Microbiome最新文献

{"title":"Steering root-associated microbiomes via direct and soil legacy effects of neighbors.","authors":"Mireadili Kuerban, Sofia I F Gomes, Ozlem Erol, T Martijn Bezemer","doi":"10.1186/s40168-026-02429-2","DOIUrl":"10.1186/s40168-026-02429-2","url":null,"abstract":"<p><strong>Background: </strong>Root-associated microbiomes are widely assumed to be primarily shaped by the host plant. However, other co-occurring plants can also influence the composition of this microbiome. This can be either directly, by stimulating or suppressing microbial recruitment of the focal plant, or indirectly, through soil legacies that shape the microbial pool encountered by the focal plant during establishment. The relative importance of these neighbor effects shaping the focal plant microbiome and the consequences for focal plant growth remain poorly known. Here, we challenge the paradigm that the host plant identity is the main driver of root-associated bacterial and fungal communities.</p><p><strong>Results: </strong>Under experimental conditions, we show that the influence of the host plant on root-associated microbiomes is dramatically reduced in the presence of neighbors and their soil legacies. Remarkably, root-associated bacterial communities were primarily shaped by co-occurring neighbor plants, while fungal communities were mainly determined by soil legacies from previously grown plants. Furthermore, culturable microbial communities (NatComs) isolated from the roots of focal plants differed greatly depending on neighbor identity and soil legacies. Inoculating new focal plants with these communities caused strong responses in growth that varied greatly depending on the history of these isolated communities, highlighting the importance of neighbor effects. Finally, we show that metabolites produced by these microbial communities are one mechanistic pathway through which neighbors influence plant growth.</p><p><strong>Conclusions: </strong>Our results stress the often-overlooked ecological and functional importance of both direct and indirect effects of neighbor plants in shaping root-associated microbiomes. By integrating neighbor effects with host identity, this work provides a starting point for understanding how neighboring plants contribute to shaping plant communities, with potential implications for sustainable agriculture. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13218040/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148032426","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":"Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge.","authors":"Alessandro N Garritano, Lilian J Hill, Bárbara Ribeiro, Taissa Damasceno, Laenne Medeiros, Gustavo Duarte, Caren L S Vilela, Marwan E Majzoub, Michelle A Allen, Jadranka Nappi, Raquel S Peixoto, Torsten Thomas","doi":"10.1186/s40168-026-02411-y","DOIUrl":"10.1186/s40168-026-02411-y","url":null,"abstract":"<p><strong>Background: </strong>Sponges are important members of shallow-water, benthic ecosystems, where they often rely on their microbial symbionts to acquire organic or inorganic carbon. Sponges are also found in the deep sea, however, how they metabolically interact there with their symbionts remains underexplored. Here, we combined metagenomic, metatranscriptomic and stable-isotope labelling approaches to investigate the metabolic activities of the microbial community of the deep-sea sponge Calyx sp.</p><p><strong>Results: </strong>Approximately 84% of the total estimated microbial abundance was composed of nine heterotrophic phyla, whilst the remaining 16% consisted of two autotrophic ammonia-oxidising archaea. Metatranscriptomic analysis revealed the high expression of genes involved in the degradation of recalcitrant polysaccharides of algal origin, suggesting that an undegraded fraction of marine snow plays a role in the nutrition of this deep-sea holobiont. Additionally, we detected active ammonia oxidation and carbon fixation pathways in the autotrophic community members and, through ex situ incubations with labelled carbonate show a potential to fix 13.67 mg CO₂ per g dry weight in a year.</p><p><strong>Conclusions: </strong>This study highlights the mixotrophic lifestyle of a deep-sea sponge microbiome, expanding our knowledge of the sponge-microbe symbiosis in the oligotrophic environment of the deep ocean. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13200403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148016461","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":"Yeast culture promotes butyrate produced fibrolytic bacteria as intracellular hydrogen sink in the rumen.","authors":"Li Wang, Fei Li, Zhiyuan Ma, Emilio M Ungerfeld, Tianxi Zhang, Zhian Zhang, Xiaozhen Liu, Qian Zhang, Xiumin Zhang","doi":"10.1186/s40168-026-02436-3","DOIUrl":"10.1186/s40168-026-02436-3","url":null,"abstract":"<p><strong>Background: </strong>Yeast culture (YC) supplementation is widely adopted to mitigate rumen pH depression and alleviate the inhibition of fiber degradation under starch-rich diets. Yet, the underlying microbial mechanisms, particularly how yeast culture orchestrates fibrolytic communities and affects metabolic hydrogen flow in the rumen, remain a critical knowledge gap. Accordingly, elucidating the microbial basis by which yeast culture modulates fiber degradation and hydrogen utilization under starch-rich diets is of both theoretical and practical importance.</p><p><strong>Methods: </strong>We conducted a study with growing lambs receiving starch-rich diets that differed only in yeast culture supplementation (CON 0%, YC 1%). We evaluated their growth performance, apparent total-tract digestibilities, rumen fermentation end-products, and the rumen metagenome.</p><p><strong>Results: </strong>The YC treatment increased the lambs' final body mass (P = 0.02), average daily gain (P = 0.03), digestibilities of neutral detergent fiber (P < 0.001) and acid detergent fiber (P < 0.001), and rumen pH (P < 0.05), and tended to increase organic matter digestibility (P = 0.09). In addition, total VFA concentrations, particularly butyrate, were higher at 6 h post-morning feeding (P = 0.01). Fibrolytic and hydrogenotrophic taxa (e.g., Ruminococcus_E and Quinella) and CAZyme families, including GH43, GH31, GH9, and GH35, were enriched by the YC treatment, as were bacteria involved in fiber degradation and butyrate production. Furthermore, none of the top five YC treatment-enriched bacterial genomes contained any hydrogenase genes, which indicates that this butyrogenic fibrolytic consortium is significantly different from the hydrogen-producing fiber-degrading microorganisms we are familiar with.</p><p><strong>Conclusion: </strong>Yeast culture supplementation promoted the proliferation of a distinct butyrogenic consortium that degrades fiber while apparently disposing intracellularly metabolic hydrogen generated during fermentation, rather than releasing it as H₂. These findings provide a microbial basis for understanding how yeast culture improves fermentation efficiency under starch-rich diets and suggest that selecting yeast culture products capable of promoting butyrogenic fibrolytic bacteria may be beneficial for ruminant performance and rumen stability. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13383528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148016416","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":"Integrated multi-omics reveals Enterococcus faecalis JM263 alleviates high-concentrate diet-induced hepatic injury via the gut-liver axis in goats.","authors":"Xinhong Zhou, Ammara Khan, Wenjie Xiang, Xiaoyun Shen","doi":"10.1186/s40168-026-02435-4","DOIUrl":"10.1186/s40168-026-02435-4","url":null,"abstract":"<p><strong>Background: </strong>In intensive ruminant production, long-term high-concentrate diets (HCD) are employed to increase short-term growth but frequently cause systemic inflammation, oxidative stress, and multiorgan damage, posing significant challenges to the sustainability of the goat industry. This study investigated the potential regulatory mechanisms of Enterococcus faecalis JM263, a strain isolated from yak gut contents, in mitigating HCD-induced inflammation and oxidative stress via the gut-liver axis. Twenty-four male Yudong black goats were randomly assigned to four groups: a control group (CON) and three treatment groups supplemented with 0.1, 0.5, or 1.0 g/kg E. faecalis JM263 (HCD1, HCD2, and HCD3, respectively) for 60 days.</p><p><strong>Results: </strong>E. faecalis JM263 supplementation significantly attenuated intestinal and hepatic injury caused by systemic inflammation and oxidative stress, thereby enhancing growth performance and immune function. Mechanistically, E. faecalis JM263 mitigated systemic inflammation by reinforcing intestinal barrier function and remodeling the gut microbiota, which was associated with increased relative abundances of Muribaculaceae and Acetatifactor. Furthermore, E. faecalis JM263 reduced hepatic oxidative stress, accompanied by coordinated changes in the Nrf2/Keap1 signaling pathway and antioxidant enzyme activity. Integrated proteomics and metabolomics analyses revealed that E. faecalis JM263 was associated with changes in hepatic inflammatory responses and apoptosis, potentially through the regulation of arachidonic acid metabolism. Correlation analysis further showed close associations among the gut microbiota, arachidonic acid-related proteins/metabolites, and host phenotypic indices.</p><p><strong>Conclusions: </strong>In summary, E. faecalis JM263 alleviates HCD-induced multiorgan damage and functional dysfunction by synergistically improving the intestinal barrier, suppressing systemic inflammation, and reducing oxidative stress. These findings highlight the efficacy of E. faecalis JM263 in promoting growth performance and maintaining health in ruminants via the gut-liver axis. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148005774","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":"Neighborhood deadwood and yard rewilding modulate commensal microbiomes and inflammatory signals among urbanites.","authors":"Marja I Roslund, Laura Uimonen, Laura Kummola, Damiano Cerrone, Ann Ojala, Anna Luukkonen, Ella Holopainen, Aku Korhonen, Reijo Penttilä, Mika Saarenpää, Martti Venäläinen, Hanna Haveri, Juho Rajaniemi, Olli H Laitinen, Aki Sinkkonen, The Biwe Research Group","doi":"10.1186/s40168-026-02413-w","DOIUrl":"10.1186/s40168-026-02413-w","url":null,"abstract":"<p><strong>Background: </strong>Urbanization and biodiversity loss reduce human exposure to diverse microbiomes. Current evidence suggests that the vanishing microbiomes in industrialized populations are a central factor in the rising prevalence of non-communicable immune-mediated diseases. Rewilding has been proposed as an approach to diversify urban microbial communities and promote immunological resilience.</p><p><strong>Results: </strong>We rewilded 21 urban private yards with deadwood, vegetation, and microbially rich soil. Control yards (15) were analyzed for comparison. We analyzed skin bacteria and oral microbiomes and used vegetation and deadwood inventories, satellite data, and questionnaires to determine the effects of rewilding, living environment, and lifestyle factors on skin and oral microbiota, functional gene pathways, and cytokine levels (IL-6, IL-10). Neighborhood deadwood within 200-m radii around home yards was used as an indicator of environmental biodiversity. Samples were collected before the rewilding in summer and three months later in autumn. Skin microbial diversity stayed constant and was associated with plant richness in the rewilding group, despite the normal seasonal decline and reduced outdoor time in autumn. Rewilding was associated with a decrease in tetrahydrofolate biosynthesis and salvage, and L-histidine degradation gene pathways and other changes in oral microbiota. In the rewilding group in autumn, picking of berries and fruits was directly associated with immunoregulatory IL-10 and pleiotropic IL-6 in saliva, and neighborhood deadwood abundance with the fatty acid biosynthesis superpathway in oral microbiomes. When groups were analyzed jointly, the diversity of oral microbial functional gene pathways was negatively correlated with IL-6 levels, and neighborhood deadwood abundance was directly linked to skin Gammaproteobacterial taxa, and typically soil-derived Cytobacillus sp. CY-G and Streptomyces sp. HSG2 in saliva.</p><p><strong>Conclusions: </strong>Our findings are consistent with the biodiversity hypothesis, suggesting that biodiversity exposure may influence commensal microbiomes and biological pathways involved in host-microbe interactions. Our results suggest that the amount of decaying deadwood in the neighborhood, in addition to conventional measures of greenness and vegetation diversity, may provide advantageous information in studies examining human-environment microbiome interactions. This may inform biodiversity-related ecosystem services related to impacts on human health. Our findings provide an incentive for future studies and strategic investments for rewilding urban microbiomes to support planetary health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13374267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147948673","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":"Bifidobacterium-driven immunoglobulin A production in pediatric patients with IgA deficiency and recurrent respiratory tract infections.","authors":"Mischa H Koenen, Marien I de Jonge, Meyke Hermsen, Geert H van Weelden, Sanne Olde Olthof, Christa E van der Gaast-de Jongh, Fred van Opzeeland, Charlene de Kluijs-Bender, Saskia van Selm, Erhard van der Vries, Debby Bogaert, Marianne Boes, Marcel R de Zoete, Lilly M Verhagen","doi":"10.1186/s40168-026-02382-0","DOIUrl":"10.1186/s40168-026-02382-0","url":null,"abstract":"<p><strong>Background: </strong>Immunoglobulin A (IgA) deficiency is the most common primary antibody deficiency and contributes to recurrent respiratory tract infections (rRTIs) in children, with prevalence rates in this group ranging from 1:4 to 1:65. Previous studies in healthy humans and animals suggest that the gut microbiota significantly influences IgA production. We investigated the role of the gut microbiota in IgA deficiency and its potential in promoting IgA induction in children with rRTIs.</p><p><strong>Results: </strong>Children under 7 years of age with rRTIs were enrolled in a prospective cohort study. Serum and feces were collected for IgA level measurement using ELISA and to determine the composition of the intestinal microbiota by 16S rRNA sequencing. We included 82 children with rRTIs, 38% of whom were IgA deficient. The microbiota composition of IgA deficient children differed from that of symptomatic non-IgA deficient children (PERMANOVA R² 2.4%, p = 0.02). Feces from a subgroup of children with and without IgA deficiency were used to inoculate germ-free mice. At baseline and after 3, 8, 12, and 16 weeks, serum and fecal samples were collected from the mice for measurement of IgA levels and microbiota composition. We also collected B-cells from lung and colon tissues for immunohistochemistry. The introduction of microbiota in germ-free mice was related to a strong induction of serum and fecal IgA levels and associated with the abundance of specific bacterial genera, including several Lachnospiraceae species. Two community clusters were associated with fecal IgA induction, one of which was a Bifidobacterium cluster, consisting of eight bacterial genera. This Bifidobacterium cluster was also associated with higher serum and lung IgA levels and increased lung B-cell density in mice. Furthermore, in children with rRTIs, Bifidobacterium abundance was negatively associated with the severity of RTI symptoms.</p><p><strong>Conclusions: </strong>This study shows that children with IgA deficiency and rRTIs harbour a distinctly altered intestinal microbiota. Using fecal transfers from pediatric donors into germ-free mice, we demonstrate robust induction of IgA across mucosal sites. Notably, a Bifidobacterium-dominated community cluster was linked to stronger IgA responses in stool, serum, and lung, highlighting a microbiota-mucosal immunity axis with translational potential. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13173950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147931071","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":"Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.","authors":"Liran Zhao, Liheng Wu, Shi Yin, Wei Gao, Xin Xiang, Yanshe Xie, Yujiao Guo, Zhengguang Wang","doi":"10.1186/s40168-026-02426-5","DOIUrl":"10.1186/s40168-026-02426-5","url":null,"abstract":"<p><strong>Background: </strong>Mounting evidence indicates that the rumen microbiota plays a crucial role in the reproductive health of sheep. However, the potential beneficial effects of rumen microbiota on lambing performance in sheep across different stages of the reproductive cycle and the precise mechanisms underlying these effects remain unclear. We aimed to elucidate the rumen microbial regulatory network underlying differences in reproductive performance in sheep by integrating multi-stage metagenomics and metabolomics.</p><p><strong>Results: </strong>No significant difference was observed in the ruminal microbial α-diversity between sheep with high and low litter size. However, significant stage-specific segregation was observed in their community structures. We identified a cohort of key species strongly associated with litter size. These included Asaia bogorensis, Methanolobus zinderi, Erwinia gerundensis, Marinobacter sp. BSs20148, and Lactobacillus amylolyticus enriched during pregnancy; Rhizobium gallicum, Aeromonas caviae, Pseudolysobacter antarcticus, Mucilaginibacter rubeus, Thermococcus paralvinellae, and Janthinobacterium svalbardensis enriched during lactation; Pseudomonas mandelii, Gordonia sp. HY186, Arachidicoccus sp. BS20, Mesotoga prima, Acidovorax ebreus, Donacia cinerea, and Salmonella enterica enriched during estrus. Host plasma metabolomics analysis further revealed an enrichment of a set of core metabolites in the blood of high-fertility sheep, including Inositol, 2-Linoleoylglycerol, lysophosphatidylcholines and neuromodulatory substances such as tyramine and sphingosine-1-phosphate. We constructed stage-specific \"rumen microbe-rumen metabolite-plasma metabolite\" regulatory axes. These results suggest the influence of the rumen microbiome on plasma metabolic profiles and subsequent fertility outcomes in sheep.</p><p><strong>Conclusion: </strong>We elucidate the dynamic mechanism by which the rumen microbiota in high-fertility sheep is associated with superior reproductive performance through stage-adaptive community succession and functional remodeling, which in turn may modulate the host's neuroendocrine and lipid metabolic profiles. These findings provide a new perspective for understanding the regulation of fertility in ruminants and lay a theoretical foundation for improving reproductive efficiency through nutritional strategies targeting the rumen microbiota. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13339425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147931080","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":"Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population.","authors":"Ziyun Zhou, Arianna Lamanna, Rashi Halder, Emeline Pansart, Shaman Narayanasamy, Besma Boussoufa, Thamila Kerkour, Paul Wilmes, Evan Williams","doi":"10.1186/s40168-026-02369-x","DOIUrl":"10.1186/s40168-026-02369-x","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota adapts to and shapes the host's metabolic state through affecting circulating metabolites and consequent gene regulatory networks, resulting in systemic influences in diverse organs via connections such as the gut-liver axis. Numerous variables such as diet, age, and host genetics modulate the composition of the gut microbiome, but their interactions and specific associative and mechanistic links to host molecular phenotypes remain incompletely unannotated. Integrated multi-omics approaches in genetically diverse populations offer an opportunity to dissect these interactions and identify predictive microbial signatures for host phenotypes, such as body weight and molecular associations with gene expression pathways in gut and liver.</p><p><strong>Results: </strong>We sequenced, aligned, and integrated the cecal metagenome, metatranscriptome, and host transcriptome from 232 mice across 175 distinct cohorts according to a low-fat chow diet (CD) or a high-fat diet (HF), four adult ages (between roughly 180 to 730 days of age), and 43 distinct genotypes (inbred BXD strains). Genetics and diet exerted the strongest influence on microbiota abundance and activity, followed by age. HF feeding significantly reduced diversity across all ages and all genotypes, altering > 300 species. Machine learning models based on microbial profiles reliably predicted body weight within dietary group (AUC = 0.84 for CD, 0.79 for HF) and chronological age (AUC = 0.84), with model performance of age prediction rising to 0.95 when integrating top microbial features with liver proteomics. Network analyses of expression data revealed links between genes, pathways, and specific microbes, including a negative association between cecal Ido1 expression and short-chain fatty acid (SCFA)-producing Lachnospiraceae, suggesting dietary fat may modulate host tryptophan metabolism through microbiota shifts.</p><p><strong>Conclusions: </strong>Whole metagenome and metatranscriptome sequencing approaches have massively expanded the landscape of microbiome analysis compared to earlier short-read 16S analyses. The resulting datasets quantify hundreds of uniquely identifiable microbes, which can be used to create sets of highly predictive microbial biomarkers for aging and obesity. When trained on controlled mouse populations, these results demonstrate that microbiome profiling can achieve high predictive capacity (AUC = 0.95 with multi-omics integration) for complex readouts such as age and body weight (AUC = 0.84), even considering genetic and dietary variation, establishing a framework for biomarker development. While at present many bacteria are still functionally unannotated at the species level, multi-omics approaches - including gene expression from the host tissues - provide insights into the functional associations of specific taxa in the microbiome. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13173809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147931144","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":"Metatranscriptomic analysis of the microbiota of tumor tissue in colon cancer.","authors":"Elena Buetas, Kelly Conde-Pérez, Ángel Concha, Catuxa Celeiro, José F Noguera, Germán Bou, Simón Pardiñas-López, Juan A Vallejo, Margarita Poza, Miguel Carda-Diéguez, Alex Mira","doi":"10.1186/s40168-026-02372-2","DOIUrl":"10.1186/s40168-026-02372-2","url":null,"abstract":"<p><strong>Background: </strong>Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, accounting for more than 900,000 deaths a year worldwide. Microbial dysbiosis, including the presence of oral bacteria in the gut, has been linked to CRC. Some mechanisms by which specific microorganisms potentially drive tumorigenesis have been described, but there is a lack of studies elucidating whole microbiota activity in the tumor and their implication for the development of the disease. Here, the metatranscriptomic data of tumor and control tissue-associated microbiota (n = 18 pairs), as well as from subgingival sulcus (n = 15) of CRC patients, was analyzed.</p><p><strong>Results: </strong>We confirmed that Fusobacterium nucleatum was more active in the tumor tissue than in the control gut mucosa. In addition, the activity of this species was positively correlated with other oral bacteria in the tumors, including Parvimonas micra, Peptostreptococcus stomatis, and Granulicatella adiacens, along with gut bacteria like Hungatella hathewayi, suggesting a potential relationship among them. Regarding bacterial gene expression, a change in the functional profile was observed, including a higher expression of genes associated with carbon metabolism in control in contrast to an increase of amino acid-related genes in tumor. Furthermore, genes implicated in the biosynthesis and transport of lipopolysaccharide were increased in tumors. Interestingly, a significantly higher expression in tumor than control tissue of potential virulence factors from F. nucleatum was found, supporting their relevance in niche colonization and tumorigenesis. Correlation analysis of the bacterial activity with the host transcriptional profile showed significant correlations of the Fusobacterium-Peptostreptotoccus-Hungatella cluster with human genes involved in inflammation and metastasis, confirming the association of this microbial consortium with tumor development. For the first time, the gene expression profiles of oral bacteria in the gut and the oral cavity were compared. The cluster of co-active bacteria identified in tumors was partially found in the oral samples, suggesting a stable interaction and potential synergy. Although there were thousands of differentially expressed genes between subgingival sulcus and tumor tissue, the expression of key virulence factors was not significantly different.</p><p><strong>Conclusions: </strong>In short, this study discovered new traits about tumor microbial-associated composition and activity and its connection with the oral composition that would be essential to unravel the translocation, colonization, and tumorigenesis of the CRC. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13218042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147874681","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":"The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.","authors":"Angela Sofia Burkhart Colorado, Nichole M Nusbacher, John O'Connor, Tyson Marden, Janine Higgins, Charles Preston Neff, Suzanne Fiorillo, Thomas B Campbell, Margaret Borok, Kathryn Boyd, John Sterrett, Brent E Palmer, Catherine Lozupone","doi":"10.1186/s40168-026-02410-z","DOIUrl":"10.1186/s40168-026-02410-z","url":null,"abstract":"<p><strong>Background: </strong>People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe. Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.</p><p><strong>Results: </strong>Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza, a subsistence staple, processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4 + T cell percentage in untreated and treated PLWH and increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24 weeks of ART. Individuals residing in the rural area had more Prevotella-rich/Bacteroides-poor microbiomes, but this was not significantly mediated by diet. Carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci, correlated with dietary intake patterns.</p><p><strong>Conclusions: </strong>Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13339530/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147931155","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}