Integrative Multi-omics Reveals Microbiota Metabolite Host Interactions Underpinning the Hybrid Advantage of Hu-East Friesian crossbred Sheep (PRJCA044440)

Background: Crossbreeding has been widely used to improve livestock performance, yet the molecular mechanisms underlying hybrid advantages in gut health remain unclear. Methods: We employed an integrative multi-omics approach, combining 16S rRNA sequencing, untargeted metabolomics, transcriptomics, and microbiota metabolite host correlation analyses, to compare the colonic microbiota, metabolites, and gene expression profiles of Hu, East Friesian (EF), and Hu*East Friesian (DH) crossbred sheep. Results: DH sheep exhibited distinct gut microbial composition, characterized by enrichment of beneficial bacteria (Lactobacillus, Bifidobacterium), higher short-chain fatty acid (butyric acid, propionic acid) levels, favorable bile acid profiles, and improved fatty acid metabolism. Transcriptomic WGCNA identified DH-specific metabolic modules, with GNB2 as a key hub gene. Microbiota metabolite host analyses revealed strong associations between Lactobacillaceae, SCFAs, bile acids, fatty acids, and host genes (CA4, ACAT2, AGPAT2). Conclusion: These findings provide mechanistic insight into how microbiota metabolite host interactions drive the hybrid advantage of DH sheep, highlighting their improved colonic metabolic capacity and intestinal health. This study offers a valuable framework for integrating multi-omics data to elucidate gut health benefits in crossbred livestock.