage colorectal cancer patients promote tumorigenesis.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21488},
pmid = {42491728},
issn = {2167-8359},
mesh = {*Colorectal Neoplasms/microbiology/pathology ; Humans ; Animals ; Mice ; *Carcinogenesis ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Metagenome ; Male ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is prevalent worldwide and is associated with gut commensals. Recent studies have highlighted the effects of gut microbes on CRC development driven by their strain diversity. Nevertheless, the impact of the gut microbial community on tumorigenesis in early-stage (ES) CRC remains unexplored.

METHODS: To assess the potential gut microbial community, which is critical to tumorigenesis in early-stage CRC, we collected publicly available shotgun metagenomes from CRC patient faecal samples from a Japanese population. Correlation analysis of the microbial profiles derived from the metagenomes revealed an ES CRC-associated community. To elucidate the strain diversity of the targeted community, we isolated strains from ES CRC patient faecal samples and employed comparative genomics. To evaluate the strain-specific effects of the community on tumorigenesis, we introduced an isolated strain cocktail into a CRC mouse model.

RESULTS: Among the most significant ES CRC-associated species, we identified Lancefieldella parvula (Lp), as reported in a previous study. The 20 species were identified as positively correlated with Lp. Seven of the 20 species were associated with ES CRC, including Actinomyces and Solobacterium. Schaalia odontolytica (So) (formerly known as Actinomyces odontolyticus) and Solobacterium moorei (Sm) were previously reported as potential species that promote CRC. Thus, we isolated clinical strains of Lp, So, and Sm from faecal samples as potential members of the ES CRC-associated community. Comparative genomics revealed that iron-related genes were shared among clinical strains. In the oral challenge with clinical strains, namely, Lp, So, and Sm, the mice exhibited shorter survival and significantly increased tumorigenesis, suggesting that the cocktail of clinical strains is more pathogenic to the CRC mouse model than the type strain is. In summary, we inferred that the ES CRC-associated community could promote CRC, and the effects depend on the strains involved.},
}

*Colorectal Neoplasms/microbiology/pathology
Humans
Animals
Mice
*Carcinogenesis
Feces/microbiology
*Gastrointestinal Microbiome/genetics
Female
Metagenome
Male

@article {pmid42493771,
year = {2026},
author = {Yi, Y and Xie, F and Xia, C and Li, J and Zhao, P and Liu, M and Ma, X and Chen, J},
title = {Hypertension and gut microbial hydrogenases: a comparison of hydrogen metabolism and etiology.},
journal = {Medical gas research},
volume = {16},
number = {4},
pages = {352-358},
doi = {10.4103/mgr.MEDGASRES-D-25-00128},
pmid = {42493771},
issn = {2045-9912},
mesh = {*Hydrogenase/metabolism/genetics ; *Hydrogen/metabolism ; *Hypertension/microbiology/etiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; },
abstract = {JOURNAL/mgres/04.03/01612956-202612000-00006/figure1/v/2026-07-23T200825Z/r/image-tiff Hypertension is a prevalent chronic condition and serves as a significant risk factor for numerous cardiovascular and cerebrovascular disorders. Gut microbiota dysbiosis has been considered to contribute to the pathogenesis of hypertension. It has been reported that a large majority of gut microbiota possess genes encoding hydrogenases. These hydrogenases are involved in the alteration of gut microbiota in non-infectious colitis, suggesting a potential link between microbial hydrogen metabolism and disease onset. This study aims to explore the relationship between hydrogenase expression patterns in the gut microbiome and the incidence of hypertension. In this study, publicly available gut microbiome metagenomic data were used to comprehensively analyze the expression patterns of hydrogenases in the gut microbiota of hypertensive patients. Compared with the control group, a 2.3-fold increase in electron bifurcating [FeFe] group A3 hydrogenases (P = 0.0299), a 55.6% decrease in [NiFe] group 1d hydrogenases (P = 0.0097), increased hydrogen-sensing hydrogenases and decreased hydrogen-uptake hydrogenases in the hypertension group. The main difference between the two groups is reflected in the abundance of [NiFe] hydrogenase subtypes. After eliminating the effects of factors such as age, sex, and lifestyle, significant differences in the abundance of [FeFe] group A3, [NiFe] group 1d, and [NiFe] group 1c were observed between the two groups, suggesting that these three indicators could serve as potential biomarkers for diagnosing the onset of hypertension. Additionally, Mendelian randomization analysis showed a protective effect of hydrogen metabolism against hypertension (odds ratio = 0.72, 95% confidence interval: 0.61-0.85, P < 0.001). Our study advances the understanding of microbiome-mediated mechanisms in hypertension by demonstrating an association between hydrogenase expression dynamics and blood pressure regulation, providing a foundation for future microbiome-based diagnostic and therapeutic strategies.},
}

*Hydrogenase/metabolism/genetics
*Hydrogen/metabolism
*Hypertension/microbiology/etiology/metabolism
Humans
*Gastrointestinal Microbiome

@article {pmid42493801,
year = {2026},
author = {Van Den Bossche, T and Grenga, L and Alves, G and Arntzen, MØ and Benndorf, D and Brauer, M and Figeys, D and Henry, C and Hettich, RL and Heyer, R and Jagtap, PD and Jehmlich, N and Kleiner, M and Li, L and Mesuere, B and Pabst, M and Pandhal, J and Pope, PB and Seifert, J and Trautwein-Schult, A and Verschaffelt, P and Wilmes, P and Armengaud, J and Kunath, BJ},
title = {The Metaproteomics Initiative: five years of community-driven progress.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42493801},
issn = {2049-2618},
mesh = {*Proteomics/methods ; *Microbiota ; Humans ; Metagenomics ; },
abstract = {The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community. Over the past 5 years, the Initiative has developed into a structured, global network of researchers. It has launched community-driven benchmark studies, helped shape emerging metadata and reporting standards, developed practical guidance and training materials, organized international symposia, and fostered connections across the microbiome research landscape (https://metaproteomics.org/). We outline the Initiative's organization, activities, achievements, and ongoing efforts, and reflect on how sustained, community-led coordination has shaped the development of metaproteomics as a field. We further position the Grand Metaproteome Challenges as a next step toward coordinated, community-scale biological research, aimed at advancing functional microbiome studies across clinical, industrial, and environmental application domains, and invite engagement from the wider microbiome and omics communities. Video Abstract.},
}

*Proteomics/methods
*Microbiota
Humans
Metagenomics

@article {pmid42494846,
year = {2026},
author = {Mthembu, TP and Hlongwane, NL and Salawu-Rotimi, A and Hadebe, K and Pierneef, R},
title = {Metagenomic analysis of fecal and environmental microbiota in rural mixed livestock farming systems in South Africa.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1828785},
pmid = {42494846},
issn = {2235-2988},
mesh = {Animals ; South Africa ; *Feces/microbiology ; *Metagenomics ; *Livestock/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Environmental Microbiology ; *Microbiota ; Cattle ; Soil Microbiology ; Phylogeny ; Metagenome ; Swine ; Sheep ; Biodiversity ; Water Microbiology ; Rural Population ; },
abstract = {In South African rural areas, farmers often practice mixed extensive livestock farming, facilitating microbial exchange among and between animal species and their environment. The composition and transmission potential of microbiomes between animals and their environments in these smallholder livestock systems remain largely unexplored, creating a gap in understanding how mixed-livestock farming affects gut and environmental microbiomes. Shotgun metagenomics was used to uncover the fecal and environmental microbiota in smallholder mixed livestock systems, aiming to understand microbiome transfer within these systems. A total of 111 samples were collected in KwaZulu-Natal and Eastern Cape provinces of South Africa, including 76 fecal samples from cattle, goats, sheep, pigs, and chickens; 18 soil samples; and 17 water samples. Taxonomic analysis of the sequencing data identified Proteobacteria as the dominant phylum across most hosts, except that pigs were dominated by Firmicutes. Moraxellaceae and Pseudomonadaceae were the differentiating families between monogastrics and ruminants. Although microbial diversity differences were significantly attributed to the host, genera such as Acinetobacter, Chryseobacterium, Flavobacterium, Pedobacter, and Pseudomonas were consistently found across all animal and environmental hosts. Cattle shared more genera with the environment than other animal species. Opportunistic pathogens, including Enterococcus spp., Escherichia coli, and Clostridium spp., were found across all the livestock species, and were highest in chickens. Additionally, some pathogens were detected in water but none in soil, suggesting water as a potential medium for pathogen transmission. The microbial exchange between livestock and their surroundings highlights the permeability of host-environment boundaries in smallholder systems.},
}

Animals
South Africa
*Feces/microbiology
*Metagenomics
*Livestock/microbiology
*Bacteria/classification/genetics/isolation & purification
*Environmental Microbiology
*Microbiota
Cattle
Soil Microbiology
Phylogeny
Metagenome
Swine
Sheep
Biodiversity
Water Microbiology
Rural Population

@article {pmid42484632,
year = {2026},
author = {Vernon, JJ and Lynch, J and Yu, X and Do, T},
title = {Clostridioides difficile in the oral microbiome: an in silico analysis.},
journal = {Journal of medical microbiology},
volume = {75},
number = {7},
pages = {},
doi = {10.1099/jmm.0.002188},
pmid = {42484632},
issn = {1473-5644},
mesh = {Humans ; *Clostridioides difficile/genetics/isolation & purification/classification ; Saliva/microbiology ; *Dental Plaque/microbiology ; *Microbiota ; *Clostridium Infections/microbiology/epidemiology ; Periodontitis/microbiology ; *Mouth/microbiology ; Computer Simulation ; Computational Biology ; Metagenomics ; Female ; Male ; },
abstract = {Introduction. High rates of recurrent Clostridioides difficile infection (CDI) and environmental contamination are attributed to its ability to form spores. Periodontal diseases are characterized by gingival inflammation, caused by dental plaque accumulation.Hypothesis. Periodontal plaque could harbour C. difficile spores, acting as a reservoir for reinfection.Aim. Compare the prevalence and abundance of C. difficile in metagenomic sequences of saliva and dental plaque from healthy and periodontal disease patients.Methodology. Publicly available metagenomic reads from oral samples of healthy (n=80) and periodontitis (n=204) patients were analysed for C. difficile presence through an in-house bioinformatic pipeline. Briefly, reads underwent quality control (cutadapt/fastQC) prior to subsampling of 3 million reads (seqtk). Reads and MEGAHIT-assembled contigs were aligned to a C. difficile reference genome (ASM1888508v1) or a full non-redundant protein DIAMOND database. Outputs were filtered, annotated (Entrez Direct) and top hits identified via National Center for Biotechnology Information blast. Abundance and prevalence were compared between cohorts.Results. Low levels of C. difficile sequences were observed, with significantly higher prevalence in periodontitis (7.4%, n=15/204) vs. healthy cohorts (5.0%, n=4/80) (P=0.0087) with reference genome alignment. Using the full non-redundant database, prevalence was also higher in periodontitis (14.2% vs. 3.8%; P=0.012), along with significantly greater average C. difficile sequence counts (0.608 vs. 0.075; P=0.018) and relative abundance (0.00029% vs. 0.0000003%; P=0.009).Conclusion. Sequences pertaining to C. difficile were detected in oral samples, with significantly more observed in periodontal disease compared to healthy cohorts. This highlights the possibility for dental plaque to act as a reservoir, potentially contributing to reinfection in CDI patients.},
}

Humans
*Clostridioides difficile/genetics/isolation & purification/classification
Saliva/microbiology
*Dental Plaque/microbiology
*Microbiota
*Clostridium Infections/microbiology/epidemiology
Periodontitis/microbiology
*Mouth/microbiology
Computer Simulation
Computational Biology
Metagenomics
Female
Male

@article {pmid42484695,
year = {2026},
author = {Vieira, CS and Lemos, LN and Morais, DK and Rosado, AS and Pylro, VS},
title = {Uneven global coverage of halophilic metagenomes limits comparative analyses of microbial adaptation to saline environments.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {42484695},
issn = {1678-4405},
mesh = {Metagenomics ; *Metagenome ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Ecosystem ; Salinity ; *Adaptation, Physiological ; Biodiversity ; },
abstract = {Halophilic microorganisms are central to biotechnology, bioremediation, and astrobiology because they persist under extreme and polyextreme conditions analogous to extraterrestrial environments. Although metagenomics has transformed the study of halophilic biodiversity, available datasets remain fragmented and unevenly documented. To assess how halophilic metagenomic research reflects the global exploration of hypersaline environments, we analyzed PubMed-indexed studies and associated sequencing metadata deposited at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) using a curation workflow. Our quantitative analysis reveals a severe geographic bias linked to uneven global research investment (Gini coefficient = 0.736), with a small number of countries contributing to many publicly available datasets. In contrast, the environmental distribution of these samples showed moderate ecological uniformity (Pielou's Evenness = 0.818), though we identified pervasive gaps in metadata completeness that hinder dataset interoperability. Our curated dataset highlights a strong research focus on polyextremophilic habitats, positioning these ecosystems as prime targets for biotechnological and astrobiological bioprospecting. Additionally, the geographical bias highlights the need for interoperable global data frameworks and more equitable investment in data generation and analysis, especially in underrepresented regions of the Global South.},
}

Metagenomics
*Metagenome
*Bacteria/genetics/classification/isolation & purification/metabolism
Ecosystem
Salinity
*Adaptation, Physiological
Biodiversity

@article {pmid42485280,
year = {2026},
author = {K V, S and Thaha, N and Dehury, B},
title = {In silico identification and biophysical characterization of candidate antimicrobial peptides from the Indian marine microbiome targeting multidrug-resistant ESKAPE pathogens.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0353985},
pmid = {42485280},
issn = {1932-6203},
mesh = {*Antimicrobial Peptides/pharmacology/chemistry ; Molecular Dynamics Simulation ; *Microbiota ; *Drug Resistance, Multiple, Bacterial/drug effects ; Acinetobacter baumannii/drug effects ; India ; Computer Simulation ; *Anti-Bacterial Agents/pharmacology/chemistry ; Klebsiella pneumoniae/drug effects ; Pseudomonas aeruginosa/drug effects ; Machine Learning ; },
abstract = {The global health crisis of antimicrobial resistance necessitates the discovery of new antibacterial agents. Underexplored marine microbiomes, particularly from the biodiverse Indian coast, represent a rich potential source of antimicrobial peptides (AMPs). Targeting the urgent threat of multidrug-resistant ESKAPE pathogens, the present study aimed to computationally identify novel, membrane-active AMPs from these unique metagenomic datasets, with a focus on inhibiting Gram-negative bacteria. In this study, we computationally mined Indian marine high-resolution shotgun metagenomic datasets through quality filtering, de novo assembly, and small open reading frame prediction. An ensemble of six machine learning-based AMP prediction tools identified over 51,000 high-confidence candidate AMPs. Subsequent filtering based on physicochemical properties and AlphaFold3-predicted structures prioritized ten peptides with favourable membrane-active characteristics. Two lead candidates, c_AMP_1 and c_AMP_2, were subjected to all-atom molecular dynamics simulations within Gram-negative membrane mimetic models of Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. Our simulations indicated distinct membrane interaction modes: c_AMP_1 adopted a stable, surface-associated α-helical orientation, while c_AMP_2 displayed a more flexible, membrane-inserting orientation in the simulations. Analysis of the MD simulations revealed distinct predicted peptide-membrane interaction profiles, characterized by specific hydrogen bonding patterns, peptide tilt angles, and membrane thinning, which collectively suggest differing biophysical interaction modes. Taken together, our work suggests the Indian marine microbiome as a promising reservoir for novel AMP candidates and suggests that an integrated computational pipeline - combining machine learning, structural biology, and biophysical simulation - may help prioritize candidate peptides for future experimental validation against critical pathogens.},
}

*Antimicrobial Peptides/pharmacology/chemistry
Molecular Dynamics Simulation
*Microbiota
*Drug Resistance, Multiple, Bacterial/drug effects
Acinetobacter baumannii/drug effects
India
Computer Simulation
*Anti-Bacterial Agents/pharmacology/chemistry
Klebsiella pneumoniae/drug effects
Pseudomonas aeruginosa/drug effects
Machine Learning

@article {pmid42478129,
year = {2026},
author = {Zhou, Y and Xu, J and Zhou, W and Wu, P and Yang, S and Ji, L and Shen, Q and Wang, X and Liu, Y and Zhou, C and Zhang, W and Xu, M},
title = {Genetic Diversity and Genomic Characteristics of the Respiratory Virome in Patients With Severe Fungal Infections.},
journal = {Journal of medical virology},
volume = {98},
number = {7},
pages = {e71063},
pmid = {42478129},
issn = {1096-9071},
support = {2023YFD1801300//National Key Research and Development Programs of China/ ; 82550118//National Natural Science Foundation of China/ ; 82341106//National Natural Science Foundation of China/ ; BK20241926//Natural Science Foundation of Jiangsu Province/ ; },
mesh = {Humans ; *Genetic Variation ; *Virome/genetics ; *Genome, Viral ; *Respiratory Tract Infections/virology/microbiology ; Sputum/virology ; Metagenomics ; Phylogeny ; *Mycoses/virology/microbiology ; *Viruses/genetics/classification/isolation & purification ; Female ; Male ; Middle Aged ; Adult ; Sequence Analysis, DNA ; },
abstract = {Respiratory tract infections represent a leading cause of morbidity and mortality globally, with viral pathogens accounting for a substantial proportion of these cases. However, research on the human respiratory virome is still in its infancy, and our understanding of this field remains relatively limited. In the present study, viral metagenomic sequencing was conducted on 65 sputum samples obtained from patients with severe fungal infections. We successfully assembled viral genome sequences belonging to four distinct viral families: Anelloviridae, Genomoviridae, Microviridae, and Inoviridae. Through systematic analysis of the virome composition, this study characterized the structural features of the respiratory virome in patients with severe fungal infections. The findings provide a foundational description of viral diversity in this specific clinical context. These findings lay a theoretical foundation for clinical pathogen detection, targeted interventions, and the development of future prevention strategies.},
}

Humans
*Genetic Variation
*Virome/genetics
*Genome, Viral
*Respiratory Tract Infections/virology/microbiology
Sputum/virology
Metagenomics
Phylogeny
*Mycoses/virology/microbiology
*Viruses/genetics/classification/isolation & purification
Female
Male
Middle Aged
Adult
Sequence Analysis, DNA