Journal Article

Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice

Suzuki, Taichi A., Nachman, Michael W.

2016

Overview

There is a growing appreciation of the role of gut microbial communities in host biology. However, the nature of variation in microbial communities among different segments of the gastrointestinal (GI) tract is not well understood. Here, we describe microbial communities from ten different segments of the GI tract (mouth, esophagus, stomach, duodenum, ileum, proximal cecum, distal cecum, colon, rectum, and feces) in wild house mice using 16S rRNA gene amplicon sequencing. We also measured carbon and nitrogen stable isotopic ratios from hair samples of individual mice as a proxy for diet. We identified factors that may explain differences in microbial composition among gut segments, and we tested for differences among individual mice in the composition of the microbiota. Consistent with previous studies, the lower GI tract was characterized by a greater relative abundance of anaerobic bacteria and greater microbial diversity relative to the upper GI tract. The upper and lower GI tracts also differed in the relative abundances of predicted microbial gene functions, including those involved in metabolic pathways. However, when the upper and lower GI tracts were considered separately, gut microbial composition was associated with individual mice. Finally, microbial communities derived from fecal samples were similar to those derived from the lower GI tract of their respective hosts, supporting the utility of fecal sampling for studying the gut microbiota of mice. These results show that while there is substantial heterogeneity among segments of the GI tract, individual hosts play a significant role in structuring microbial communities within particular segments of the GI tract.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Anaerobic bacteria / Anaerobic microorganisms / Bioinformatics / Biology / Biology and Life Sciences / Cecum / Colon / Communities / Computer and Information Sciences / Diet / Digestive system / Digestive tract / Duodenum / Ecology / Esophagus / Feces / Gastrointestinal system / Gastrointestinal tract / Gene sequencing / Heterogeneity / House mouse / Ileum / Intestinal microflora / Laboratories / Medicine and Health Sciences / Metabolic pathways / Mice / Microbial activity / Microbiota / Microbiota (Symbiotic organisms) / Microorganisms / Museums / Natural populations / Phylogenetics / Physical Sciences / Rectum / Relative abundance / Research and Analysis Methods / RNA / rRNA 16S / Segments / Spatial heterogeneity / Stomach / Zoology