Segment-specific intestinal bacterial community structure is associated with short-chain fatty acid profiles and mucosal morphology in two high-altitude sheep breeds.

The gastrointestinal tract of grazing ruminants contains segment-specific microbial niches that contribute to fermentation metabolism and intestinal function. However, the intestinal bacterial communities and their relationships with fermentation products and mucosal morphology remain insufficiently characterized in alpine sheep breeds. In this study, Tianhua mutton sheep and Gansu Alpine fine-wool sheep maintained under the same grazing conditions were compared using the techniques of hematoxylin and eosin (H&E) staining, gas chromatography, and full-length 16S rRNA sequencing. Histological analysis showed that Tianhua mutton sheep had lower crypt depth and higher villus-height-to-crypt-depth ratios in the duodenum and ileum, while muscular layer thickness differed between breeds in a segment-dependent manner. Short-chain fatty acids (SCFAs) analysis revealed breed-related differences in specific intestinal segments, with Tianhua mutton sheep showing higher levels of several major SCFAs components and total SCFA in the duodenum, jejunum, cecum, and colon. Full-length 16S rRNA sequencing demonstrated distinct bacterial community structures between the two breeds and clear spatial variation along the intestinal tract. Tianhua mutton sheep exhibited higher bacterial richness in several segments and enrichment of Firmicutes and Christensenellaceae_R_7_group, whereas Gansu Alpine fine-wool sheep showed higher abundances of Bacteroidota, Verrucomicrobiota, and Akkermansia in specific segments. Functional prediction indicated that KEGG level 3 differences were mainly concentrated in the cecum and colon, involving pathways related to microbial metabolism, carbon metabolism, ABC transporters, and two-component systems. Spearman correlation analysis further linked selected genera with SCFA traits, whereas fewer associations were observed with small-intestinal histomorphological indices. These findings suggest that Tianhua mutton sheep and Gansu Alpine fine-wool sheep differ in intestinal morphology, fermentation characteristics, and microbial structure and function, providing new information for understanding breed-specific host-microbiota interactions in alpine grazing sheep.