Gut microbiota and multi-omics analysis identify candidate gut-muscle associations underlying breast muscle quality differences between Mimas pigeon and pigeon Tianxiang 1 strain

Pigeon meat is increasingly favored by the public for its unique flavor and nutritional value. Previous studies have identified meat quality differences between Mimas pigeon and pigeon Tianxiang 1 strain. To investigate the biological basis of these differences, this study conducted an integrated analysis of intestinal morphology, gut microbiome, and breast muscle metabolomics and transcriptomics. The pigeon Tianxiang 1 strain exhibited enhanced intestinal development and immune characteristics, as evidenced by significantly higher villus height, villus height-to-crypt depth (V/C) ratio, and goblet cell density, along with reduced intestinal wall thickness. Marked differences in ileal microbiota composition were observed between the two breeds. Functional enrichment indicated that the microbiota of pigeon Tianxiang 1 strain was mainly associated with intestinal growth and immune regulation, whereas that of Mimas pigeon was predominantly involved in carbohydrate metabolism and lipid biosynthesis. GO and KEGG enrichment analyses of the breast muscle transcriptome further revealed significant enrichment of lipid metabolism-related pathways in Mimas pigeon, raising the possibility of coordinated variation between intestinal microbial function and muscle metabolism. Exploratory multi-omics correlation analysis showed that Turicibacter and Lactobacillus in pigeon Tianxiang 1 strain were associated with intestinal morphological parameters, whereas Acinetobacter and Pseudomonas in Mimas pigeon were positively associated with the expression levels of KIF2C , BIRC5 , PRC1 , and RACGAP1 genes, and negatively associated with glycolytic intermediates. The pigeon Tianxiang 1 strain exhibited intestinal morphological features under H&E-stained sections that may be associated with improved digestive and absorptive capacity and immune function. Together with its characteristic genera, such as Turicibacter and Lactobacillus , these features may synergistically support intestinal development and immune function, potentially contributing to a greater digestive capacity than that of the Mimas pigeon. In contrast, Mimas pigeon showed an exploratory gut-muscle association pattern in which Acinetobacter and Pseudomonas were associated with higher expression of KIF2C and BIRC5 in breast muscle and with changes in glycolytic metabolism and intramuscular fat deposition. These findings provide candidate links between gut microbiota and meat quality that require further validation in larger and mechanistic studies.