Abstract
Objective: Feed conversion ratio (FCR) is a crucial economic trait in animal breeding and management and is also important for environmental sustainability. This study aimed to investigate the putative regulatory mechanisms of FCR in sheep by integrating rumen microbiota and host metabolome through multi-omics analysis.Methods: FCR data were collected from 127 male Hu sheep. Extreme individuals were selected for rumen metagenomic and serum metabolomic analyses to identify key factors driving FCR across early and late fattening stages.Results: Bacteroides, Prevotella, and other genera were identified as dominant taxa in the rumen across both stages, suggesting their ipotential role in FCR regulation. Notably, Nocardia tengcongensis differed significantly between the highest FCR values (HF) and lowest FCR values (LF) groups at different stages, indicating its potential as a predictive biomarker of feed efficiency. Functional analysis revealed that the pentose phosphate pathway (M00004) and lysine biosynthesis via the succinyl-DAP pathway (M00016) were enriched in the LF group, whereas the methanogenesis pathway (M00357) was significantly enriched in the HF group, indicating increased methane production. Thirteen metabolites consistently differed between HF and LF across fattening stages and they may be used as predictive biomarkers. Furthermore, the abundance of Prevotella and Bacteroides increased over time and showed significant correlations with key metabolites.Conclusion: These findings suggest strong interactions between rumen microbiota and host metabolites that may collectively influence FCR, providing new insights into microbial and metabolic regulation of feed efficiency and a theoretical basis for optimizing feeding strategies in sheep.