Multi-omics evaluation of feeding strategies on yak meat quality: insights from eDNA, metagenomics, and metabolomics

This study investigates how seasonal grazing and housed feeding regimes alter the rumen microbiome and metabolite networks in yaks, thereby influencing meat quality. We evaluated the effects of these feeding strategies on Warner-Bratzler shear force (WBSF) and other key meat quality parameters using an integrated approach combining eDNA-metagenomics and metabolomics. This study revealed that warm-season forages, which are abundant in n-3 polyunsaturated fatty acids (n-3 PUFA), promote rumen metabolites associated with PUFA retention. This process resulted in an increased n-3 PUFA content in yak meat. Housed yaks fed high-energy diets exhibited increased Bacillota abundance and acetate biosynthesis, changes that enhanced IMF and crude protein levels, thereby improving meat tenderness and marbling. In contrast, cold-season grazing yaks ingested a higher proportion of Fabaceae and Ranunculaceae species. A high-fibre diet increased the abundance of Prevotella and Fibrobacter, genera that mitigate cold stress through enhanced propionate production and fatty acid catabolism. However, this dietary pattern led to a reduction in key meat quality indicators. In conclusion, the yak rumen microbiome employs distinct adaptive strategies under different feeding systems, thereby exerting differential effects on meat quality.