Metabolic And Spatial Competition For Dietary Fiber Between Commensal And Pathogenic Gut Microbes

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PROJECT SUMMARY The microbial community that resides in the human intestine profoundly influences host metabolism, immune homeostasis, and the outcome of enteric infections. Dietary fiber is a promising tool for manipulating the gut microbiota to promote organisms that provide beneficial functions to the host. Though, it is currently difficult to predict which gut bacterial species will respond to fiber-based dietary interventions, interspecies competition makes it possible to precisely target beneficial species of interest using a particular fiber type. Bacterial species with pathogenic potential, such as uropathogenic E. coli (UPEC), are present in the gut microbiota of asymptomatic individuals and these species have the capacity to expand in response to fiber. Exploiting competition between pathogens and their non-pathogenic relatives to reduce pathogen load in the gut will require detailed knowledge of the genes underlying these species’ overlapping nutrient harvesting strategies, including genes mediating adhesion to nutrient-rich diet-derived particles. The following aims will test the hypotheses that (i) expansion of commensal E. coli in the gut in response to dietary fiber can reduce the fitness of pathogenic E. coli, and that (ii) commensal and pathogenic bacterial species compete for adhesion to the same diet-derived surfaces in the intestinal lumen. In Aim1, I will identify dietary fibers that selectively increase the abundance of commensal E. coli in vivo. Preliminary studies have identified a widely consumed fiber that increases the abundance of commensal E. coli in a model microbial community. I will define the mechanism of action by colonizing these mice with an E. coli transposon mutant library and performing community-wide quantitative proteomics and forward genetic analyses. To model a gut reservoir of pathogenic E. coli, I will substitute UPEC for commensal E. coli in this community, and then administer commensal E. coli with or without fiber to identify interventions that reduce UPEC abundance. In Aim2, I will determine whether commensal and pathogenic microbes adhere to the same surfaces in the gut. A multiplex adhesion assay, using glycan-coated magnetic beads, identified dietary fibers that support adhesion of both UPEC and commensal E. coli. I will validate adhesive interactions in vivo by administering these particles to mice and measuring bacterial localization around beads in situ. Application of the bead-based adhesion assay to cecal microbiota of mice colonized with uncultured human fecal samples will identify additional E. coli strains, as well as uncharacterized gut microbes, that adhere to dietary glycans in vivo. This research will (i) provide insights into the ecological relationships that determine the outcome of dietary interventions designed to promote beneficial species at the expense of known pathogens and ii) provide candidate dietary components, bacterial strains, and microbial genetic targets for manipulating these relationships to enhance human health.