Mapping the Interplay Between Bacterial and Fungal Microbiota During Health and Intestinal Disease

The mammalian gastrointestinal (GI) tract is compartmentalized and each compartment provides unique environment where nutrients, metabolites and other factors differ depending on the site. Bacteria, viruses and fungi cohabitate in this environment. It is currently unknown whether bacterial and fungal communities are interdependent, and whether some fungi would prefer certain GI sites over the other.

Using deep sequencing technology we surveyed the mycobiomes and the respective bacterial communities in the entire murine GI tract. We found that few abundant fungal genera are ubiquitously present at the intestinal mucosa. Notably, site specificity was also observed and fungal genera such as Fusarium and Candida were always found at specific location. The murine mycobiome structure and diversity were significantly affected by intestinal inflammation and by bacterial dysbiosis. To access whether intestinal pathology affects the mycobiome structure in humans, we analyzed fungal and bacterial communities in a cohort of Ulcerative colitis patients and healthy controls. We conclude that fungal and bacterial communities are interdependent and are both affected by the physiological status of the host. Altogether our results demonstrate specific distribution of fungal genera throughout the GI tract which might be associated with site specific immune responses to fungi.