Ecological niche assignment in the gut microbiome on an ecosystem-level scale

PROJECT SUMMARY The gut microbiome comprises hundreds of microbial species that inhabit the human gastrointestinal tract and impact host health in a myriad of ways. Diverse microbes coexist in the gut by specializing in distinct colonization strategies which collectively give rise to a complex microbial ecosystem with emergent functional properties. Despite the critical nature of the specialized ecological roles in explaining the composition and function of the microbiome, colonization strategies employed by the majority of gut microbes remains poorly defined. The proposed research will take two approaches to broadly assign colonization strategies to diverse gut microbes. A first part of the proposed project will employ comparative genome analyses to determine the distribution of established microbial functions across the gut microbiome and to guide the discovery of novel colonization strategies. A second part of the project will utilize unbiased growth assays to identify members of the microbial community adapted for diverse colonization strategies. The molecular basis of identified colonization strategies will be further interrogated through the application of genetic and biochemical approaches. By assigning ecological context to diverse members of the gut microbiota, these studies will advance a basic understanding of the gut ecosystem that could benefit the development of diagnostic and therapeutic microbiome-based technologies.