The microbial community composition of the human intestine is receiving a lot of attention and now is fairly well characterized. Yet the functional roles of individual microorganisms in the intestinal ecosystem and the dynamic interactions of its community members remain largely uncharacterized, including those interactions that drive competition for resources (i.e., the food web) and those that create conditions favorable for success of the community (e.g., anaerobiosis). Experiments that address these issues cannot be done in humans;they require an animal model that allows testing of the basic ecological principles that underpin the human microbiome. For over a decade, we have used the streptomycin-treated mouse model of intestinal colonization to characterize the functional role of Escherichia coli in the intestine. We learned that different E. coli strains execute different nutritional programs, allowing them to co-colonize the gut. Importantly, we learned that E. coli respires oxygen and thereby lowers the oxygen tension of the cecum, creating conditions that favor growth of the predominantly anaerobic microbial community. Therefore, we hypothesize that E. coli lives in symbiotic relationship with the anaerobes. Since anaerobes are sensitive to oxygen, we predict that the community composition of the intestine depends at least in part on the oxygen scavenging function contributed by E. coli. Since E. coli is unable to hydrolyze complex polysaccharides, which are the primary nutrient source in the gut, and because E. coli can grow only on the degradation products, we predict that anaerobic polysaccharide degradation releases simple sugars that cross-feed E. coli. And, since different E. coli strains execute different nutritional programs in the intestine, we predict that each E. coli strain will interact with distinct subpopulations of the microbial community. Here we outline a Research Plan designed to test these predictions.
In Aim 1 we will use high-throughput sequencing of 16S rRNA gene tags and molecular phylogenetic analysis to examine the microbial composition of the streptomycin-treated mouse intestine as it is affected by E. coli colonization. Using isogenic E. coli strains that can and cannot respire oxygen, we will test the prediction that oxygen scavenging in the intestine affects the composition of the anaerobic microbial community. In addition, we will test the prediction that colonization of the intestine with different strains of E. coli, each of which consumes different nutrients in the intestine, will influence the microbial community composition.
In Aim 2 we will test the prediction that different E. coli strains physically associate with different members of the microbial community by using 16S analysis of microbes sampled from the intestine by laser capture micro-dissection. Furthermore, we will characterize nutrient flow between E. coli and individual members of the intestinal microbial community in co-cultures.
In Aim 3 we wil determine whether surface structures, including O-polysaccharides, flagella, and capsule, target E. coli to specific microhabitats where they could interact with different members of the microbiota. Thus we will characterize the interactions of E. coli with the microbial community in the intestine.
We will use a mouse model of intestinal colonization to explore and characterize the symbiotic relationship in which we hypothesize that E. coli generates anaerobic conditions to stimulate growth of anaerobes that degrade complex polysaccharides, which in turn release simple sugars that cross-feed E. coli. We will use the tools of genomics to determine the microbial community composition as it is impacted by scavenging of oxygen by E. coli and, in addition, we will couple the community analysis with sophisticated microscopic techniques to determine the specific organisms that E. coli physically associates with in the intestine and we will determine nutrient flow between these organisms in co-culture experiments. Our research represents an unprecedented step forward in the effort to characterize the functional roles of individual microbes in the human microbiome.
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