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Here, we used germ\u2010free (GF) and specific pathogen\u2010free (SPF) Rongcheng piglets to explore how microbial absence influences muscle development. GF piglets showed significantly reduced body weight and an increased proportion of fast\u2010twitch fibers compared with SPF controls. Transcriptome sequencing identified 1332 differentially expressed genes (DEGs), notably those involved in cGMP\u2010PKG, Thyroid hormone, HIF\u20101, VEGF, and Butanoate metabolism signaling pathways, which are essential for myofiber specification. Non\u2010targeted metabolomic profiling revealed 320 differentially expressed metabolites (DEMs), with major alterations in Bile secretion. Integrated transcriptomic and metabolomic uncovered 10 KEGG pathways co\u2010enriched with DEGs and metabolites, including Bile secretion, Ferroptosis, Inflammatory mediator regulation of TRP channels, and HIF\u20101 signaling pathway. Correlation analysis revealed that strong positive correlations were observed between fast\u2010twitch fiber genes (e.g.,\n                    <jats:italic>PRKCA<\/jats:italic>\n                    ,\n                    <jats:italic>MYOZ3<\/jats:italic>\n                    ,\n                    <jats:italic>NFATC1<\/jats:italic>\n                    ) and fatty acid\u2010related metabolites (e.g., Dodecanoic acid, Valproic Acid, and Decanoic acid), whereas negative correlations were detected between these genes and bile acid\u2010related metabolites (e.g., Cholic acid and 7\u2010Ketolithocholic acid), suggesting microbial metabolites is associated with muscle fiber phenotype via metabolic and signaling crosstalk. Collectively, our findings demonstrate that gut microbial absence in pigs disrupts bile acid metabolism and fatty acid metabolism, which in turn drives the shift of skeletal muscle fiber composition toward fast\u2010twitch glycolytic fibers. These metabolites are identified as key microbial mediators linking the gut microbiota to the transcriptional regulatory function of porcine muscle fiber type specialization, providing new insights into the gut\u2013muscle axis and highlighting the important role of microbiota\u2010derived metabolites in maintaining porcine muscle fiber composition and metabolic balance.\n                  <\/jats:p>","DOI":"10.1002\/age.70124","type":"journal-article","created":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T08:09:41Z","timestamp":1779178181000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Integrated Transcriptomic and Metabolomic Analysis Reveals Gut Microbiota\u2013Mediated Regulation of Muscle Fiber Composition and Metabolism in Germ\u2010Free Pigs"],"prefix":"10.1002","volume":"57","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2795-2648","authenticated-orcid":false,"given":"Yaxin","family":"Peng","sequence":"first","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural University  Wuhan China"},{"name":"Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs Huazhong Agricultural University  Wuhan China"},{"name":"Hubei Hongshan Laboratory  Wuhan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5038-1943","authenticated-orcid":false,"given":"Yapeng","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural University  Wuhan China"},{"name":"Fujian Provincial University Engineering Research Center for Animal Breeding and Sustainable Production, College of Animal Sciences Fujian Agriculture and Forestry University  Fuzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunpeng","family":"He","sequence":"additional","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural University  Wuhan China"},{"name":"Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs Huazhong Agricultural University  Wuhan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Zuo","sequence":"additional","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural University  Wuhan China"},{"name":"Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs Huazhong Agricultural University  Wuhan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhifeng","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural University  Wuhan China"},{"name":"Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs Huazhong Agricultural University  Wuhan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Panpan","family":"Yang","sequence":"additional","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural University  Wuhan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Ma","sequence":"additional","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural University  Wuhan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuaifei","family":"Feng","sequence":"additional","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural University  Wuhan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang","family":"Tan","sequence":"additional","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural University  Wuhan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zaiyan","family":"Xu","sequence":"additional","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural University  Wuhan China"},{"name":"Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs Huazhong Agricultural University  Wuhan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Wei","sequence":"additional","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural University  Wuhan China"},{"name":"Yu\u2010Yue Pathology Scientific Research Center  Chongqing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5653-0797","authenticated-orcid":false,"given":"Bo","family":"Zuo","sequence":"additional","affiliation":[{"name":"College of Animal Sciences &amp; Technology Huazhong Agricultural 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