Gut Mycobiome: Latest Findings and Current Knowledge Regarding Its Significance in Human Health and Disease

Abstract

The gut mycobiome, the fungal component of the gut microbiota, plays a crucial role in health and disease. Although fungi represent a small fraction of the gut ecosystem, they influence immune responses, gut homeostasis, and disease progression. The mycobiome's composition varies with age, diet, and host factors, and its imbalance has been linked to conditions such as inflammatory bowel disease (IBD) and metabolic disorders. Advances in sequencing have expanded our understanding of gut fungi, but challenges remain due to methodological limitations and high variability between individuals. Emerging therapeutic strategies, including antifungals, probiotics, fecal microbiota transplantation, and dietary interventions, show promise but require further study. This review highlights recent discoveries on the gut mycobiome, its interactions with bacteria, its role in disease, and potential clinical applications. A deeper understanding of fungal contributions to gut health will help develop targeted microbiome-based therapies.

Keywords: dysbiosis; fungi; gut microbiota; gut mycobiome.

Figure 1

A balanced microbial environment and dysbiosis influence the interactions between bacteria and fungi within the gut microbiota. Under normal conditions, these microorganisms engage in cooperative relationships that support gut health. However, in dysbiosis, their interactions can become antagonistic, potentially disrupting immune regulation and contributing to disease development and progression. Created with Biorender.com (accessed on 16 February 2025).

Figure 2

Updated dynamics of early-life gut fungal colonization. This figure illustrates the revised pattern of gut fungal colonization in infants, integrating longitudinal data from the recent studies. The updated data indicate that initial colonization occurs more rapidly than previously reported, with significant shifts in fungal diversity observed following dietary transitions and environmental exposures during the first year of life. These findings redefine our understanding of the establishment and maturation of the gut mycobiome compared to earlier studies. Created with Biorender.com (accessed on 20 April 2025).

Figure 3

The relationship between the gut mycobiome and the main affected organs, highlighting the gut–brain, gut–lung, gut–liver, gut–kidney, and gut–pancreas axes. At the center of the image, the intestine is depicted as the primary reservoir of fungi, including species such as Candida, Malassezia, and Saccharomyces. Arrows indicate interactions between the gut and different organs. Created with Biorender.com (accessed on 20 April 2025).

Figure 4

Different methods for calibrating the gut mycobiome. Most approaches target infections caused by C. albicans, while some studies suggest that certain methods are effective against both C. albicans and other fungal species or exclusively against non-Candida fungi. Created with Biorender.com (accessed on 1 March 2025). CDI = Clostridium difficile infection; IBD = inflammatory bowel disease.