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

View Article: PubMed Central - PubMed

ABSTRACT

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.

No MeSH data available.


Spatial heterogeneity of microbial composition along the gastrointestinal (GI) tract.Ten samples were collected along the GI tract per individual (A). The averages of relative abundance of bacterial families (B), the microbial diversity measures (C), and the first principle component value from predicted gene function categories (D) across the GI tract are shown. The error bars are standard deviations. Asterisks denote unclassified families within the listed order.
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pone.0163720.g001: Spatial heterogeneity of microbial composition along the gastrointestinal (GI) tract.Ten samples were collected along the GI tract per individual (A). The averages of relative abundance of bacterial families (B), the microbial diversity measures (C), and the first principle component value from predicted gene function categories (D) across the GI tract are shown. The error bars are standard deviations. Asterisks denote unclassified families within the listed order.

Mentions: The samples were collected from the following 10 locations along the GI tract under sterile conditions: oral cavity, esophagus, stomach, duodenum, ileum, proximal half of cecum, distal half of cecum, proximal colon, rectum, and fresh feces (Fig 1A). The oral cavity was swabbed using 1 cm2 kimwipe. All tissues were collected immediately after the animal was euthanized. All samples were stored immediately at -80°C.


Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice
Spatial heterogeneity of microbial composition along the gastrointestinal (GI) tract.Ten samples were collected along the GI tract per individual (A). The averages of relative abundance of bacterial families (B), the microbial diversity measures (C), and the first principle component value from predicted gene function categories (D) across the GI tract are shown. The error bars are standard deviations. Asterisks denote unclassified families within the listed order.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036816&req=5

pone.0163720.g001: Spatial heterogeneity of microbial composition along the gastrointestinal (GI) tract.Ten samples were collected along the GI tract per individual (A). The averages of relative abundance of bacterial families (B), the microbial diversity measures (C), and the first principle component value from predicted gene function categories (D) across the GI tract are shown. The error bars are standard deviations. Asterisks denote unclassified families within the listed order.
Mentions: The samples were collected from the following 10 locations along the GI tract under sterile conditions: oral cavity, esophagus, stomach, duodenum, ileum, proximal half of cecum, distal half of cecum, proximal colon, rectum, and fresh feces (Fig 1A). The oral cavity was swabbed using 1 cm2 kimwipe. All tissues were collected immediately after the animal was euthanized. All samples were stored immediately at -80°C.

View Article: PubMed Central - PubMed

ABSTRACT

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.

No MeSH data available.