The Metabolome in Different Sites of Gut Tract Regulates the Meat Quality of Longissimus Dorsi Muscle

Meat quality is influenced by genetic, nutritional, and microbial factors, with increasing attention on the role of gut-derived metabolites. In this study, we conducted untargeted metabolomics of 10 gut tract sites and RNA sequencing (RNA-seq) of longissimus dorsi muscles in Meigu goats and Liangshan black sheep raised under standardized conditions. Results showed that goat muscle contained significantly higher levels of essential amino acids (e.g., methionine) and specific fatty acids (e.g., C18:3_N6, C20:4_N6), suggesting improved nutritional quality. Transcriptomic analysis identified 3133 differentially expressed genes (DEGs), among which <i>ADCY1</i> and <i>SLC38A4</i> were upregulated in goats and strongly associated with meat traits. Using integrative correlation analysis, we uncovered 17 genes and 19 gut metabolites that were significantly correlated with more than eight meat quality parameters across multiple gut sites. Notably, these metabolites included bioactive compounds such as L-tyrosine ethyl ester and pelargonidin 3-O-glucoside, while genes were enriched in pathways related to amino acid transport, cAMP signaling, and muscle development. Together, these findings highlight a potential gut-muscle axis involving metabolite-mediated modulation of muscle gene expression, contributing to breed-specific differences in meat composition and quality. This study provides a valuable framework for improving ruminant meat quality through integrative multi-omics analysis.