{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T16:15:52Z","timestamp":1792080952560,"version":"4.4.0"},"reference-count":71,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,9,27]],"date-time":"2022-09-27T00:00:00Z","timestamp":1664236800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Med."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Fungal microbiota's involvement in the pathogenesis of Crohn's disease (CD) is incompletely understood. The terminal ileum is a predilection site both for primary involvement and recurrences of CD. We, therefore, assessed the mucosa-associated mycobiota in the inflamed and non-inflamed ileum in patients with CD.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>The mucosa-associated mycobiota was assessed by ITS2 sequencing in a total of 168 biopsies sampled 5 and 15 cm proximal of the ileocecal valve or ileocolic anastomosis in 44 CD patients and 40 healthy controls (HC). CD patients with terminal ileitis, with endoscopic inflammation at 5 cm and normal mucosa at 15 cm and no history of upper CD involvement, were analyzed separately. The need for additional CD treatment the year following biopsy collection was recorded.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>CD patients had reduced mycobiota evenness, increased Basidiomycota\/Ascomycota ratio, and reduced abundance of Chytridiomycota compared to HC. The mycobiota of CD patients were characterized by an expansion of <jats:italic>Malassezia<\/jats:italic> and a depletion of <jats:italic>Saccharomyces<\/jats:italic>, along with increased abundances of <jats:italic>Candida albicans<\/jats:italic> and <jats:italic>Malassezia restricta<\/jats:italic>. <jats:italic>Malassezia<\/jats:italic> was associated with the need for treatment escalation during follow-up. Current anti-TNF treatment was associated with lower abundances of Basidiomycota. The alpha diversity of the inflamed and proximal non-inflamed mucosa within the same patients was similar. However, the inflamed mucosa had a more dysbiotic composition with increased abundances of <jats:italic>Candida sake<\/jats:italic> and reduced abundances of <jats:italic>Exophiala equina<\/jats:italic> and <jats:italic>Debaryomyces hansenii<\/jats:italic>.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The ileal mucosa-associated mycobiota in CD patients is altered compared to HC. The mycobiota in the inflamed and proximal non-inflamed ileum within the same patients harbor structural differences which may play a role in the CD pathogenesis. Increased abundance of <jats:italic>Malassezia<\/jats:italic> was associated with an unfavorable disease course.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fmed.2022.868812","type":"journal-article","created":{"date-parts":[[2022,9,27]],"date-time":"2022-09-27T05:34:18Z","timestamp":1664256858000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":24,"title":["The ileal fungal microbiota is altered in Crohn's disease and is associated with the disease course"],"prefix":"10.3389","volume":"9","author":[{"given":"Maya","family":"Olaisen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mathias L.","family":"Richard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vidar","family":"Beisv\u00e5g","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atle van Beelen","family":"Granlund","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elin S.","family":"R\u00f8yset","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier","family":"Ru\u00e9","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom Christian","family":"Martinsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arne Kristian","family":"Sandvik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harry","family":"Sokol","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reidar","family":"Fossmark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2022,9,27]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1741","DOI":"10.1016\/S0140-6736(16)31711-1","article-title":"Crohn's Disease","volume":"389","author":"Torres","year":"2017","journal-title":"Lancet."},{"key":"B2","doi-asserted-by":"publisher","first-page":"771","DOI":"10.1016\/0140-6736(91)90663-A","article-title":"Effect of faecal stream diversion on recurrence of crohn's disease in the neoterminal ileum","volume":"338","author":"Rutgeerts","year":"1991","journal-title":"Lancet."},{"key":"B3","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1016\/S0016-5085(98)70476-7","article-title":"Early lesions of recurrent crohn's disease caused by infusion of intestinal contents in excluded ileum","volume":"114","author":"D'Haens","year":"1998","journal-title":"Gastroenterology."},{"key":"B4","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1016\/j.surge.2015.04.002","article-title":"Post-operative recurrence in crohn's disease. 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