Characterizing bacterial and fungal communities along the longitudinal axis of the intestine in cynomolgus monkeys

Abstract

ABSTRACT The gut microbiota develops specialized local communities along the gastrointestinal (GI) tract of the host. Among these microbes, intestinal bacteria and fungi interact closely with the host and play vital roles in their health. However, the gut biogeography of bacteria and fungi has rarely been studied simultaneously, and their correlations have not been reported. In this study, we collected the intestinal luminal contents from different gastrointestinal regions (the ileum, caecum, and colon) of wild-type female cynomolgus monkeys and performed 16S and 18S rRNA gene sequencing to determine the gut biogeography of bacterial and fungal communities. The richness and diversity of bacteria and fungi increased gradually from the small to the large intestine. The bacterial and fungal composition of ileum differed significantly from that of the colon. Specifically, Bacteroidia and Spirochaetia were abundant in the caecum and colon, while Actinobacteria and Cyanobacteria were enriched in the ileum. As for fungal taxa, the genera Aspergillus , Wallemia , and Cryptococcus_f_Tremellaceae were enriched in the colon, while the genus Fusarium was abundant in the caecum. Consequently, the bacterial and fungal functions of the ileum differed from those of the caecum and colon. Notably, we characterized the correlations between intestinal bacteria and fungi at different gastrointestinal regions of cynomolgus monkeys using Spearman correlation analysis. In summary, our results contribute to a more comprehensive understanding of the composition and function of intestinal bacteria and fungi in non-human primates (NHPs) and reveal their correlations along the longitudinal axis of the intestine. IMPORTANCE Gut microbiota varies along the gastrointestinal (GI) tract and exerts profound influences on the host’s physiology, immunity, and nutrition. Given that gut microbes interact with the host closely and the gastrointestinal function differed from the small to the large intestine, it is essential to characterize the gut biogeography of the microbial community. Here, we focused on intestinal bacteria and fungi in cynomolgus monkeys and determined their spatial distribution along the GI tract by performing 16S and 18S rRNA gene sequencing. The composition and function of bacterial and fungal communities differed significantly at different biogeographic sites of the intestine, and the site-specific correlations between intestinal bacteria and fungi were revealed. Thus, our studies characterized the gut biogeography of bacteria and fungi in NHPs and revealed their site-specific correlations along the GI tract.