Gut mycobiome in IBD

December 16, 2025

Issue 24

Clinical Question

Does the gut mycobiome differ between patients with inflammatory bowel disease and controls?

Editor’s Bottom Line

Although the mycobiome of patients with IBD differs from that of healthy controls, it remains unclear whether this is a cause or a consequence of intestinal inflammation and its therapy.

Reference

Füchtbauer JD, Brovkina O, Sivickis K, et al. Gut Mycobiome in Inflammatory Bowel Disease: A Systematic Review of Case-Control Studies. Inflamm Bowel Dis. 2025 Nov 1;31(11):3213–24; https://pmc.ncbi.nlm.nih.gov

Synopsis

This systematic review evaluated the gut mycobiome in IBD by examining 27 case-control studies with 1,406 IBD patients (816 Crohn’s disease [CD], 590 ulcerative colitis [UC]) and 1,060 controls included in EMBASE and MEDLINE between database inception and June 2024. The studies used a variety of sequencing technologies, including, most commonly, ITS sequencing, 18S sequencing, culture with qPCR, or metagenomics. Twenty-one studies analyzed stool samples while the remainder studied biopsies or colonic lavage. The patient populations were heterogeneous, with a range in disease activity and use of a variety of medications.

Alpha diversity (fungal diversity within a sample) showed inconsistent results across studies. In CD, eight of 10 studies found no differences compared to non-IBD controls, while two studies reported decreases in diversity. In UC, five studies found no differences, two found decreases, and one found an increase in diversity compared to non-IBD controls. Geographic location was strongly associated with alpha diversity findings.

Beta diversity (dissimilarity between communities) was more consistent. In CD, seven of 11 studies demonstrated significant differences between patients and controls. In UC, five of eight studies showed significant differences. The type of specimen and country of origin were strongly associated with beta diversity findings.

At the genus level, the most consistent finding in CD was increased Candida (four studies; 1.8 to 20-fold range) and Malassezia (five studies; 1.1 to 20.4-fold range), with decreased Saccharomyces (three studies, 0.7 to 0.9-fold range). In UC, Candida was increased in three studies (1.2 to 3.6-fold range) and Alternaria in two studies. However, results were often contradictory, with some genera showing increases in some studies and decreases in others.

Quality assessment revealed that 11 of 29 studies did not adequately report on the representativeness of cases, and baseline characteristics were inadequately reported or imbalanced in more than half of studies.

 

Details

Study Design: Systematic review of case-control studies
Funding: National Odense University Hospital PhD Fund, NordForsk, Innovation Fund Denmark, Research Council of Norway, Deutsche Forschungsgemeinschaft
Allocation: Not applicable
Setting: Multicenter
Level of Evidence: 1a