Limits...
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.


PCoA plots of microbial community membership (unweighted UniFrac distance).Each dot represents a microbial community from one gut segment in one individual. The first principle component (PC1) mostly accounts for differences between the upper and lower GI tract (A). Within the upper GI tract, microbial communities were grouped by host individual to some degree (B). Within the lower GI tract, microbial communities were strongly grouped by host individual (C).
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5036816&req=5

pone.0163720.g003: PCoA plots of microbial community membership (unweighted UniFrac distance).Each dot represents a microbial community from one gut segment in one individual. The first principle component (PC1) mostly accounts for differences between the upper and lower GI tract (A). Within the upper GI tract, microbial communities were grouped by host individual to some degree (B). Within the lower GI tract, microbial communities were strongly grouped by host individual (C).

Mentions: For the complete GI tract dataset, gut segment best explained the variation in microbial community membership (R2 = 0.31, P < 0.001) (Fig 3A) and structure (R2 = 0.76, P < 0.001) based on ADONIS (Table 1). Analyses using generalized linear models (GLMs) showed a similar pattern (Table B in S1 File). The model excluding gut segment (model 2) had a significantly lower log likelihood score compared to the full model (Likelihood ratio test, P <0.001). In contrast, the model excluding diet (model 3) and the model excluding individual (model 4) were not significantly different from the full model (Table B in S1 File). This indicates that variation in diet and variation among individuals are not contributing to variation in gut microbial composition when the entire GI tract is considered. Given the large differences in microbial communities between the upper and lower GI tract, we next restricted our analyses to datasets consisting of samples from the upper GI tract alone and the lower GI tract alone.


Spatial Heterogeneity of Gut Microbial Composition along the Gastrointestinal Tract in Natural Populations of House Mice
PCoA plots of microbial community membership (unweighted UniFrac distance).Each dot represents a microbial community from one gut segment in one individual. The first principle component (PC1) mostly accounts for differences between the upper and lower GI tract (A). Within the upper GI tract, microbial communities were grouped by host individual to some degree (B). Within the lower GI tract, microbial communities were strongly grouped by host individual (C).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0163720.g003: PCoA plots of microbial community membership (unweighted UniFrac distance).Each dot represents a microbial community from one gut segment in one individual. The first principle component (PC1) mostly accounts for differences between the upper and lower GI tract (A). Within the upper GI tract, microbial communities were grouped by host individual to some degree (B). Within the lower GI tract, microbial communities were strongly grouped by host individual (C).
Mentions: For the complete GI tract dataset, gut segment best explained the variation in microbial community membership (R2 = 0.31, P < 0.001) (Fig 3A) and structure (R2 = 0.76, P < 0.001) based on ADONIS (Table 1). Analyses using generalized linear models (GLMs) showed a similar pattern (Table B in S1 File). The model excluding gut segment (model 2) had a significantly lower log likelihood score compared to the full model (Likelihood ratio test, P <0.001). In contrast, the model excluding diet (model 3) and the model excluding individual (model 4) were not significantly different from the full model (Table B in S1 File). This indicates that variation in diet and variation among individuals are not contributing to variation in gut microbial composition when the entire GI tract is considered. Given the large differences in microbial communities between the upper and lower GI tract, we next restricted our analyses to datasets consisting of samples from the upper GI tract alone and the lower GI tract alone.

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.