Microbiome最新文献

{"title":"Convergent evolution of intestinal lineages in the phylum Methanobacteriota.","authors":"Evgenii Protasov, Undine S Mies, Cathrin Spröer, Boyke Bunk, Sebastian Cristian Treitli, Katja Platt, Andreas Brune","doi":"10.1186/s40168-026-02434-5","DOIUrl":"10.1186/s40168-026-02434-5","url":null,"abstract":"<p><strong>Background: </strong>Representatives of the phylum Methanobacteriota occur in various anoxic environments, but only members of the genera Methanosphaera and Methanobrevibacter exclusively colonize the digestive tract of animals. Recent phylogenomic analyses revealed that the genus Methanobrevibacter, which harbors the majority of the intestinal species, is severely underclassified and represents a family-level taxon, \"Methanobrevibacteraceae\", that evolved entirely in the digestive tract of animals.</p><p><strong>Results: </strong>Comparative genome analysis of 158 species of Methanobacteriota, including uncultured representatives in the Genome Taxonomy Database (GTDB), demonstrated that the intestinal lineages are clearly separated from the remaining members of the phylum. They differ from the non-intestinal lineages in genome size, GC content, coding density, an increased number of pseudogenes and adhesin-like proteins, and show numerous adaptations to the copiotrophic gut environment. A decreased biosynthetic potential led to a dependence on other community members and limits the dispersal of intestinal species into other habitats, which is reflected in coevolutionary patterns with their major host groups among arthropods, ungulates, and primates. Certain lineages even engaged in symbiotic associations with intestinal protists, presumably benefiting from the H₂ produced by the hydrogenosomes of their anaerobic hosts.</p><p><strong>Conclusions: </strong>Our results reveal that the transition of free-living Methanobacteriota to a host-associated lifestyle involves the same genomic changes that were previously recognized in gut bacteria and bacterial endosymbionts of protists, reflecting resemblances between the two prokaryotic domains that are caused by evolutionary convergence in similar environments.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"14 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13135261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147817193","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":"Capsaicin ameliorates glycemic levels via gut microbiota-derived 5-aminolevulinic acid in mice.","authors":"Qingying Fang, Shi Huang, Chengcheng Zhang, Mingyang Li, Zi Ye, Hang Guo, Meifang Xiao, Shunhe Wang, Leilei Yu, Hao Zhang, Jianxin Zhao, Fengwei Tian, Wei Chen, Qixiao Zhai","doi":"10.1186/s40168-026-02415-8","DOIUrl":"10.1186/s40168-026-02415-8","url":null,"abstract":"<p><strong>Background: </strong>Capsaicin, a natural alkaloid in chili peppers, regulates glycemic levels; however, its mechanisms and therapeutic potential remain unclear. This study aimed to elucidate the role of gut microbiota and their metabolites in mediating capsaicin's glycemic regulatory effects. We conducted experiments in specific pathogen-free (SPF) and germ-free (GF) mice, transient receptor potential vanilloid 1 (TRPV1) receptor ablation studies, and fecal microbiota transplantation (FMT) to demonstrate the involvement of gut microbiota in capsaicin-mediated glycemic control. Metagenomics and metabolomics analyses were employed to identify key microbial strains and metabolic pathways. Keystone strains and metabolites were supplemented in GF mice without capsaicin intervention to validate their effects on glycemic regulation. In vitro co-culture experiments were performed to investigate the mutualistic relationships among keystone strains under capsaicin treatment.</p><p><strong>Results: </strong>Gut microbiota constitute an important component of capsaicin-mediated glycemic regulation, acting in concert with but not solely dependent on TRPV1 signaling. Gut microbiota altered by capsaicin promote the production of 5-aminolevulinic acid (5-ALA), which contributes to heme synthesis and enhances glycemic control. Supplementation with Akkermansia muciniphila, Ligilactobacillus murinus, or 5-ALA in GF mice recapitulates the glycemic benefits of capsaicin. Furthermore, capsaicin enriches Akkermansia muciniphila, which in turn supports the growth of Ligilactobacillus murinus.</p><p><strong>Conclusion: </strong>Capsaicin-induced changes in the gut microbiota promote 5-ALA synthesis, leading to improved glycemic control. These findings suggest that dietary or probiotic interventions targeting gut microbiota, particularly Akkermansia muciniphila and 5-ALA, may offer promising strategies for managing glycemic disorders, including type 2 diabetes (T2D). Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13151249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147817187","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":"Puerarin modulates the gut-liver-ovarian axis to ameliorate reproductive aging in breeder hens.","authors":"Zhenwu Huang, Dandan Ma, Guangju Wang, Yanru Shi, Jinghai Feng, Chunmei Li, Minhong Zhang","doi":"10.1186/s40168-026-02404-x","DOIUrl":"10.1186/s40168-026-02404-x","url":null,"abstract":"<p><strong>Background: </strong>Puerarin (PU), a natural bioactive isoflavone derived from the edible root of Pueraria lobata, exhibits multi-pharmacological activities, including antioxidant, lipid metabolism-regulating, and immunomodulatory properties. The decline in the reproductive performance of hens is primarily attributed to age-related dysbiosis of gut function and reduced function of the liver-ovary axis. However, the systemic mechanisms linking puerarin-induced microbiota changes to improvements in hepatic and ovarian function in aged hens remain poorly defined. In this study, we performed a multi-omics investigation to explore the effects on gut microbiota, liver metabolism, ovarian function, and the associations among them induced by dietary puerarin in aged hens.</p><p><strong>Results: </strong>The results demonstrated that dietary supplementation with 200 mg/kg puerarin significantly improved egg quality, laying rate, and feed conversion efficiency, restored endocrine hormone homeostasis, and reduced ovarian oxidative stress and apoptosis. Puerarin stimulated carbon flux partitioning through the hepatic citrate cycle (TCA) and pentose phosphate pathway, thereby enhancing vitellogenin (VTG) synthesis and its transport to the ovary. Furthermore, puerarin activated the cytokine-cytokine receptor interaction pathway and reversed microbial dysbiosis (e.g., Lactobacillus and Bacteroides), thereby ameliorating intestinal functional decline. Significant correlations were also observed among hepatic tauroursodeoxycholic acid levels, intestinal expression of the lipid metabolism genes CD36 and GPAT3, and the relative abundance of Lactobacillus. Multi-omics analyses revealed that puerarin ameliorated age-related hepatic lipid metabolism disorders by targeted regulation of the peroxisome proliferator-activated receptor (PPAR) signaling pathway in the gut and liver. We elucidated the direct effects of puerarin-induced alterations in gut microbial abundance and reproductive performance in aging hens, highlighting the mediating role of liver function.</p><p><strong>Conclusions: </strong>These findings collectively indicate that puerarin positively redirected the gut-liver-ovary axis function to mitigate reproductive aging, suggesting potential to improve metabolic health in aging hens.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13227894/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147775644","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":"Gut microbiota induces dysspermatogenesis via microbial-derived phenylacetylglycine in Ggt1-deficient mice.","authors":"Jinhua Tang, Ling Wang, Zhaolin Yang, Yuyang Song, Shang Wu, Qiqi Liang, Zesheng Li, Shiqin Zhou, Hao Xiong, Dake Chen, Jialian Li, Fenge Li","doi":"10.1186/s40168-026-02401-0","DOIUrl":"10.1186/s40168-026-02401-0","url":null,"abstract":"<p><strong>Background: </strong>Male infertility represents a global health concern, with emerging evidence linking gut microbiota dysbiosis to dysspermatogenesis and subfertility. However, the molecular mediators and regulatory mechanisms by which gut microbiota influences testicular functions remain poorly defined.</p><p><strong>Results: </strong>This study demonstrates that male gamma-glutamyl transferase 1-deletion (Ggt1^-/-) mice exhibits infertility phenotypes, including reduced germ and testicular Leydig cell numbers, increased rates of abnormal sperm, and altered reproductive hormone levels. Metabolomic analysis reveals elevated levels of the gut microbial-derived metabolite phenylacetylglycine (PAGly) in serum and testes of Ggt1^-/- mice, with in vivo injection experiments indicating its role in impairing spermatogenesis. Moreover, blocking PAGly effectively restores the impaired spermatogenesis in Ggt1^-/- mice. Fecal metagenomic and metabolomic analyses show that gut microbiota in Ggt1^-/- mice induces elevation of phenylacetic acid, a precursor metabolite of PAGly. Strikingly, fecal microbiota transplantation from Ggt1^-/- mice (Ggt1^-/--FMT) recapitulates the infertility phenotypes including reduced germ cells and increased rates of abnormal sperm. Mechanistically, integrated CUT&Tag and ATAC-Seq analyses reveal that transcription factor STAT5B occupies regulatory elements near Klk1b transcription start sites (TSS), confirming that transcription factor STAT5B directly regulates Klk1b gene transcription. Concretely, PAGly activates β2-adrenergic receptor (β2AR) on Leydig cells, triggering STAT3 phosphorylation, subsequent SOCS3 upregulation, and STAT5B phosphorylation suppression; p-STAT5B with transcriptional activation function is reduced, then Klk1b gene transcription is compromised, and therefore spermatogenesis is disrupted.</p><p><strong>Conclusion: </strong>Ggt1 deletion-induced gut microbiota dysbiosis disrupts spermatogenesis via β2AR-STAT3-SOCS3-STAT5B-Klk1bs signaling pathway. Specifically, PAGly-induced β2AR activation promotes STAT3 phosphorylation, which induces SOCS3 to suppress p-STAT5B dependent Klk1bs transcription. This mechanism underscores the critical role of gut-derived metabolites in regulating testicular function and identifies potential targets for microbiota-modulated male infertility. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13227699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147729510","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":"Gastrointestinal microbial nitrogen metabolic landscape underlies nitrogen utilization efficiency of goats fed distinct dietary protein sources.","authors":"Yechan Zhao, Zhiliang Tan, Zhixiong He, Jian Wu, Jinzhen Jiao","doi":"10.1186/s40168-026-02398-6","DOIUrl":"10.1186/s40168-026-02398-6","url":null,"abstract":"<p><strong>Background: </strong>Improving nitrogen (N) utilization efficiency in ruminant livestock is vital for coping with global protein scarcity and lowering environmental pollution. The biogeographically stratified microorganisms in the gastrointestinal tract (GIT) fulfill the pivotal role of metabolizing dietary N into bioavailable nutrients. In this study, we deciphered the microbial N utilization dynamics in the rumen and colon under different protein source interventions, soybean meal (SBM) and corn gluten meal (CGM) which differed in rumen degradation rate and amino acid (AA) profile, using goats as a model.</p><p><strong>Results: </strong>Goats fed with the SBM diet exhibited greater N utilization efficiency, as characterized by greater average daily gain (ADG), nutrient digestibility, and the concentration of free amino acids (AAs) in the GIT. The SBM diet, with its higher rumen-degradable protein (RDP) content, selectively enriched protein degraders Sodaliphilus, Limivicinus, and RUG472 spp., and upregulated genes encoding key peptidases (pepT, pepDA/B) in the rumen. Conversely, aligning with its higher rumen-undegradable protein (RUP) content, the CGM diet promoted the enrichment of proteolytic bacteria Alistipes spp. in the colon. Notably, in response to dietary AA deficiency, the CGM diet enriched AA producers-Ruminococcus, RUG563, UBA1179 spp. in the rumen, Treponema, UBA737, and Firm-07 spp. in the colon. This is accompanied by greater abundances of genes involved in de novo biosynthesis of aromatic AAs (trpA, trpB), lysine (dapA), and histidine (hisG), suggesting a microbial compensatory response for dietary deficiencies, though insufficient to fully offset the nutritional shortfall.</p><p><strong>Conclusions: </strong>This study depicts the microbial nitrogen metabolic landscapes integrating protein degradation, AA biosynthesis, and AA catabolism under distinct dietary protein sources, and provides potential microbial targets for optimizing N utilization efficiency in ruminants. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13227792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147729558","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":"Trimethylamine-producing microbe Bacillus megaterium KCTC 3007 promotes antitumor immunity in endometrial cancer via type I interferon response pathways.","authors":"Kyungchan Min, Se Ik Kim, Minji Lee, Yunjae Kim, Chanyeong Jeong, Sujeong Kim, Sang Jin Kim, Hyun Kim, Beomki Cho, Yanghyun Joo, Hansoo Park, Maria Lee","doi":"10.1186/s40168-026-02373-1","DOIUrl":"10.1186/s40168-026-02373-1","url":null,"abstract":"<p><strong>Background: </strong>Endometrial cancer (ECa) is one of the most common gynecologic malignancies, with limited therapeutic responses in metastatic or recurrent cases. The bacterial microbiota has emerged as a key modulator of carcinogenesis and antitumor immunity. However, the role of endometrial microbiota in ECa pathogenesis and prognosis remains poorly understood.</p><p><strong>Methods: </strong>We performed comprehensive multi-omics analysis integrating metatranscriptomics, transcriptomics, and targeted metabolomics from 60 ECa and 18 benign patients. RNA sequencing enabled simultaneous profiling of active tissue-resident microbiota and host gene expression. Serum metabolomics was conducted on all patients. Identified microbial-metabolite associations were validated through in vitro co-culture experiments using peripheral blood mononuclear cells (PBMCs), cancer cell lines, RNA sequencing, and live cell imaging.</p><p><strong>Results: </strong>ECa patients exhibited significantly altered microbial diversity and composition compared to benign controls. Through integrated multi-omics analysis, we identified Bacillus megaterium (BM) KCTC 3007 as a beneficial microbe associated with prolonged recurrence-free survival. In an exploratory analysis of ECa subtypes, Cupriavidus taiwanensis and Marinomonas primoryensis showed potential links to poor prognosis, although these observations warrant caution due to the limited size of certain subgroups. Tissue BM abundance positively correlated with serum trimethylamine N-oxide (TMAO) levels, particularly in postmenopausal women. In vitro experiments demonstrated that BM KCTC 3007 enhanced antitumor immunity by promoting interleukin and type I interferon expression, expanding CD8 + T cell populations, and increasing immune cell-tumor cell interactions. RNA sequencing revealed activation of interferon alpha response and immune cell proliferation pathways, with IFNAR1 identified as a key upstream regulator. TMAO treatment recapitulated these immune-activating effects, enhancing CD8 + T cell responses and preferentially inducing pyroptotic cancer cell death.</p><p><strong>Conclusions: </strong>We provide the first evidence that tissue-resident BM KCTC 3007 promotes antitumor immunity in ECa through TMAO production and subsequent type I interferon-mediated immune activation. This integrated multi-omics approach establishes a complete microbe-metabolite-host mechanistic pathway and highlights the therapeutic potential of TMAO-producing probiotic strains for ECa treatment. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13104324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147729518","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":"Unveiling microbial risks in Chinese household dust: a comprehensive analysis from absolute abundance to virulence unit.","authors":"Lu Long, Yan An, Li-Ting Zhu, Xue-Li Xu, Jing-Jing Lin, Wen-Juan Xu, Jing-Yu Chen, Fang-Yu Liu, Xu-Yi Liu, Qiansheng Huang","doi":"10.1186/s40168-026-02353-5","DOIUrl":"10.1186/s40168-026-02353-5","url":null,"abstract":"<p><strong>Background: </strong>People spend the majority of their lives indoors, yet the risk and virulence potential of household microbiota remain largely unexplored, particularly in developing countries.</p><p><strong>Results: </strong>Here, we conducted a nationwide survey on both dust samples and health information across 118 Chinese households. The microbiota composition and its functional units were analyzed using absolute 16S rRNA/ITS sequencing, metagenomics, and metaproteomics. Cross-domain network analysis of the core microbial communities revealed robust co-occurrence patterns in household dust. The mean absolute abundance of potentially pathogenic bacteria and fungi in households was 2.39 × 10⁵ and 2.83 × 10⁶ DNA copies/g dust. The potentially pathogenic community was primarily influenced by latitude, relative humidity, and average temperature. Although total absolute abundance was substantially lower in urban areas, the relative abundance of potentially pathogenic bacteria was markedly higher compared to rural environments. While urban-rural differences existed, the underlying statistical drivers were the environmental variables. The absolute abundance of potential pathogens was significantly associated with the prevalence of rhinitis, wheeze, and dermatitis in 266 participants. Children were identified as the highest-risk group from inhalation exposure of average daily dose. A total of 170 bacterial, 223 fungal virulence factors (VFs), and 370 antibiotic resistance genes (ARGs) were detected in dust and dust extracellular vesicle (EV)-associated DNA. EV-associated cargoes contributed 47.13% to the bacterial VF profiles, 11.90% to fungal VF profiles, and 44.45% to ARG profiles. Metaproteomic analysis confirmed the presence of VF profiles in dust EVs, which was further verified by curated proteomics data from 35 household pathogens.</p><p><strong>Conclusions: </strong>This study provides a comprehensive, quantitative framework linking indoor microbial exposure to health risks, highlighting EVs as a non-negligible, novel, extracellular mechanistic pathway for health impact in household environments. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13227884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147729537","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":"Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot.","authors":"Chuan You, Weiqi Zhang, Ying Guan, Qingqing Liang, Chuanjiang Nong, Tianjie Yang, Mengfei Li, Samiran Banerjee, Xingang Zhou, Xiaofang Wang, Yangchun Xu, Qirong Shen, Zhong Wei","doi":"10.1186/s40168-026-02393-x","DOIUrl":"10.1186/s40168-026-02393-x","url":null,"abstract":"<p><strong>Background: </strong>The rhizosphere-associated microbiota plays a crucial role in plant responses to disease stress. Plant secondary metabolites are recognized as crucial mediators in the assembly of rhizosphere microbial communities, particularly by enhancing the colonization of beneficial microorganisms. Despite this recognized importance, a deeper understanding of how such metabolome-driven microbiome assembly specifically determines plant resistance against soil-borne diseases is still lacking.</p><p><strong>Results: </strong>Here, we focused on the widely planted medicinal plant Angelica sinensis and demonstrated that root rot-diseased rhizosphere soils (DRS) exhibited a higher relative abundance of Fusarium and a lower relative abundance of Streptomyces compared to healthy rhizosphere soils (HRS). Shotgun metagenomic sequencing revealed that metabolism-associated genes, particularly those related to steroid degradation, are significantly enriched in HRS samples. Subsequent genome and functional gene analysis of Streptomyces revealed that the steroid degradation-related genes are associated with rhizosphere colonization in hosts. Rhizosphere Streptomyces S15 directly antagonized Fusarium and enhanced the root resistance of A. sinensis. Comparative metabolomics showed that A. sinensis plants from HRS secreted more lipid and lipid-like molecules than those from DRS, especially sterol lipids and long-chain fatty acids, which promoted the growth of Streptomyces S15 isolates. Transcriptome analysis validated that the lipid hormones are essential for sporulation, biofilm formation, and streptomycin biosynthesis of S15 strain. Finally, exogenous application of synbiotics (lipid prebiotics and S15) to A. sinensis resulted in the enrichment of S15-homologous Streptomyces amplicon sequence variant (ASV), further establishing beneficial bacterial communities in Fusarium-stressed rhizospheres.</p><p><strong>Conclusions: </strong>Our study proposes that A. sinensis recruits steroid-metabolizing Streptomyces species by exuding key lipid compounds (i.e., methyl jasmonate and brassinolide) to combat Fusarium root rot. This study provides novel insights into using functional synbiotics as a promising strategy for manipulating plant-microbiome interactions to promote sustainable agriculture. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13227790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147729477","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":"Curcumin modulates hepatic pyroptosis-autophagy crosstalk induced by aflatoxin B1 via rumen microbiota-blood-liver axis.","authors":"Tongwei Liu, Shijie Fan, Jiefeng Li, Ting Wang, Jing Zhang, Chuanqi Wang","doi":"10.1186/s40168-026-02396-8","DOIUrl":"10.1186/s40168-026-02396-8","url":null,"abstract":"<p><strong>Background: </strong>Aflatoxins, fungal secondary metabolites from Aspergillus species, primarily causes liver and gastrointestinal damage in ruminant. Curcumin, a plant polyphenol, has been shown to possess both anti-inflammatory and antioxidant properties, in addition to regulatory effects on gut microbiota. However, research on curcumin's impact against AFB1 toxicity in ruminants is limited. This study aims to elucidate whether AFB1 induces hepatic pyroptosis and autophagy in ruminants via the rumen microbiota-blood-liver axis and the regulatory role of curcumin. The experimental design involves the administration of AFB1 and curcumin to sheep, followed by a comprehensive observation of alterations in rumen microbiota, barrier function, and the occurrence of hepatic pyroptosis and autophagy, with the aim of elucidating the mechanism of curcumin in ameliorating AFB1-induced liver injury in sheep.</p><p><strong>Results: </strong>In the experimental setup, 800 mg/kg dry matter (DM) curcumin was administered as a dietary supplement to alleviate the adverse effects of AFB1 (500 μg/kg DM) on the rumen and liver of sheep. AFB1 suppressed NH₃-N and VFAs production, whereas curcumin improved VFA generation and fermentation efficiency. Curcumin mitigated AFB1-induced rumen barrier impairment by upregulating tight junction proteins (ZO-1, Occludin, Claudin-1) and reducing LPS levels, which was consistent with metagenomic data showing amelioration of microbiota dysbiosis and reduced lysis of Gram-negative bacteria. At hepatic level, curcumin downregulated the principal mediators of the TLR4-NF-κB-NLRP3 signaling pathway (TLR4, p65, and NLRP3), attenuating pyroptosis and reducing serum AST, ALT, and LDH concentrations, while reversing inflammatory infiltration and hepatic cord disruption. Furthermore, curcumin restored autophagic flux by increasing the LC3-II/LC3-I ratio and decreasing p62 accumulation, counteracting AFB1-induced autophagy inhibition.</p><p><strong>Conclusions: </strong>Curcumin counteracts AFB1-induced rumen-liver axis dysfunction. It works by stabilizing the microbiota, maintaining barrier integrity, and dually regulating pyroptosis and autophagy. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13224419/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147722647","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":"Genome-resolved multi-omics provide new insights into microbial nitrogen utilization by the rumen microbiota.","authors":"Ming Yan, Jeffrey Firkins, Jiarong Guo, Alejandro Relling, Zhongtang Yu","doi":"10.1186/s40168-026-02422-9","DOIUrl":"10.1186/s40168-026-02422-9","url":null,"abstract":"<p><strong>Background: </strong>Optimizing nitrogen (N) utilization in ruminant production systems holds both economic and environmental significance. However, traditional paradigms of N metabolism, derived primarily from well-studied model rumen bacteria, do not fully reflect the diverse and complex N metabolism in the rumen ecosystem.</p><p><strong>Results: </strong>To address this gap, we utilized comparative genomics and genome-resolved multi-omics analyses using a curated set of microbial genomes to investigate N assimilation and regulation in rumen microbes. We discovered that well-established mechanisms of ammonia assimilation and regulation, such as the glutamine synthetase (GS)/glutamate synthase (GOGAT) pathways and their regulatory proteins, are absent in many of the predominant rumen microbes, which likely utilize alternative pathways for ammonia assimilation. These findings challenge the applicability of E. coli-based N regulation models to rumen bacteria in response to ammonia availability. We further linked polysaccharide utilization and ammonia assimilation across hundreds of rumen microbial species. Furthermore, we identified specific microbial species involved in ureolysis and denitrification, as well as phages carrying auxiliary metabolic genes involved in N assimilation. Using an animal trial involving 11 pairs of lamb twins in a crossover design, we demonstrated that dietary crude protein (CP) at 10% and 13% had minimal impact on rumen microbiome composition and expression of N assimilation genes. Instead, changes in concentrate levels altered N assimilation, notably increasing expression of amino acid biosynthesis pathways.</p><p><strong>Conclusion: </strong>These findings indicate a nuanced, species-specific microbial response to dietary interventions, highlighting the limitations of traditional N metabolism models applied to rumen microbes and the need for more granular studies of rumen microbial ecosystems.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":" ","pages":""},"PeriodicalIF":14.9,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13196213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147690292","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}