Host genome regulation of the porcine gut microbiota and its impact on feed conversion efficiency

This study aims to elucidate the regulatory mechanisms of host genetics on the porcine gut microbiota and their subsequent impact on the feed conversion ratio (FCR). While initial genome-wide association studies (GWAS) did not identify significant SNPs directly associated with FCR, we investigated the gut microbiota as a potential intermediate phenotype influencing feed efficiency. Nonmetric multidimensional scaling (NMDS) based on Bray–Curtis distances demonstrated a distinct separation in microbial community structure between the high-feed conversion ratio (HFCR) and low-feed conversion ratio (LFCR) groups (stress = 0.19), suggesting a link between FCR and gut microbial composition. Furthermore, a significant, albeit weak, negative correlation was observed between the genomic relatedness matrices and microbial Bray‒Curtis dissimilarity (r = −0.0143, p = 0.0031), indicating host genetic control over the microbiome. Microbiome genome-wide association study (mGWAS) identified 117 significant SNPs associated with 28 microbial taxa. Functional annotation highlighted eight candidate genes (DCY8, PATJ, PTPN2, FTO, SLC13A1, ADAM28, MGST1, and PTGS2) involved in the regulation of taxa, including Campylobacter, Faecalibacterium, Streptococcus, Succinivibrio, Treponema, Turicibacter, uncultured Erysipelotrichales, and uncultured Peptococcaceae 2. Collectively, these findings establish that the gut microbiota is a heritable trait influenced by the host genome, providing novel targets for breeding strategies designed to optimize microbial composition for improved feed efficiency.