Spatial heterogeneity of gut microbiota reveals multiple bacterial communities with distinct characteristics

Abstract

We analyzed bacterial communities of six distinct gut sites (the food bolus and mucus layer of the proximal small intestine, cecum and distal large intestine), using wild folivorous flying squirrels. We found significant spatial heterogeneity in composition, diversity, and species abundance distributions (SADs) of gut microbiota, corresponding to physicochemical conditions. High diversity was detected in the mucus layer of small intestine and the food bolus of cecum, followed by the food bolus of large intestine and the mucus layer of cecum, and relatively low diversity in the food bolus of small intestine and the mucus layer of large intestine, likely due to disturbance and resource partitioning. The SADs showed succession-like patterns in the food bolus communities from the proximal to distal gut. Notably, each mucus layer community had a unique pattern different from the food bolus community of the same compartment, with distinct relative abundances of dominant species. In combination with data from other mammalian fecal samples, we concluded that gut microbiota were apparently dynamic in community structure, from low species richness with unequal abundances to high species richness with equal abundances; these findings were interpreted as strong habitat effects on bacterial communities.

Comparative analysis of microbiota along the length of the gastrointestinal tract of two tree squirrel species (Sciurus aberti and S. niger) living in sympatry

“…Despite these limitations, our findings strengthen previous assertions that the high‐fiber diet of Abert's squirrels has shaped the evolution of the GI tract of this species (Murphy & Linhart, ). Moreover, our data corroborate previous research documenting distinct microbial communities in the upper and lower GI tract (Gu et al, ; Kohl, Dearing, et al, ; Lu et al, ; Suzuki & Nachman, ). Although few studies have compared microbial communities along the length of the GI tract in different species, our findings align with previous research suggesting the microbiota of the lower GI tract may be more divergent between species than microbial communities inhabiting the upper GI tract (Kohl, Dearing, et al, ).…”

“…Furthermore, most alpha ‐diversity measurements were higher in samples from the lower GI tract than the upper GI tract. These results parallel findings in several other rodent species where samples from the upper and lower GI tract are clearly delineated by community membership, and lower GI samples typically have higher diversity (Gu et al, ; Kohl, Dearing, et al, ; Lu et al, ; Suzuki & Nachman, ). Consistent with lower overall diversity in the upper GI tract, the core microbiota of upper GI samples were comprised of few species, which also indicates high individual heterogeneity in this community.…”

Age‐related changes in the gut microbiota of the Chinese giant salamander (Andrias davidianus)

“…Within the posterior gastrointestinal tract, the ileum and rectum harbored more complex microbial assemblages (e.g., high alpha diversity). Previous studies have demonstrated that the neutral pH maintained within this region of the digestive tract offers a more conducive internal environment for the maintenance of larger microbial assemblages than those found in highly acidic stomachs (Lu et al, ). The length of the gastrointestinal tract chambers increases significantly following this compartmentalization process.…”

Gut biogeography of the bacterial microbiota

“…Divergence between the mucosal and digesta - associated colonic communities has been observed in several mammals including humans 28 , macaques 29 , mice 30 , cows 31 , and flying squirrels 32 . More specifically, human colon biopsy and swab samples have revealed a distinct mucosal community enriched in Actinobacteria and Proteobacteria compared to the lumen community 33 .…”