Summary The fungus Candida albicans is a ubiquitous pathobiont of the human gastrointestinal tract (GIT). It is also the most common cause of life-threatening fungal infections in the United States and other developed countries. These infections generally arise as a result of dissemination from the GIT; therefore, the biology of this species in its native niche is relevant to the initiation of disease, yet it has been neglected in molecular, immunological, and genomic studies. To understand this important biology, it is paramount to diversify the spectrum of C. albicans strains that are studied by including isolates derived from the human GIT. To date, GIT isolates represent a tiny minority of publicly available C. albicans strains and genome sequences. We hypothesize that there is a wide diversity of C. albicans strains in the human GIT and that these strains engage in a broad spectrum of interactions with the intestinal epithelium reflecting differences in their ability to attach to, and invade, the intestinal mucosa and to eschew local host defenses. The research proposed herein will define the genomic diversity of this fungal species in the human GIT, illuminate the range of responses that distinct C. albicans isolates elicit in the intestinal epithelium, and identify Candida loci associated with fitness of the fungus in the GIT. The project builds upon world-class sequencing, computational, and experimental capabilities at Baylor College of Medicine and The University of Texas Health Science Center at Houston, leverages the largest medical center in the world for human GIT-derived Candida isolates, and takes advantage of state-of-the-art human organoid technology as well as mouse models of GIT colonization to probe the diversity of this medically important fungus. Identifying fungal genetic markers associated with dissemination from the GIT will have profound implications for the management of patients at particular risk for candidiasis.