Gut Mycobiome in Inflammatory Bowel Disease: A Systematic Review of Case-Control Studies.

Background: The bacterial composition of the microbiome in inflammatory bowel disease (IBD) has been the focus of substantial interest. In contrast, the fungal part of the microbiome, the mycobiome, has only rarely been investigated-although anti-Saccharomyces cerevisiae antibodies, an antibody against fungal mannan, have been known for years as a biomarker for Crohn's disease (CD), but not for ulcerative colitis (UC).

Methods: A systematic review of case-control studies on the human gut mycobiome in IBD was conducted using searches in EMBASE and MEDLINE.

Results: Twenty-seven studies, with a total of 1406 IBD patients and 1060 controls were identified. The differences in alpha diversity varied across studies and were related to geography, whereas differences in beta diversity between cases and controls were found in a large majority of the studies. Overall, the results were inconsistent at different taxonomic levels, and the studied populations were heterogeneous, as were the methodological approaches. The most consistent finding was an increase of Candida for both CD and UC and of Malassezia in CD, where it was often linked to a decrease of Saccharomyces.

Conclusions: The mycobiome is altered in IBD, as differences in beta diversity were found between cases and controls consistently. Future studies should carefully standardize every step from sample collection through analysis and data processing, allowing external validation of findings. Inclusion of treatment naïve patients and symptomatic controls could further advance this field.