Integrated analyses of the intestinal microbiome and transcriptome in NingXiang piglets

NingXiang (NX) pig has been recognized as one of the most famous Chinese indigenous breeds due to its characteristics in high fertility and stress resistance. However, the global intestinal gene expression profiling and the feature of gut microorganisms in NX piglets have not been studied. Here, we compared the intestinal microbiome and transcriptome between NX and Duroc × Landrace × Large white (DLY) piglets and found the high enrichment of several colonic Bacteroides, Prevotella and Clostridium species in NX piglets than DLY piglets. Further functional analyses of these microbes revealed their predominant function in methane, glycolysis and gluconeogenesis metabolism. Our mRNA-sequencing data unraveled the distinct colonic gene expression between these two pig breeds. In particular, NX piglets exhibited improved intestinal barrier function and cellulose digestibility, as well as varied immune features than DLY piglets. Finally, by integrating metagenomic and transcriptomic analyses, we further showed that the improved intestinal function in NX piglets may be determined by intestinal genes through modulating the composition of the gut microbes. Together, our study revealed the intestinal characteristics of NX piglets, providing their potential application in improving breeding strategies and developing dietary interventions.