The genetic and evolution characterization of the gut microbiota in pigs

Abstract

Abstract Intestinal microbiota plays significant roles in the physiology and functioning of their host organisms. However, there is limited knowledge of the evolution and genetic of microbiota-host relationships from wild ancestors to modern domesticated species. In this study, the 16S rRNA gene V3 -V4 was analyzed by high-throughput sequencing in the intestinal contents of different pig breeds which were then compared. This identified 18 323 amplicon sequence variants, of which the Firmicutes and Actinobacteria phyla and Bifidobacterium and Allobaculum genera were most prevalent in wild pigs (WP). In contrast, Proteobacteria and Firmicutes predominated in Chinese Shanxi Black pigs (CSB), while Firmicutes were the most prevalent phylum in Large White pigs (LW) and Iberian pigs (IB), followed by Bacteroidetes in IB and Proteobacteria in LW. At the genus level, Shigella and Lactobacillus were most prevalent in CSB and LW, while Actinobacillus and Sarcina predominated in IB. Differential gene expression together with phylogenetic and functional analyses indicated significant differences in the relative abundance of microbial taxa between different pig breeds. Although many microbial taxa were common to both wild and domestic pigs, significant diversification was observed in bacterial genes that may influence host phenotypic traits. Overall, these findings suggested that both the composition and functional of the microbiota were closely associated with the domestication and resultant genetic and evolutionary changes in the host. The members of the microbial communities were vertically transmitted in pigs, with evidence of co-evolution of both the hosts and their intestinal microbial communities. These results enhance our understanding and appreciation of the complex interactions between intestinal microbes and hosts and highlight the importance of applying this knowledge in agricultural and microbiological research.