Comprehensive analysis of host genetics and gut microbiota co-regulatory network provides new insights into improving pork quality in pigs

Pork quality is co-regulated by host genetics and gut microbiota, though their interplay remains elusive. We conducted integrated genome-wide and microbiome-wide association studies on 257 commercial Duroc×(Landrace×Yorkshire) pigs, assessing genetic and microbial influences on intramuscular fat, meat color, marbling, and moisture. Meat quality traits exhibited moderate heritability (0.13–0.60) but low microbiability (0.00-0.07). Thirty host SNPs affecting microbial abundance were identified, including loci near CDH13 , APOB , LDAH , and ACSL1 genes implicated in lipid metabolism. Seven bacterial taxa showed meat quality associations, with improved traits linked to reduced Anaerobiospirillum , Parvimonas , Anaerovibrio , Oscillospira and enriched Anaeroplasma , WAL_1855D , and Prevotella . This tripartite interaction pattern between porcine genotypes, microbial consortia, and meat phenotypes suggests coordinated, although quantitatively modest host–microbiome association. The identification of genomic loci and bacterial taxa therefore represents candidate components of a host-microbiome network potentially involved in lipid deposition and muscle characteristics. These findings provide a basis for further mechanistic and validation studies, with potential implications for the future development of precision breeding and microbiome-informed management strategies in pigs.