ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Microorganisms in Vertebrate Digestive Systems
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1648896
This article is part of the Research TopicNew Horizons in Gut Microbiome Research for Enhancing Livestock ProductivityView all 13 articles
Bile acid pathways in Caprinae gut microbiota: Adaptive shifts in microbial metabolism and community structure
Provisionally accepted
Kai-Meng Shang1,2,3Rui Liu4
Hong-Bo Ni3
He Ma3Jin-Wen Su3
Hai-Long Yu3Guo Li5Bei-Ni Chen2*
Xiao-Xuan Zhang3*
Xing Yang1*- 1Dali University, Dali, China
- 2Changchun Sci-Tech University, Changchun, China
- 3Qingdao Agricultural University, Qingdao, China
- 4Other
- 5Jilin Agricultural Science and Technology University, Jilin, China
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This study presents a comprehensive analysis of the gut microbiota in Caprinae animals, focusing on the role of microbial taxa in bile acid (BA) metabolism. A total of 63,126 metagenome-assembled genomes (MAGs) were retrieved from 779 samples, of which 7,530 high-quality, non-redundant MAGs were retained after stringent quality assessment and dereplication. The constructed gene catalog encompassed 14,840,909 genes, facilitating taxonomic annotation and functional analysis. The results revealed a diverse gut microbiota across 28 phyla, with Bacillota_A being the most dominant. A significant number of genes (8,290) from 5,217 genomes were identified to be involved in BA transformation pathways, including deconjugation, oxidation, and dehydroxylation. Bacteria from the Bacillota_A phylum were the primary carriers of BA-related genes. Among the MAGs, 1,845 encoded bile salt hydrolase (BSH), an enzyme crucial for the initial step of BA metabolism. Comparative analysis with human and pig gut microbiota highlighted a distinct BA metabolic profile in Caprinae animals, characterized by a higher proportion of BSH-related genes. Functional profiling of BSH-carrying MAGs within the genus Alistipes revealed significant differences in carbohydrate-active enzymes (CAZymes), indicating distinct metabolic repertoires that may reflect divergent ecological roles in the intestinal environment. Microbial taxonomic composition and bile acid (BA)-metabolizing potential varied markedly across the ten intestinal segments of Ovis aries, with the colon, cecum, and rectum showing the highest microbial diversity and functional gene abundance. Key BA-transforming enzymes (BSH, 7α-HSDH, and baiB) were widely distributed, with particularly high abundances in the jejunum and ileum, indicating region-specific specialization in BA metabolism. This study provides new insights into the ecological and metabolic functions of gut microbiota in Caprinae animals, emphasizing the unique BA metabolic profiles and the functional potential of BSH-carrying MAGs, which have broader implications for understanding host-microbiota interactions in health and disease.
Keywords: Gut Microbiota, microbial functional profiling, Metagenomic, Bile acid metabolism, Caprinae
Received: 17 Jun 2025; Accepted: 29 Aug 2025.
Copyright: © 2025 Shang, Liu, Ni, Ma, Su, Yu, Li, Chen, Zhang and Yang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Bei-Ni Chen, Changchun Sci-Tech University, Changchun, China
Xiao-Xuan Zhang, Qingdao Agricultural University, Qingdao, China
Xing Yang, Dali University, Dali, China
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