Revealing the Social Biomarkers of Residual Feed Intake by Using 16s rRNA and LC-MS in Duroc Pig Ileum

Abstract Feed efficiency (FE) is a typical social affected trait. However, the mechanisms involved are not fully elucidated. According to the rank of residual feed intake (RFI)’s social genetic effect (SGE), ten high and low pigs were selected, named LRI and HRI groups. A sampling of ileal chyme after slaughter. Liquid chromatography-mass spectrometry (LC-MS) and 16S rRNA were conducted to investigate the relationship between the gut microbiome or metabolites and the SGE of RFI. The results showed significant differences between HRI and LRI groups. Compared with the HRI group, Escherichia, Eubacterium, and Gemmiger were enriched in the LRI group (P < 0.01), whereas the abundance of Fusobacterium, Eubacterium, and Desulfovibrio in the HRI group were significantly higher than that in the LRI group (P < 0.01). In the metabolome, we found that Glycine, L-lysine, and L-tryptophan were positively correlated with RFI’s SGE. KEGG pathway analysis revealed that most differential metabolites were involved in amino acid metabolism. The Pearson correlation analysis of the candidate social biomarkers was carried out. Amino acid metabolites were discovered to have significant correlations with Escherichia and Fusobacterium. Therefore, Escherichia and Fusobacterium may influence the SGE of RFI through amino acid metabolism, thereby affecting feed efficiency.