npj Biofilms and Microbiomes最新文献

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MeeY and YybP, two proteins regulated by manganese-sensing riboswitches, are required for Bacillus subtilis biofilm formation. MeeY和YybP是枯草芽孢杆菌生物膜形成所必需的两种由锰传感核开关调节的蛋白。
IF 11.4 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2026-06-10 DOI: 10.1038/s41522-026-01045-0
Ankita J Sachla, Miguel Piñeros, John D Helmann
{"title":"MeeY and YybP, two proteins regulated by manganese-sensing riboswitches, are required for Bacillus subtilis biofilm formation.","authors":"Ankita J Sachla, Miguel Piñeros, John D Helmann","doi":"10.1038/s41522-026-01045-0","DOIUrl":"10.1038/s41522-026-01045-0","url":null,"abstract":"<p><p>In the rhizosphere, Bacillus subtilis forms biofilms on plant roots and contributes to improved plant growth and disease resistance. Manganese stimulates biofilm formation in B. subtilis 3610, but the underlying mechanism is unknown. Here, we show that YybP and MeeY (formerly YkoY), two proteins regulated by the eponymous manganese-sensing yybP-ykoY riboswitches, are required for biofilm formation. MeeY is a TerC family membrane protein implicated in manganese export and YybP is of unknown function. Inactivation of either meeY or yybP leads to reduced synthesis of matrix-associated exopolysaccharide and a loss of biofilm-associated divalent cations.Deletion of sinR restores exopolysaccharide but does not restore normal metalation of the biofilm matrix. We conclude that the YybP and MeeY membrane proteins are previously unappreciated regulators of biofilm formation important for the production and metalation of exopolysaccharide.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13598126/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148218742","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}
引用次数: 0
Strontium ameliorates tibial dyschondroplasia in broilers through gut microbiota-mediated retinoic acid metabolism. 锶通过肠道菌群介导的维甲酸代谢改善肉仔鸡胫骨软骨发育不良。
IF 11.4 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2026-06-09 DOI: 10.1038/s41522-026-01026-3
Shu-Cheng Huang, Bo-Wen Xu, Ya-Nan Lu, Tao-Jing Yue, Wen-Li Ding, Fang-Fang Guo, Zi-Qun Zhang, Xi-Shuai Tong, Cai Zhang, Li Wang
{"title":"Strontium ameliorates tibial dyschondroplasia in broilers through gut microbiota-mediated retinoic acid metabolism.","authors":"Shu-Cheng Huang, Bo-Wen Xu, Ya-Nan Lu, Tao-Jing Yue, Wen-Li Ding, Fang-Fang Guo, Zi-Qun Zhang, Xi-Shuai Tong, Cai Zhang, Li Wang","doi":"10.1038/s41522-026-01026-3","DOIUrl":"10.1038/s41522-026-01026-3","url":null,"abstract":"<p><p>Tibial dyschondroplasia (TD) is a prevalent skeletal disorder in fast-growing broilers that impairs animal welfare and production efficiency. Although strontium (Sr) is known to support bone-strengthening properties, its protective mechanisms against TD, particularly those involving the gut‒bone axis, remain unclear. This study showed that dietary Sr supplementation (200 mg/kg) significantly improved growth performance, restored the tibial microstructure, corrected plasma calcium/phosphorus imbalances, enhanced chondrocyte alignment, increased the osteoblast density, increased the bone mineral density, and improved vascularization in the proximal tibial growth plate in TD broilers. Moreover, the Sr intervention upregulated the bone morphogenetic protein-mediated osteogenic pathway while suppressing RANKL activity and promoted angiogenesis by activating the VEGFA and PI3K/AKT/eNOS signaling pathways, thereby restoring bone remodeling. Interestingly, Sr remodeled the gut microbiota of TD broilers, enriching the beneficial species Pediococcus pentosaceus and reducing the abundance of Levilactobacillus brevis, changes that were correlated with the level of the osteotoxic metabolite 9-cis-retinoic acid (9-cis-RA). Furthermore, exogenous retinoic acid (RA) administration induced TD-like damage, whereas Sr cotreatment mitigated the RA-induced tibial impairment, vascular defects, and dysregulation of the PI3K/AKT/eNOS pathway. Collectively, these results demonstrated that Sr alleviated TD by modulating the gut microbiota to inhibit 9-cis-RA accumulation, thereby normalizing retinoic acid metabolism, promoting vascularization and enhancing osteogenesis; these findings provide novel insights for preventing leg disorders in poultry.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13590495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148212066","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}
引用次数: 0
The Wor2 phenotypic switching regulator controls biofilm formation in Candida auris. Wor2表型开关调节因子控制耳念珠菌生物膜的形成。
IF 11.4 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2026-06-08 DOI: 10.1038/s41522-026-01043-2
Weihong Liang, Shuyun Guan, Jian Bing, Han Du, Qiushi Zheng, Li Tao, Bing Li, Guanghua Huang, Haiqing Chu
{"title":"The Wor2 phenotypic switching regulator controls biofilm formation in Candida auris.","authors":"Weihong Liang, Shuyun Guan, Jian Bing, Han Du, Qiushi Zheng, Li Tao, Bing Li, Guanghua Huang, Haiqing Chu","doi":"10.1038/s41522-026-01043-2","DOIUrl":"10.1038/s41522-026-01043-2","url":null,"abstract":"<p><p>The emerging fungal pathogen Candida auris is a serious global public health threat due to its ability to persist in healthcare environments and on human skin. Here, we report a prevalent cluster of clinical C. auris strains with enhanced biofilm formation, a contributor to environmental and skin persistence. Genomic analyses show that the clinical isolates with enhanced biofilm formation ability carry a loss-of-function mutation in the WOR2 locus, which encodes a white-opaque switching regulator in Candida species. Analysis of 13,314 published genomes revealed that 3104 strains (23.3%) harbor nonsense or frameshift mutations in WOR2, indicating frequent clinical occurrence. Deletion of WOR2 in a clinical strain markedly increased biofilm formation, whereas reintroduction of an intact WOR2 significantly attenuated biofilm development. Further analyses show that Wor2 inactivation upregulates GFC1, ALS4, and multiple biofilm-associated genes. Together, these findings reveal a key regulatory mechanism underlying biofilm development, environmental persistence, and transmission of C. auris.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13586155/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148205602","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}
引用次数: 0
Genome-resolved and culture-based atlas of the feline gut microbiome enables host-adapted probiotic development. 基因组解析和基于培养的猫肠道微生物组图谱使宿主适应的益生菌发展。
IF 11.4 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2026-06-08 DOI: 10.1038/s41522-026-01038-z
Feilong Deng, Ying Fan, Jinxia Yan, Xingyin Zhang, Yan Guo, Minghui Li, Yunjuan Peng, Lingling Zhao, Feitong Liu, Yanyi Zheng, Baichuan Deng, Jinping Deng, Shengfeng Chen, Hui Jiang, Jianmin Chai, Jiangchao Zhao, Ying Li
{"title":"Genome-resolved and culture-based atlas of the feline gut microbiome enables host-adapted probiotic development.","authors":"Feilong Deng, Ying Fan, Jinxia Yan, Xingyin Zhang, Yan Guo, Minghui Li, Yunjuan Peng, Lingling Zhao, Feitong Liu, Yanyi Zheng, Baichuan Deng, Jinping Deng, Shengfeng Chen, Hui Jiang, Jianmin Chai, Jiangchao Zhao, Ying Li","doi":"10.1038/s41522-026-01038-z","DOIUrl":"10.1038/s41522-026-01038-z","url":null,"abstract":"<p><p>Domestic cats (Felis catus) depend on their gut microbiome for metabolism, immunity, and pathogen defense, yet its genomic characterization remains limited. We combined large-scale metagenomics and culturomics to define the feline gut microbiome and identify indigenous probiotic candidates. Analysis of 412 feline fecal metagenomes produced 2852 strain-resolved metagenome-assembled genomes (MAGs) grouped into 514 species-level genome bins, including 106 putative novel taxa. This catalog revealed 24 core species and two enterotypes: ET-P, deaminated by Prevotella, and ET-CB, enriched for Collinsella, Blautia, Bifidobacterium, Ligilactobacillus, MAG-based screening prioritized 113 candidate probiotic species. Culturomics recovered 2904 isolates representing 110 species-level taxa, including 75 putative novel species and a candidate novel genus. Six feline-derived isolates were selected for downstream testing, and five exhibited favorable probiotic traits in vitro, including acid and bile tolerance, anti-Escherichia coli activity, and favorable cytokine responses. In a pathogenic Escherichia coli-induced dirrhea model in cats, a five-strain indigenous consortium improved fecal scores and reduced IL-2, IL-1β, and IL-6, with TNF-α suppression superior to antibiotics or a commercial probiotic. These results establish FelMGDB as a resource for feline microbiome research and highlights indigenous probiotics as promising interventions for feline gut health.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13586241/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148205613","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}
引用次数: 0
Faecalibacterium-derived spermidine mediates the amelioration of fatty liver hemorrhagic syndrome by inulin in laying hens. 粪杆菌衍生亚精胺介导菊粉对蛋鸡脂肪肝出血综合征的改善作用。
IF 11.4 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2026-06-08 DOI: 10.1038/s41522-026-01037-0
Xinyue Yang, Xin Li, Dahai Xu, Yuqing Feng, Yuming Guo, Yongfei Hu
{"title":"Faecalibacterium-derived spermidine mediates the amelioration of fatty liver hemorrhagic syndrome by inulin in laying hens.","authors":"Xinyue Yang, Xin Li, Dahai Xu, Yuqing Feng, Yuming Guo, Yongfei Hu","doi":"10.1038/s41522-026-01037-0","DOIUrl":"10.1038/s41522-026-01037-0","url":null,"abstract":"<p><p>Fatty liver hemorrhagic syndrome (FLHS) is a critical disease threatening the laying hen industry. Inulin, a widely used prebiotic, has shown promise in alleviating metabolic disorders, but its role in mitigating FLHS in laying hens is not fully understood. Here, we investigated the effects and underlying mechanisms of inulin-mediated alleviation of FLHS in a high-carbohydrate low-protein diet (HCD)-induced laying hen model. We found that inulin supplementation significantly ameliorated HCD-induced hyperlipidemia, hyperglycemia, hepatic steatosis, liver injury, and oxidative stress. These phenotypic improvements were accompanied by enhanced fatty acid oxidation and suppressed lipid synthesis and inflammation. Microbiota analysis revealed that inulin reshaped the HCD-perturbed cecal microbiota, with Faecalibacterium identified as the only dominant genus substantially depleted by HCD and restored by inulin. Targeted metabolomics showed that inulin elevated cecal spermidine levels, which strongly correlated with Faecalibacterium abundance and improved metabolic traits. Fecal microbiota transplantation (FMT) from inulin-treated donors replicated the protective effects, confirming the causal role of gut microbiota in mediating inulin's anti-FLHS activity. Further mechanistic investigation using the representative species Faecalibacterium prausnitzii demonstrated that inulin enhanced spermidine production through transcriptional activation of the spermidine biosynthetic pathway. Spermidine, in turn, upregulated hepatic ALDH1A2 expression, enhancing retinoic acid synthesis and activating the AMPK-SIRT1 axis, thereby reducing lipid accumulation in hepatocytes. Collectively, these findings establish a novel Faecalibacterium-spermidine-ALDH1A2-retinoic acid-AMPK-SIRT1 axis through which inulin alleviates FLHS, highlighting inulin as a dietary intervention targeting the gut-liver axis and offering novel therapeutic avenues for preventing this disorder in laying hens.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13578277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148205623","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}
引用次数: 0
Lactiplantibacillus plantarum-inoculated silage improves milk fat in dairy goats by reprogramming rumen microbiota to promote pyruvate metabolism. 接种植物乳杆菌的青贮饲料通过重组瘤胃微生物群促进丙酮酸代谢来改善奶山羊的乳脂。
IF 11.4 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2026-06-06 DOI: 10.1038/s41522-026-01031-6
Jing Ma, Qiang Li, Guanghao Xia, Jiayao Zhang, Samaila Usman, Xusheng Guo
{"title":"Lactiplantibacillus plantarum-inoculated silage improves milk fat in dairy goats by reprogramming rumen microbiota to promote pyruvate metabolism.","authors":"Jing Ma, Qiang Li, Guanghao Xia, Jiayao Zhang, Samaila Usman, Xusheng Guo","doi":"10.1038/s41522-026-01031-6","DOIUrl":"10.1038/s41522-026-01031-6","url":null,"abstract":"<p><p>Silage inoculated with homofermentative lactic acid bacteria exhibits superior nutritional quality and improves ruminant production performance. However, the mechanisms by which the inoculated silage modulates microbial and metabolic alterations along the rumen-mammary gland axis remain unclear. Here, Lactiplantibacillus plantarum BX62 inoculation enhanced silage quality and flavonoid content through reshaping the microbiome, which promotes carbohydrate-active enzyme secretion. Feeding the silage to dairy goats modulated ruminal microbiota through changes in silage flavonoid, fiber, and crude protein contents. Notably, increased flavonoid intake enriched ruminal flavonoid-degrading bacteria, leading to enhanced flavonoid transformation, fiber degradation, and pyruvate-centered carbohydrate metabolism, promoting acetate production. The increased ruminal acetate and upregulated expression of mammary lipogenic genes ultimately improved milk fat synthesis. Our findings reveal how L. plantarum links silage quality to rumen function and mammary gland metabolism, offering a mechanistic basis for improving lactation performance of dairy goats via modulating silage fermentation.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13562649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148176432","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}
引用次数: 0
Gut commensal Parabacteroides goldsteinii-derived CDCA mediates FXR signalling to improve mucosal barrier function. 肠道共生金斯坦副杆菌来源的CDCA介导FXR信号通路改善粘膜屏障功能。
IF 11.4 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2026-06-06 DOI: 10.1038/s41522-026-01035-2
Jiantao Yang, Kailong Qin, Qianggang Wang, Wei Guo, Xiaojun Yang
{"title":"Gut commensal Parabacteroides goldsteinii-derived CDCA mediates FXR signalling to improve mucosal barrier function.","authors":"Jiantao Yang, Kailong Qin, Qianggang Wang, Wei Guo, Xiaojun Yang","doi":"10.1038/s41522-026-01035-2","DOIUrl":"10.1038/s41522-026-01035-2","url":null,"abstract":"<p><p>The gut microbiome plays a crucial role in maintaining barrier integrity. However, it remains urgently needed to mining the gut microbiota that contribute to intestinal mucus barrier and to understand their biological mechanisms. In this study, the Lueyang black-boned chicken (LBC, a Chinese native breed) exhibited higher abundances of Bacteroidetes and Parabacteroides and stronger intestinal barrier function than Arbor Acres (AA, a commercial breed) broilers. Microbiota transplantation from LBC to AA broilers improved the intestinal barrier function. Bacteroides expanded the exclusive metabolic niche of Parabacteroides goldsteinii by producing small metabolites, thereby increasing P. goldsteinii abundance within the gut. P. goldsteinii was identified as the main contributor to the enhanced intestinal mucosal barrier. P. goldsteinii bio-transformed the taurochenodeoxycholic acid into chenodeoxycholic acid, promoting mucin production via farnesoid X receptor activation. Collectively, these findings highlight that the gut microbiota of LBC creates an exclusive metabolic niche for P. goldsteinii through cross-feeding, and reveal the critical role of P. goldsteinii-mediated bile acid biotransformation in enhancing intestinal mucosal barrier function.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13562522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148194930","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}
引用次数: 0
The precisely regulated keystone taxa facilitate microbial mineralization of soil organic phosphorus via niche partitioning. 精确调控的关键类群通过生态位分配促进土壤有机磷的微生物矿化。
IF 11.4 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2026-06-05 DOI: 10.1038/s41522-026-01036-1
Wenhui Yan, Chengdong Huang, Dandan Li, Jiayin Feng, Gu Feng, Hang Ma, Jan Jansa, John Klironomos, Minghao Zhuang, Fusuo Zhang, Lin Zhang
{"title":"The precisely regulated keystone taxa facilitate microbial mineralization of soil organic phosphorus via niche partitioning.","authors":"Wenhui Yan, Chengdong Huang, Dandan Li, Jiayin Feng, Gu Feng, Hang Ma, Jan Jansa, John Klironomos, Minghao Zhuang, Fusuo Zhang, Lin Zhang","doi":"10.1038/s41522-026-01036-1","DOIUrl":"10.1038/s41522-026-01036-1","url":null,"abstract":"<p><p>Rhizosphere keystone taxa critically drive microbial community stability and soil biogeochemical cycles. However, the manipulation of such taxa remains a challenge. This study simulated plant-mediated modulation of keystone taxa via simplified synthetic root exudates to track their compositional shifts. The combination of luteolin, myristic acid, and glucose enhanced rhizosphere phosphatase activity, significantly enriched Domibacillus indicus D99, and converted it into a keystone taxon. This precise regulation was driven by transcriptional upregulation of C metabolism and an unusual fatty acid assimilation pathway. Additionally, metabolites produced by D. indicus D99 (such as bergapten and lactate) were preferentially utilized by phosphate-mineralizing bacteria, Bacillus sp. C67 and Domibacillus sp. C94. These partner bacteria exhibited less substrate overlap and pronounced resource partitioning, forming an efficient synergistic relationship with D. indicus D99 that amplified rhizosphere phosphatase activity and plant growth. This study highlights opportunities to utilize the ecological roles of keystone taxa in manipulating the microbiome.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13562629/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148175836","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}
引用次数: 0
Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows. 瘤胃源性膜性毕赤酵母调节奶牛瘤胃微生物组和代谢组,减少甲烷排放。
IF 11.4 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2026-06-02 DOI: 10.1038/s41522-026-01029-0
Jichao Li, Xu Liang, Pengyu Liu, Weiyun Zhu, Wei Jin, Shengyong Mao, Fei Xie
{"title":"Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.","authors":"Jichao Li, Xu Liang, Pengyu Liu, Weiyun Zhu, Wei Jin, Shengyong Mao, Fei Xie","doi":"10.1038/s41522-026-01029-0","DOIUrl":"10.1038/s41522-026-01029-0","url":null,"abstract":"<p><p>Methane emissions from ruminants represent a significant environmental challenge and dietary energy loss. While yeasts are potential rumen modulators, specific methane-mitigating species remain poorly characterized. Here, we screened 73 rumen-derived strains in vitro, identifying Pichia membranifaciens M12 as the most effective candidate, reducing methane output by 17.1%. Subsequently, a randomized block trial with 36 dairy cows compared a control group with P. membranifaciens M12 supplementation at 2.5 and 5 × 10<sup>11</sup> CFU/cow/day. Methane yield per unit of dry matter intake significantly decreased in the high-dose group (18.7%, P = 0.003), without compromising lactation performance and animal health. Multi-omics analyses revealed that M12 suppressed hydrogenotrophic methanogens (e.g., Methanobrevibacter) and hydrogen-producing bacteria (e.g., Ruminococcus and Fibrobacter), while enriching specific eukaryotic taxa like Orpinomyces and Entodinium. Metabolomic profiling indicated a significant dose-dependent accumulation of metabolites. Metagenomic function analysis demonstrated the decreased abundance of key methanogenesis genes (e.g., mcrABCDG) and increased abundance of hydrogenase (hyaABC), lactate-forming (ghrB), and propionate-forming (mcmA1 and lcdB), suggesting a redirection of reducing equivalents from methanogenesis toward propionate synthesis, alongside enhanced butyrate production. These findings demonstrate that P. membranifaciens M12 mitigates methane emissions via coordinated ecological and metabolic modulation, highlighting its potential as a sustainable strategy for low-carbon ruminant production.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13526788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148150631","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}
引用次数: 0
Choline counteracts pregnancy undernutrition-associated colitis in sheep by restoring microbiota driven bile acid metabolism. 胆碱通过恢复微生物群驱动的胆汁酸代谢来抵消妊娠期营养不良引起的绵羊结肠炎。
IF 11.4 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2026-05-30 DOI: 10.1038/s41522-026-01027-2
Weibin Wu, Peng Jiao, Yamei Gu, Huizhen Lu, Caiyun Fan, Zheng Sun, Lizhuang Hao, Shengyong Mao, Jianbo Cheng, Yanfeng Xue
{"title":"Choline counteracts pregnancy undernutrition-associated colitis in sheep by restoring microbiota driven bile acid metabolism.","authors":"Weibin Wu, Peng Jiao, Yamei Gu, Huizhen Lu, Caiyun Fan, Zheng Sun, Lizhuang Hao, Shengyong Mao, Jianbo Cheng, Yanfeng Xue","doi":"10.1038/s41522-026-01027-2","DOIUrl":"10.1038/s41522-026-01027-2","url":null,"abstract":"<p><p>High-fertility sheep experience undernutrition during late gestation, which induces body metabolic disruption and intestinal inflammation. Crucially, the gut microbiota-bile acid axis is a promising intestinal inflammation target, but how choline modulates this axis in livestock enteritis is unknown. This study investigated choline's protective mechanisms against undernutrition-induced intestinal inflammation in sheep, focusing on gut microbiota and bile acid regulation. Choline consistently alleviates colitis severity, restores epithelial barrier integrity, and suppresses intestinal inflammation. These protective effects are accompanied by pronounced remodeling of the colonic microbial ecosystem, characterized by the enrichment of Clostridiales bacterium to elevate bile salt hydrolase activity and regulate bile acid homeostasis. Concomitantly, choline reshapes colonic bile acid profiles, normalizing total bile acid levels and selectively restoring DCA abundances. Mechanistically, the anti-inflammatory effects of DCA depend on Nur77 activation and subsequent suppression of NF-κB signaling across in vivo and in vitro systems. These findings provide preliminary evidence for a putative choline-microbiota-bile acid-immune signaling axis that confers protection against undernutrition-associated colitis and support choline intervention as a pregnancy-compatible nutritional strategy for intestinal inflammatory disorders in animal.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":" ","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13518997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148101597","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}
引用次数: 0
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