Exploring the Spatial Variation in the Microbiota and Bile Acid Metabolism of the Compound Stomach in Intensively Farmed Yaks

Yaks are one of the important livestock on the Qinghai–Tibet Plateau, providing abundant dairy and meat products for the local people. The formation of these dairy and meat products mainly relies on the microbiota in their gastrointestinal tract, which digests and metabolizes plant feed. The yak’s gastrointestinal microbiota is closely related to the health and production performance of the host, but the molecular mechanisms of diet-induced effects in intensively farmed yaks remain to be elucidated. In this study, 40 chyme samples were collected from the four stomach chambers of 10 intensively farmed yaks, and the bacterial diversity and bile acid changes in the rumen (SFRM), reticulum (SFRC), omasum (SFOM), and abomasum (SFAM) were systematically analyzed using 16S rRNA sequencing and bile acid metabolism. Our results showed that the gastrointestinal microbiota mainly distributes in the four-chambered stomach, with the highest microbial diversity in the reticulum. There is a highly negative correlation among the microbiota in the four chambers. The dominant bacterial phyla, Bacteroidota and Firmicutes, were identified, with Rikenellaceae_RC9_gut_group being the dominant genus, which potentially helps maintain short-chain fatty acid levels in the stomach. In contrast, the microbiome within the four stomach chambers synergistically and selectively altered the content and diversity of bile acid metabolites in response to intensive feeding. The results of this study provide new insights into the microbiota and bile acid metabolism functions in the rumen, reticulum, omasum, and abomasum of yaks. This can help uncover the role of gastrointestinal microbiota in yak growth and metabolic regulation, while also providing references for improving the production efficiency and health of ruminants.