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Nicole Koropatkin

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Primary Appointment: Microbiology and Immunology
Primary PIBS Dept.: Microbiology and Immunology
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  The microorganisms that reside in our intestinal tract have a profound impact on both our systemic and intestinal health. These organisms are essential for stimulation of the immune system, maturation of the intestinal tract, and provide short chain fatty acids that we absorb as a result of dietary carbohydrate fermentation. The ability to extract carbohydrate nutrition from the intestinal environment is a key driving force shaping the structure of this microbial community. The composition of this community (ie the types and abundance of certain species) dictates its metabolic output, which in turn influences the progression and outcome of various disorders and diseases such as diabetes, obesity, colorectal cancer and inflammatory bowel diseases.

The intestinal ecosystem is one of the most overpopulated and competitive ecosystems on earth, and the microorganisms that have adapted to this niche have evolved strategies to scavenge or degrade dietary and host mucosal carbohydrates that exist in this environment. Many prominent human gut symbionts display a greatly expanded capacity for glycan utilization; while the human genome contains approximately 99 glycoside hydrolases (carbohydrate-degrading enzymes), individual bacteria within the human intestinal tract encode upwards of 250 such enzymes. Despite the multitude of different bacterial species that inhabit the distal intestinal tract, two phyla predominate: the Bacteroidetes and the Firmicutes. These organisms have different fundamental physiologies, can degrade different repertoires of carbohydrates, and have different strategies for capturing glycans from their environment. The goal of my research is to understand the molecular details of how each class of bacteria recognizes and degrades polysaccharides in their environment so that we can develop effective dietary-based therapies for manipulating the structure and composition of the human gut microbial community towards better overall human health, and specifically prevent or treat microbiota-associated diseases.