title: 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.
authors.affiliation: State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China.
authors.forename: Dongyao
authors.initials: D
authors.lastname: Li
authors.affiliation: State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China.
authors.forename: Haiqin
authors.initials: H
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China.
authors.forename: Bingyong
authors.initials: B
authors.lastname: Mao
authors.affiliation: State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China.
authors.forename: Qin
authors.initials: Q
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China.
authors.forename: Jianxin
authors.initials: J
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China.
authors.forename: Zhennan
authors.initials: Z
authors.lastname: Gu
authors.affiliation: State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China.
authors.forename: Hao
authors.initials: H
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China.|Departments of Cancer Biology and Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
authors.forename: Yong Q
authors.initials: YQ
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi 214122, P.R. China.|Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, P.R. China.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D000068536:Bacillota / Q000235:genetics / Q000302:isolation & purification; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D041981:Gastrointestinal Tract / Q000382:microbiology*; D007421:Intestine, Small / Q000382:microbiology; D007778:Lactobacillus / Q000235:genetics / Q000302:isolation & purification; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D051381:Rats; D017422:Sequence Analysis, DNA; D013291:Streptococcus
chemical_list: D012336:RNA, Ribosomal, 16S