Microbial Biogeography and Core Microbiota of the Rat Digestive Tract

Dongyao Li,Haiqin Chen,Yong Q Chen,Jianxin Zhao,Zhennan Gu,Wei Chen,Qin Yang,Hao Zhang,Bingyong Mao

doi:10.1038/srep45840

Abstract

As a long-standing biomedical model, rats have been frequently used in studies exploring the correlations between gastrointestinal (GI) bacterial biota and diseases. In the present study, luminal and mucosal samples taken along the longitudinal axis of the rat digestive tract were subjected to 16S rRNA gene sequencing-based analysis to determine the baseline microbial composition. Results showed that the community diversity increased from the upper to lower GI segments and that the stratification of microbial communities as well as shift of microbial metabolites were driven by biogeographic location. A greater proportion of lactate-producing bacteria (such as Lactobacillus, Turicibacter and Streptococcus) were found in the stomach and small intestine, while anaerobic Lachnospiraceae and Ruminococcaceae, fermenting carbohydrates and plant aromatic compounds, constituted the bulk of the large-intestinal core microbiota where topologically distinct co-occurrence networks were constructed for the adjacent luminal and mucosal compartments. When comparing the GI microbiota from different hosts, we found that the rat microbial biogeography might represent a new reference, distinct from other murine animals. Our study provides the first comprehensive characterization of the rat GI microbiota landscape for the research community, laying the foundation for better understanding and predicting the disease-related alterations in microbial communities.

Highlights

A large variety of symbiotic microorganisms coexist in the mammalian digestive tract, with their number around 10 times greater than the total number of mammalian somatic and germ cells[1]
The relative abundance of Proteobacteria was highest in the cecal mucus and stomach, while the dominant genera within this phylum were completely different in these sampling sites (Fig. 2 and Supplemental Table S4)
The stomachs of the 6 rat subjects shared a small set of microbial community composed of 8 bacterial genera (Fig. 6e), with Turicibacter occupying more than half of this core

Summary

Introduction

A large variety of symbiotic microorganisms coexist in the mammalian digestive tract, with their number around 10 times greater than the total number of mammalian somatic and germ cells[1]. The relative abundance of Proteobacteria was highest in the cecal mucus and stomach, while the dominant genera within this phylum were completely different in these sampling sites (Fig. 2 and Supplemental Table S4).

Results

Conclusion