Microbial Biogeography and Core Microbiota of the Rat Digestive Tract

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.

High‐Fat Diet Enriched with Bilberry Modifies Colonic Mucus Dynamics and Restores Marked Alterations of Gut Microbiome in Rats

“…Analysis of bacterial composition by 16S rRNA sequencing showed that HFD treatment reduced α‐diversity of gut microbiome (Figure C), which was normalized when high‐fat feeding was enriched with bilberry ( p < 0.01). The rat microbiota was found dominated by the phyla Firmicutes and Bacteroidetes , consistent with previous descriptions . HFD profoundly increased the Firmicutes / Bacteroidetes ratio in fecal samples (Figure D, p < 0.001), whereas HFD+BB normalized this ratio to the level of LFD and LFD+BB group ( p < 0.001).…”

Six‐Week High‐Fat Diet Alters the Gut Microbiome and Promotes Cecal Inflammation, Endotoxin Production, and Simple Steatosis without Obesity in Male Rats

“…Interestingly, Actinobacteria (subclass: Rothia , Micrococcaceae , Corynebacterium , Corynebacteriaceae , and Actinomyocytes ) and Bacteroidetes (subclass: Bacteroidales ), common phyla associated with a “healthy gut” (Clarke et al, ), were also significantly abundant in the cecal contents of HFD‐fed rats. This is consistent with research that has shown the abundance of Actinobacteria and Bacteroidetes are high in the large intestine of rats (Li et al, ). Moreover, rats in the current study were fed a 60% HFD that contained 6.5% of a dietary fiber called Solka Floc (FCC200).…”

Genetic determinants of gut microbiota composition and bile acid profiles in mice

“…Due to the strong correlative relationship between the QTL, we tested whether there was a direct interaction between bile acids and Turicibacter . Turicibacter inhabits the small intestine where BAs are secreted upon consumption of a meal (73,74). We screened the human isolate Turicibacter sanguinis for deconjugation and transformation activity in vitro by HPLC/MS-MS. We found that T. sanguinis deconjugated ∼96-100% of taurocholic acid and glycochenodeoxycholic acid (Fig 5A) within 24 hours.…”