Yuyang Ma, Min Yang, Andi Xu, Xueni Zhao, Xiao Dong, Wenyuan Li, Huakang Tu, Yi Guo, Zhengya Song, Xifeng Wu
{"title":"Characterization of gut microbiome signatures in metabolic dysfunction associated steatotic liver disease.","authors":"Yuyang Ma, Min Yang, Andi Xu, Xueni Zhao, Xiao Dong, Wenyuan Li, Huakang Tu, Yi Guo, Zhengya Song, Xifeng Wu","doi":"10.1038/s41522-026-01059-8","DOIUrl":"10.1038/s41522-026-01059-8","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13444103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148295453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Elizabeth V K Ledger, Niamh E Horgan, Denis Lynch, Lorraine M Bateman, Ruth C Massey
{"title":"Human serum triglycerides promote Staphylococcus aureus biofilm formation and antibiotic tolerance.","authors":"Elizabeth V K Ledger, Niamh E Horgan, Denis Lynch, Lorraine M Bateman, Ruth C Massey","doi":"10.1038/s41522-026-01064-x","DOIUrl":"10.1038/s41522-026-01064-x","url":null,"abstract":"<p><p>Biofilm formation and antibiotic tolerance are major contributors to the persistence of Staphylococcus aureus infections, yet how the host environment affects these phenotypes remains poorly understood. Here, we show that incubation in human serum primes S. aureus to form robust biofilms and tolerate vancomycin and daptomycin, last resort antibiotics for the treatment of antibiotic-resistant staphylococcal infections. Mechanistically, we demonstrate that the staphylococcal Geh lipase is essential for serum-induced biofilm formation by liberating glycerol from host lipids, which is then used to promote increased synthesis of D-alanylated wall teichoic acids, driving biofilm development. Inhibition of the Geh lipase or wall teichoic acid synthesis markedly reduces biofilm formation and restores antibiotic susceptibility, highlighting clinically achievable strategies to inhibit host-induced biofilm formation and prevent the associated antibiotic tolerance. Together, our findings reveal a host-driven mechanism of biofilm-associated antibiotic tolerance in S. aureus and provide rational targets for therapeutic intervention.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13631273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148295468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Runlai Xu, Chenghang Du, Yutian Gao, Kunhu Chen, Jieru Guo, Jun Ma, Yinghua Zhang, Zhimin Wang, Zhencai Sun
{"title":"Distinct rhizosphere microbiomes and metabolomes mediate Fusarium crown rot resistance across wheat cultivars.","authors":"Runlai Xu, Chenghang Du, Yutian Gao, Kunhu Chen, Jieru Guo, Jun Ma, Yinghua Zhang, Zhimin Wang, Zhencai Sun","doi":"10.1038/s41522-026-01065-w","DOIUrl":"10.1038/s41522-026-01065-w","url":null,"abstract":"<p><p>Soil-borne Fusarium crown rot (FCR) poses a major challenge to wheat production. Plants can recruit beneficial microbes through a \"cry-for-help\" strategy in response to pathogen attack, yet how different wheat genotypes modulate this response remains unclear. In FCR-affected wheat fields, we systematically investigated the interactions among wheat, pathogens, rhizosphere microbes, and metabolites using a combination of phenotypic assessment, molecular detection, and microbiome and metabolome profiling. Our results showed that wheat genotype and plant health jointly shaped rhizosphere microbial communities and metabolite profiles. Beneficial Bacillus species were key taxa in healthy rhizosphere communities, whereas the susceptible cultivar additionally relied on Pseudomonas to maintain plant health. In vitro assays and a pot experiment confirmed that these microbes antagonize the pathogen and enhance wheat performance, thereby alleviating FCR. Furthermore, the tolerant cultivar exhibited more complex rhizosphere microbial co-occurrence networks and harbored conserved taxa, such as Devosia. Microbe-metabolite interaction networks revealed strong associations between beneficial rhizosphere microbes (e.g., Bacillus and Pseudomonas) and specific metabolites, such as tritrans-heptacis-undecaprenyl phosphate, PE(14:1(9Z)/20:5(5Z,8Z,11Z,14Z,17Z)), and 1,2-Dioleoyl-sn-glycerol-3-phosphate. Collectively, our results provide novel evidence that rhizosphere metabolite-mediated plant-microbe interactions contribute to the suppression of soil-borne diseases.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13642924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148295435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yuchao Zhao, Ying Wang, Sarula Bai, Jian Tan, Haoyu Niu, Ao Zhang, Gang Guo, Luoyun Fang, Linshu Jiang
{"title":"Reprogramming hydrogen metabolism for methane mitigation in dairy cows: mechanistic insights from polyphenols using meta-omics approaches.","authors":"Yuchao Zhao, Ying Wang, Sarula Bai, Jian Tan, Haoyu Niu, Ao Zhang, Gang Guo, Luoyun Fang, Linshu Jiang","doi":"10.1038/s41522-026-01068-7","DOIUrl":"10.1038/s41522-026-01068-7","url":null,"abstract":"<p><p>Enteric methane emissions from ruminants contribute significantly to agricultural greenhouse gases. Plant-derived phytochemicals such as grape seed proanthocyanidins (GSP) are promising natural antimethanogenic feed additives, yet their modes of action remain incompletely understood. This study aimed to comprehensively elucidate the microbiological and functional mechanisms underlying phytochemical-induced methane mitigation using integrative meta-omics. Both in vivo and in vitro experiments demonstrated that GSP supplementation significantly reduced methane emissions; in lactating dairy cows, GSP decreased methane emission intensity by 16.5% (g/kg energy-corrected milk). Metagenomic and metatranscriptomic analyses revealed a reprogramming of microbial communities, with decreased abundance and transcriptional activity of methanogenic archaea (e.g., Methanobrevibacter) and enhanced activity of alternative hydrogenotrophic bacteria (Selenomonas, Veillonella, Sharpea). Functionally, GSP elevated expression of genes involved in reductive acetogenesis (e.g., acsB), nitrate ammonification (narG, nrfA), and sulfate reduction (dsrA), thereby redirecting hydrogen flux away from methanogenesis. These shifts were accompanied by increased microbial carbohydrate metabolism and antioxidative responses. Our findings provide the first meta-omics-based mechanistic framework for understanding methanogenesis suppression by phytochemicals in ruminants. GSP modulates microbial composition and function to reroute reductant flows and suppress archaeal methanogenesis through enhanced bacterial electron sinks. This work highlights the potential of polyphenols to modulate the rumen microbiome for sustainable methane mitigation, supporting the development of next-generation feed additives.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13642931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148284142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Adrien Sarlet, Anja K Ehrmann, Namiko Mitarai, Liselotte Jauffred
{"title":"Wrinkle-like structures emerge from matrix complementarity and mechanical discontinuity in heterogenous biofilms.","authors":"Adrien Sarlet, Anja K Ehrmann, Namiko Mitarai, Liselotte Jauffred","doi":"10.1038/s41522-026-01048-x","DOIUrl":"10.1038/s41522-026-01048-x","url":null,"abstract":"<p><p>Biofilms are dynamic communities of microorganisms encased in a self-produced extracellular matrix. The mechanical behaviour of a biofilm is shaped by the heterogenous composition of its matrix, both spatially and chemically. In turn, these mechanics influence the biofilm's architecture at micro- and macroscopic scales, driving its complexity and adaptability. Morphologically, this is reflected in mechanical deformations of the biofilm known as wrinkles. In nature, biofilms often host different species of bacteria, allowing for a great diversity of matrix components. Here, we use a combination of two Escherichia coli strains as a model for a multispecies biofilm in which each bacterial strain produces one of two complementary matrix fibres: an amyloid protein (curli) or a polysaccharide (phosphoethanolamine-cellulose). Using fluorescence microscopy, we confirm that the two bacterial strains rapidly segregate into isogenic sectors, decreasing local heterogeneity. Furthermore, we show how wrinkles form, both in the homogenous central region of the biofilm, as well as at the boundary between sectors (i.e. where the two matrix producers co-localize). Finally, we show that increasing strain intermixing via the addition of bacteriophages results in thicker, taller wrinkles, irrespective of whether the two fibres are produced by two different strains or co-produced by the same bacteria.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13639082/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148284156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Ligilactobacillus murinus modulates gut microbiota-derived 5-hydroxyindole to inhibit pseudorabies virus infection via activation of the aryl hydrocarbon receptor.","authors":"Man-Jie Hu, Yong-Lei Yang, Ya-Xin Yang, Rong-Rong Zhang, Tian-Kui Guo, Jun-Hong Xing, Bing Liu, M Azeem Riaz, Ying-Shi Yang, Lin-Jiao Yu, Jing-Yi Pang, Ying Zhao, Chun-Wei Shi, Gui-Lian Yang, Hai-Bin Huang, Yan-Long Jiang, Jian-Zhong Wang, Xin Cao, Nan Wang, Yan Zeng, Wen-Tao Yang, Chun-Feng Wang","doi":"10.1038/s41522-026-01025-4","DOIUrl":"https://doi.org/10.1038/s41522-026-01025-4","url":null,"abstract":"<p><p>Pseudorabies virus (PRV) infects a wide range of mammals and poses a potential threat to human health. The stimulator of interferon genes (STING) is crucial for innate immunity against DNA viruses and intestinal homeostasis; however, its influence on gut microbiota-mediated antiviral immunity is unclear. Here, we demonstrate that deletion of the STING gene or the IFNAR1 gene in mice aggravates PRV-induced lung pathology, increases viral load and inflammatory cytokine expression, reduces type I interferon transcription, and ultimately decreases survival of STING-KO mice and IFNAR1-KO mice. Additionally, STING deficiency causes rapid loss of alveolar macrophages (AMs) in the lungs following PRV infection, promotes neutrophil and monocyte recruitment through activation of inflammation-related signaling pathways, and disrupts the pulmonary immune cell balance. Furthermore, STING-deficient mice exhibit a markedly reduced abundance of Ligilactobacillus murinus (L. murinus) in the gut after PRV infection, and the level of 5-hydroxyindole (5-HI) correlates positively with intestinal Ligilactobacillus abundance. L. murinus modulates gut microbiota-derived 5-hydroxyindole. Moreover, L. murinus and 5-HI protect antibiotic (Abx)-treated mice from PRV infection by activating the aryl hydrocarbon receptor (AhR) in a STING-dependent manner, and this protective effect is abolished in Ahr<sup>-</sup><sup>/</sup><sup>-</sup> mice. Collectively, these findings highlight that STING inhibits PRV infection by regulating L. murinus and 5-HI, which leads to activation of AhR.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148272236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Maxime Amoyel, André Bado, Tigran Poghosyan, Tiphaine Le Roy, Maude Le Gall
{"title":"The gastric ecosystem: assessing resident microbiome vs. transient microorganisms in obesity and following bariatric interventions.","authors":"Maxime Amoyel, André Bado, Tigran Poghosyan, Tiphaine Le Roy, Maude Le Gall","doi":"10.1038/s41522-026-01058-9","DOIUrl":"10.1038/s41522-026-01058-9","url":null,"abstract":"<p><p>Long considered a sterile environment due to its acidity, the stomach is increasingly recognized as a low-biomass but structured microbial ecosystem. Advances in culture-independent sequencing reveal a diverse gastric microbiome shaped by acid secretion, mucosal physiology, diet, medication use, and Helicobacter pylori colonization, although distinguishing metabolically active residents from transient oropharyngeal or dietary microorganisms remains a significant challenge. In healthy individuals, gastric mucosal communities primarily consist of Bacillota, Pseudomonadota, Actinomycetota, Bacteroidota, and Fusobacteriota, with genera such as Streptococcus, Prevotella, Rothia, and Veillonella consistently detected. Obesity is associated with altered gastric physiology, including higher pH, delayed emptying, and increased bile reflux, alongside distinct microbial signatures. Helicobacter pylori remains a dominant ecological factor modifying acidity, inflammation, and niche structure, while proton-pump inhibitors significantly \"oralize\" the gastric microbiome. Although animal models suggest that bariatric surgery can remodel the gastric microbiome, no human study has yet characterized gastric microbial changes following sleeve gastrectomy, gastric bypass, or endoscopic bariatric therapies, leaving the translational relevance of preclinical findings uncertain. Given the central role of the stomach in nutrient sensing and metabolic hormone secretion, its microbial ecosystem warrants dedicated investigation.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13443172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148265426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Li Zhang, Chenrui Lv, Wenqiang Guo, Qiuyue Fu, Yilang Li, Xiaomeng Liu
{"title":"Multi-omics insights into isovaleric acid effects on broiler performance, physiological health, and meat quality.","authors":"Li Zhang, Chenrui Lv, Wenqiang Guo, Qiuyue Fu, Yilang Li, Xiaomeng Liu","doi":"10.1038/s41522-026-01053-0","DOIUrl":"https://doi.org/10.1038/s41522-026-01053-0","url":null,"abstract":"<p><p>Isovaleric acid (IVA) has been shown to benefit gut health, but its effects on broiler meat quality remain unclear. A total of 864 broilers were assigned to control or 0.05%, 0.1%, or 0.2% IVA groups to evaluate the effects of IVA supplementation on performance, blood biochemistry, immunity, gut microbiota, metabolome, and meat quality. IVA increased average daily gain and, at some doses, feed intake and villus height, while reducing feed conversion ratio. It also lowered serum blood urea nitrogen at 21 and 42 days and modulated inflammatory and immune indices. IVA improved meat quality by increasing breast and leg muscle protein content at 42 days, reducing drip loss and shear force, and improving color parameters. Microbiome analysis showed that IVA reduced Ace index and altered bacterial and fungal β-diversity at 21 days, whereas at 42 days it increased bacterial Shannon index and shifted community composition, while fungal α-diversity remained largely unchanged. Metabolomics revealed marked changes in lipid and amino acid metabolism. Integrative analysis identified Collinsella, norank_f__Ruminococcaceae, and unclassified_f__Oxalobacteraceae as key taxa associated with beneficial muscle metabolites. These findings highlight a gut microbiota-metabolome-muscle axis contributing to improved broiler meat quality and inform nutritional interventions in poultry production.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148284111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kaile Ma, Qiqi Zhang, Rui Hao, Xiao Sun, Jing Jia, Min Li
{"title":"The microbiota-gut-brain axis: novel mechanisms and therapeutic frontiers in obesity and type 2 diabetes.","authors":"Kaile Ma, Qiqi Zhang, Rui Hao, Xiao Sun, Jing Jia, Min Li","doi":"10.1038/s41522-026-01039-y","DOIUrl":"10.1038/s41522-026-01039-y","url":null,"abstract":"<p><p>The microbiota-gut-brain axis (MGBA) is a bidirectional network linking gut microbes to the CNS. This review elucidates how microbial messengers-short-chain fatty acids, bile acids, neuroactive metabolites, and extracellular vesicles-drive obesity and type 2 diabetes via neural, endocrine, and immune pathways. MGBA dysregulation triggers hypothalamic dysfunction, adipose inflammation, incretin axis impairment, and β‑cell failure. We discuss MGBA-targeted therapies and their translational challenges.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13631225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148265464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"From diet to function: using synthetic microbial communities to map gut microbial interactions.","authors":"Dodzi Kwaku Jnr Senoo, Luke Acton, Lindsay J Hall","doi":"10.1038/s41522-026-01012-9","DOIUrl":"10.1038/s41522-026-01012-9","url":null,"abstract":"<p><p>Diet shapes gut microbial ecology and function, but causal mechanisms are hard to resolve in native communities. Synthetic microbial communities provide defined systems to test how dietary substrates alter community structure, metabolism, and host responses. This review summarises SynCom design, experimental platforms, and dietary applications, highlights multi-omics and modelling approaches, proposes reporting standards, and considers challenges and future directions, including multi-kingdom and AI-enabled function-first SynComs.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13631285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148258897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}