Rumen and colon-centered microbiota-liver interactions associated with bile acid-related metabolic regulation in sheep.

Background: Ruminant gastrointestinal microbiota are spatially heterogeneous, yet whether the rumen microbiota contributes to bile acid-related gut-liver associations beyond its local fermentative role remains unclear. Here, paired rumen, ileum, and colon microbiota were integrated with liver transcriptomic data, blood biochemical and tail fat-related phenotypes to determine which gastrointestinal sector microbiota play prioritized host interactions in a sheep model. Results: The rumen, ileum, and colon showed marked taxonomic and predicted functional divergence, indicating strong spatial restructuring along the digestive tract. Distinct patterns included rumen-enriched taxa, coordinated rumen-colon taxa, and taxa showing progressive shifts across compartments. Representative genera included Conclusions: These findings indicate that the rumen is not merely a local fermentation chamber but may represent an important upstream microbial component associated with the bile acid-related gut-liver axis. Our results support consideration of an expanded, rumen-inclusive framework for investigating bile acid-related gut-liver associations in ruminants.