Regional Diversity of the Gastrointestinal Microbiome

Abstract

The role of gut microbes in health and disease has often been surmised from stool, which is easily sampled and rich in microbial diversity, density, and abundance. Microbial analyses of stool have been accepted as measures to determine the relationship of gut microbiomes with host health and disease, based on the belief that it represents all microbial populations throughout the gut. However, functional heterogeneity of each gastrointestinal tract (GIT) segment gives rise to regional differences in gut microbial populations. Herein, we summarize the literature regarding the microbial landscape along the rostral to caudal, i.e., horizontal mouth to anus, axis of the GIT. We aim to identify gaps in the literature, particularly regarding small intestinal microbiota abundance and diversity, highlight the importance of regional microbiota on host health and disease, as well as discuss opportunities to advance this line of research.

Figure 1.. Representative host and microbial factors and community membership along the rostral to caudal (horizontal) axis of the GI tract.

Different regions of the GI tract perform unique functions in regards to macro- and micronutrient digestion and absorption. These unique features along with a number of host derived factors, such as epithelial cell types and surfaces, mucus thickness, motility and contractility, pH, oxygen tension, and flow rate drive diversity and abundance of gut microbes from mouth to anus. Additionally, each area of the intestine secretes unique immune factors that can interact with the intestinal microbiota, shaping the community membership in a region-specific manner. Several host factors secreted into the intestine, such as primary bile acids (BAs), are important for digestion, but can also elicit direct antimicrobial effects i.e., primary vs. secondary BAs. Other regions of the intestine, due to pH and oxygen tension support microbial fermentation of complex fiber sources, resulting in an increasing abundance of short chain fatty acids in the distal portions of the GI tract that not only impact local epithelial cells, but further influence the regional microbial communities and distal tissue sites important for health and disease.