Fecal Mycobiota in Patients with Inflammatory Bowel Diseases and Extraintestinal Manifestations

Inflammatory Bowel Disease (IBD), a chronic inflammatory condition affecting the gastrointestinal tract, is associated with extraintestinal manifestations (EIMs) in up to 50% of patients, significantly impacting quality of life and causing serious complications. Reduced gut microbiota bacterial diversity is a characteristic of IBD, and emerging evidence suggests fungal changes, such as an increase in Candida, are also present. However, the mycobiota in patients with IBD, particularly those with EIMs, remains sparsely investigated. Fecal samples from 107 patients with IBD and 43 healthy controls (HC) underwent Internal Transcribed Spacer 2 (ITS2) sequencing using Oxford Nanopore technology. Fecal mycobiota composition differed between patients with IBD and HC, with increased Malassezia in IBD. Patients with IBD and EIMs exhibited lower fungal richness compared to those without EIMs, however did not differ in beta diversity. Patients with IBD and primary sclerosing cholangitis (PSC, n = 7) possessed a distinct mycobiota composition compared with HC and IBD without EIMs, characterized by lower diversity and decreased relative abundance of Saccharomyces cerevisiae and unspecified Dipodascaceae. Overall, the fecal mycobiota of the whole study group (n = 150) exhibits heterogeneity and low richness, primarily shaped by the dominant genus. In conclusion, minor fecal mycobiota differences related to EIMs were observed, particularly in PSCs.