O-013 Characterization of Gut Fungal Communities and their Role in Colitis

Changes in the composition of gut bacterial communities have been associated with intestinal inflammation and obesity. Recent studies have begun to note that a fraction of mucosa-associated microorganisms are not bacterial and a few mycobiome studies have characterized the fungal communities at different mucosal surfaces of the body and the skin. Because intestinal mucosal tissue is often hard to access, we and others have previously characterized the gut mycobiome in feces. However what fungi populate different gut mucosal surfaces and how immunity to them might play a role in inflammatory disease is currently unknown. Commensal fungi were visualized and quantified by staining with Dectin-1 probe followed by microscopy and FACS analysis, and additionally detected in fecal samples by qPCR for fungal 18S rDNA. To define the mouse intestinal fungal microbiome (the mycobiome), we isolated DNA from murine feces and mucosa, amplified the internal transcribed spacer region (ITS1-2) of fungal rDNA, and performed high-throughput sequencing. To induce colitis, wild type and Dectin-1−/− mice were treated with DSS. To determine whether the altered fungal burden during colitis contributes to disease severity, we suppressed fungal growth with fluconazole, a specific antifungal drug. We found that different sites of the murine gastrointestinal tract (GI) are all colonized with diverse fungal communities. More abundant fungal communities were found in the mouth and in the stomach, whereas less fungi colonize internal sites such as the small intestine and the stomach. The most abundant member of the gut mycobiome belonged to a few fungal genera, whereas 2% of the mycobiome harbored the most diverse fungal community. We found that Candida is present at all sites of the murine GI tract and is often the most abundant genera found in colonic mucosa. Consistently we found that mice lacking Dectin-1, recognizing fungal cell wall β-glucan, are more susceptible to experimental colitis characterized by increased infiltration of Th17 and Th1 cells in the colon. This pathology was associated with Candida invasion of the colon of Dectin-1−/− mice and was ameliorated upon treatment with an anti-fungal drug fluconazole. We found that a specific variant of the gene for Dectin-1 is strongly associated with a severe form of ulcerative colitis in humans. Using deep sequencing technology we surveyed the mycobiomes of the entire murine gastrointestinal tract, as well as other mucosal sites throughout the body. Our findings reveal that a few abundant fungal genera are present throughout the GI tract and Candida in particular contributes to colitis in mice lacking Dectin-1. In contrast, highly diverse fungal community makes a small fraction of the gut mycobiome. Our results show specific distribution of certain fungal genera which might be associated with site specific immune responses to fungi and might promote inflammatory conditions at those sites as a result of aberrant immunity to fungi. A deeper understanding of the mechanisms by which fungi stimulate inflammatory immune responses in the gut may lead to better therapies for IBD in a population of individuals with polymorphism in gene coding for Dectin-1.