The Qianqiu goat is a high-quality indigenous breed in China, known for its excellent adaptability, carcass yield, and quality. It is primarily found along the border between Tianchang City and Lai’an County in Anhui Province, where the local environment shapes its habitat. Despite over a thousand years of domestication, the mechanisms behind its germplasm traits, particularly the roles of its gastrointestinal microbiota, key host genes, and metabolites, remain poorly understood. Using modern omics technologies, we studied the microbe–gene–metabolite axis in Qianqiu goats within a multi-omics framework to support genetic improvement and goat husbandry. Our findings are as follows: (1) Tukey’s HSD tests identified 18 differentially abundant genera across gut segments, mainly enriched in the small intestine, with Methanobrevibacter reaching 24.51% relative abundance. Qianqiu goats showed high microbial diversity compared to other goat breeds, with core genera in the rumen, small intestine, and large intestine. (2) Whole-transcriptome analysis revealed 7,465 differentially expressed genes (DEGs) in small intestine vs. rumen and 4,645 DEGs in large intestine vs. small intestine. WGCNA identified hub genes involved in muscle contraction, immune response, and transport processes across different gut segments. (3) Metabolomics analysis identified 273 upregulated and 348 downregulated metabolites in the small intestine vs. rumen, and 363 upregulated and 232 downregulated metabolites in the large intestine vs. small intestine. Key metabolites were involved in lipid signaling, sulfur-amino-acid metabolism, and immune homeostasis. In conclusion, our multi-omics analysis reveals that the Qianqiu goat's gastrointestinal microbiota, genes, and metabolites form a coordinated system that influences gastrointestinal health, offering valuable targets for breeding and resource utilization.

Goat, Germplasm Resources, Gene