Fungi participate in the dysbiosis of gut microbiota in patients with primary sclerosing cholangitis

<jats:sec> <jats:title>Objective</jats:title> <jats:p>Patients with primary sclerosing cholangitis (PSC) were previously shown to display a bacterial gut dysbiosis but fungal microbiota has never been examined in these patients. The aim of this study was to assess the fungal gut microbiota in patients with PSC.</jats:p> </jats:sec> <jats:sec> <jats:title>Design</jats:title> <jats:p>We analysed the faecal microbiota of patients with PSC and concomitant IBD (n=27), patients with PSC and no IBD (n=22), patients with IBD and no PSC (n=33) and healthy subjects (n=30). Bacterial and fungal composition of the faecal microbiota was determined using 16S and ITS2 sequencing, respectively.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p> We found that patients with PSC harboured bacterial dysbiosis characterised by a decreased biodiversity, an altered composition and a decreased correlation network density. These alterations of the microbiota were associated with PSC, independently of IBD status. For the first time, we showed that patients with PSC displayed a fungal gut dysbiosis, characterised by a relative increase in biodiversity and an altered composition. Notably, we observed an increased proportion of <jats:italic>Exophiala</jats:italic> and a decreased proportion of <jats:italic>Saccharomyces cerevisiae</jats:italic> . Compared with patients with IBD and healthy subjects, the gut microbiota of patients with PSC exhibited a strong disruption in bacteria-fungi correlation network, suggesting an alteration in the interkingdom crosstalk. </jats:p> </jats:sec> <jats:sec> <jats:title>Conclusion</jats:title> <jats:p>This study demonstrates that bacteria and fungi contribute to gut dysbiosis in PSC.</jats:p> </jats:sec>