Integrated analyses of the intestinal microbiome and transcriptome in NingXiang piglets

Abstract

Background NingXiang (NX) pig has been characterized as one of the best Chinese indigenous pig breeds, with high fertility and disease resistance. However, its intestinal gene expression and gut microbial characteristics have not been studied. Results Here, we delineated and compared the profile of intestinal microbiome and transcriptome between NX and Duroc × Landrace × Large white (DLY) piglets by integrating metagenomic and transcriptomic analyses. We found that the abundance of several colonic Bacteroides species (B. fragilis, B. thetaiotaomicron and B. sp_PHL_2737), Prevotella species (P. intermedia, P. dentalis and P. enoeca), Clostridium species (C. scindens, C. butyricum and C. botulinum), Anaerrobutyricum and Lactobacillus_saerimneri are significantly increased in NX piglets than DLY piglets. Additionally, several archaea and fungal species were also dominantly enriched in the colon of NX piglets. Then, we identified some unique colonic bacterial species that may act as characteristics of these two pig breeds. Functional analyses of NX piglets-enriched microbes revealed their dominant function in methane, glycolysis and gluconeogenesis metabolism. Strikingly, the composition and function of the gut microbiota were significantly correlated with growth performance both in NX and DLY piglets. Finally, our mRNA-sequencing revealed the distinct intestinal gene expression pattern between NX and DLY piglets, and NX piglets exhibit improved intestinal barrier function and varied immune features than DLY piglets. Conclusion Together, our study revealed the characteristics of the gut microbiota and intestinal gene expression in NX piglets, providing the potential to explore its mechanisms in disease resistance and gut development.