Mycobiota of the human gastrointestinal tract

Fungi (Mycota) that colonize the human digestive tract are collectively referred to as gastrointestinal mycobiota. The most common method of fungi identification is based on the culture of a clinical sample with subsequent classic phenotypic identification detailed by biochemical and/or molecular (e.g. sequencing of ITS regions of rDNA) tests in some cases. Additionally, the culture-independent identification is gaining popularity, especially in scientific research. The composition of the human mycobiota significantly differs across the digestive tract. In the oral cavity of healthy people, Candida, Cladosporium, Auerobasidium, and Aspergillus are most often identified fungi genera; however, in recent studies the presence of Malassezia spp. has been also emphasized. In the case of the lower gastrointestinal tract, Candida, Saccharomyces, Penicillium, Aspergillus, Cryptococcus, Malassezia, Cladosporium, Galactomyces, Debaryomyces, and Trichosporon genera are most often reported. This paper summarizes the factors that are associated with the composition of mycobiota in both children (age, type of delivery, breastfeeding) and adults (age, gender, diet, saliva flow rate and composition). Changes in the composition of mycobiota also occur in pathological conditions, including both gastrointestinal diseases (Crohn’s disease, oral lichen planus) and metabolic diseases (diabetes, obesity). Additionally, this paper summarizes the already known, putative interactions between fungi and bacteria colonizing the human digestive tract.