Role of the human gut mycobiome in healthy individuals

Abstract

The gut microbiome is a complex ecosystem. Interest in this area tends to focus on the gut bacteriome, and the more dynamic gut mycobiome is seldom researched. Some studies have suggested an association between distinct fungal species and disease; however, these studies tend to focus on diseased individuals, rather than characterising gut fungi from a healthy population. Few studies have attempted to determine which fungi are active in the human gut, and which are transient. This thesis explores the diversity of the healthy human gut mycobiome and the role of cultured fungal isolates in the metabolism of short- and medium-chain fatty acids to methyl ketones in the human gut mimicking conditions. Culture-dependent techniques were employed to gain insight into the diversity of fungal species in the healthy human gut. Faecal samples from 21 healthy, non-obese volunteers were cultured under dark, anaerobic and aerobic conditions at body temperature, using Sabouraud dextrose agar. Twenty different fungal species were identified using the Internal Transcribed Spacer (ITS)-based sequencing method. The number of different fungal species cultured from any single individual ranged from zero to six. The most prevalent species were Candida albicans, Candida parapsilosis, and Saccharomyces cerevisiae, which is consistent with the reports by other researchers. Additionally, six fungal species identified in this study do not appear to have been reported previously from a healthy human gut, signifying the importance of baseline studies from the general population. Further, fungal isolates obtained from faecal samples provided by the study volunteers were cultured in broth chemically mimicking human gut conditions with isotopically-labelled short- and medium-chain fatty acids. The volatile organic compounds emitted from the broths were analysed using Solid Phase Micro-Extraction Gas Chromatography-Mass Spectrometry in order to detect metabolite by-products. Results suggest faecal fungi may have distinct metabolic profiles and could inhibit the breakdown of fatty acids in the human gut, although the biotransformation of fatty acids to methyl ketones by the fungal species is yet to be determined. The identification of symbiotic fungi in the human gut has the potential to inform future research and development of obesity preventative action and treatment options via diet or transfer of microbial consortia.