Fungi make up a very small portion of the gut microbiome, with a population estimated at around 1 billion out of the 10 trillion microbes residing there.[1] Most fungi in the gut are forms of yeast, such as Candida, Saccharomyces, and Malassezia. The genus Candida includes many species, but the most common is C. albicans. Depending on the sampling site and preparation, yeasts are detected in the feces of 4–97% of healthy people.[2][3]
The fungal microbiome, or mycobiome, of the human gut is poorly understood. It is much lower in abundance, diversity, and stability than the bacterial microbiome but more unique to each individual.[3] Some evidence suggests that most fungi aren’t inhabitants of the gut at all, but rather ingested with food and saliva (from the oral mycobiome).[1]
To further complicate matters, fungi are dimorphic, meaning they can exist in different forms, and can change to a hyphal form, which is less adapted to the human gastrointestinal (GI) tract and potentially more pathogenic (likely to cause disease). Because gene expression differs between the fungal and hyphal forms of the same species, accurate identification and quantification (measuring the number) is challenging.[3]
The role of the mycobiome in human health and disease is largely unknown. Some yeast species, such as C. albicans, exist as pathobionts, which are potential pathogens that remain harmless or even beneficial under normal conditions. Others, such as Saccharomyces boulardii, have known probiotic effects.[4]
Though intestinal colonization is normal and harmless in healthy individuals, certain species of yeast can cause disease in immunocompromised individuals, premature newborns, and cases of surgery or inflammatory bowel disease (IBD) that damage the physical barrier of the intestinal wall.[5][6][7] In these cases, microbes that reside in the gut can easily overcome the cellular or physical defenses of the immune system, escaping the intestines and entering the circulatory system. Yeast may also play a role in the development of antibiotic-associated diarrhea and certain respiratory and skin allergies, but more research is needed to establish causality.[2]