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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.


Microbial community membership is strongly associated with host individual in the lower GI tract.Tree is based on UPGMA clustering of unweighted UniFrac distance. Different colors show different gut segments (see Fig 3A). Larger node sizes indicate stronger jackknife support. The brackets show the clustering by individuals in the lower GI tract with a jackknife support of 1.0.
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pone.0163720.g004: Microbial community membership is strongly associated with host individual in the lower GI tract.Tree is based on UPGMA clustering of unweighted UniFrac distance. Different colors show different gut segments (see Fig 3A). Larger node sizes indicate stronger jackknife support. The brackets show the clustering by individuals in the lower GI tract with a jackknife support of 1.0.

Mentions: The stronger effect of individuals on microbial variation in the lower GI tract is further supported by UPGMA trees of community membership, where the samples (cecum to feces) from the same individual were each clustered with a jackknife support of 1.0, unlike the pattern seen in samples from the upper GI tract (Fig 4). Although the lower GI tract samples from the same individual did not always form a clade when the taxa were weighted by relative abundances, the UPGMA tree based on community structure also showed a similar trend (Figure D in S1 File). Samples collected from the same geographic site grouped individuals in some cases (Female 1 and Male 1) but not in others (Female 2 and Male 2) (Fig 4). Although the sample size is very small, there seemed to be no obvious associations between geographic site and diet measures in the current dataset (Figure E in S1 File).


Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice
Microbial community membership is strongly associated with host individual in the lower GI tract.Tree is based on UPGMA clustering of unweighted UniFrac distance. Different colors show different gut segments (see Fig 3A). Larger node sizes indicate stronger jackknife support. The brackets show the clustering by individuals in the lower GI tract with a jackknife support of 1.0.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0163720.g004: Microbial community membership is strongly associated with host individual in the lower GI tract.Tree is based on UPGMA clustering of unweighted UniFrac distance. Different colors show different gut segments (see Fig 3A). Larger node sizes indicate stronger jackknife support. The brackets show the clustering by individuals in the lower GI tract with a jackknife support of 1.0.
Mentions: The stronger effect of individuals on microbial variation in the lower GI tract is further supported by UPGMA trees of community membership, where the samples (cecum to feces) from the same individual were each clustered with a jackknife support of 1.0, unlike the pattern seen in samples from the upper GI tract (Fig 4). Although the lower GI tract samples from the same individual did not always form a clade when the taxa were weighted by relative abundances, the UPGMA tree based on community structure also showed a similar trend (Figure D in S1 File). Samples collected from the same geographic site grouped individuals in some cases (Female 1 and Male 1) but not in others (Female 2 and Male 2) (Fig 4). Although the sample size is very small, there seemed to be no obvious associations between geographic site and diet measures in the current dataset (Figure E in S1 File).

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.