Multi-omics reveals the associations between cecal candidate bacteria and muscle fatty acid composition variations in Daheng and Luning chickens.

INTRODUCTION: Accumulating evidence underscores the profound impact of the gastrointestinal ecosystem on skeletal muscle lipid dynamics. METHODS: This study was designed to investigate the systemic associations connecting the gut microbiota, intermediate metabolomes, and intramuscular fatty acid (FA) deposition in chicken. RESULTS: Phenotypic and lipophilic profiling revealed distinct FA compositions between Daheng chickens (DHC) and Luning chickens (LNC), with DHC exhibiting significantly higher concentrations of 26 distinct FAs including flavor-precursor MUFAs (C18:1n9c) and functional omega-3 (n-3) PUFAs (C20:5n3 and C22:5n3) within the leg muscle. High-throughput metagenomic sequencing subsequently identified positive correlations between dominant cecal bacterial taxa and these specific muscle FAs. Concurrently, multi-compartment metabolomics mapped a spectrum of differential metabolites spanning the cecum, serum, and leg muscle, which were fundamentally enriched in the "cysteine and methionine metabolism" and "pantothenate and CoA biosynthesis" pathways. Through an integrative multi-omics framework paired with statistical mediation modeling, we identified a candidate functional axis: the Agathobaculum-Collinsella-Enorma consortium strongly co-varies with muscle FA deposition, a process bridged by key intermediate nodes including Pyruvic acid, S-adenosylmethionine, and Spermine. CONCLUSION: Collectively, these findings suggest that the gut microbiota is closely coupled with muscle lipid composition via a structured gut-metabolite-muscle axis, offering candidate microbial markers for precision management of meat quality in poultry production.