Microbiome Research

David Underhill, PhD, and his laboratory group have discovered that fungi are among the microbes normally found in the gastrointestinal tract and on the skin surface. Fungi play a role in inflammation and inflammatory bowel disease. He has shown people with Crohn's disease have increased amounts of several fungi in their intestinal mucosa. Dr. Underhill's team is working to determine how the interaction between these fungi and the immune system contributes to the inflammatory response. Innate immune response to the microbiome.

Jonathan Braun, MD, PhD, and team study the biology of mucosal-microbiome interaction and its impact on mucosal inflammation and cancer. The focus of his research is to define how host genetics and mucosal microbial ecology shape intestinal immunoregulation, inflammatory bowel pathogenesis and intestinal carcinogenesis. This work is based in both human and murine models using innovative 'omic' and bioinformatic-based approaches (functional immune assessment, tissue proteomics, genome-wide genetics, and microbiome metagenomics and metabolomics).

Projects underway include metaboproteomic assessment of microbiome ecology, the development of an innovative tool to impute intestinal microbiome composition and function from the plasma metabolome, and studies of epithelial autoimmunity in IBD pathogenesis.

Suzanne Devkota, PhD, and her laboratory group are interested in the effect of diet on microbial composition and inflammation. She has shown that nutrients are mediators of health through interaction with the gut microbiome. She has also shown a direct mechanism between an opportunistic microbe and Th-1 mediated colitis. Dr. Devkota's lab also focuses on intestinal permeability and bacterial translocation. They have discovered that creeping fat provides a mechanism for transporting bacteria into the intestine.

Ivan Vujkovic-Cvijin, PhD, and his team seek to identify gut microbes that spur harmful inflammation in IBD as well as other human inflammatory diseases. Vujkovic-Cvijin has identified gut microbial signatures that may contribute to HIV-associated inflammatory diseases, to immunotherapy responses in the setting of cancer, and various monogenic immune diseases. Vujkovic-Cvijin's Lab is actively seeking to uncover methods by which to modulate the human gut microbiota for therapeutic benefit.