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Original article
Fungal microbiota dysbiosis in IBD
  1. Harry Sokol1,2,3,4,
  2. Valentin Leducq1,4,
  3. Hugues Aschard5,
  4. Hang-Phuong Pham6,
  5. Sarah Jegou1,4,
  6. Cecilia Landman3,4,
  7. David Cohen1,2,
  8. Giuseppina Liguori7,
  9. Anne Bourrier3,4,
  10. Isabelle Nion-Larmurier3,4,
  11. Jacques Cosnes3,4,
  12. Philippe Seksik3,4,
  13. Philippe Langella2,4,
  14. David Skurnik8,9,
  15. Mathias L Richard2,4,
  16. Laurent Beaugerie3,4
  1. 1Sorbonne University—UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, UMR 7203, Saint-Antoine Hospital, AP-HP, UPMC Univ Paris 06, Paris, France
  2. 2Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
  3. 3Department of Gastroenterology, Saint Antoine Hospital, Paris, France
  4. 4Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France
  5. 5Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
  6. 6ILTOO Pharma, iPEPS ICM, Hôpital Pitié Salpêtrière, Paris, France
  7. 7Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
  8. 8Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
  9. 9Massachusetts Technology and Analytics, Brookline, Massachusetts, USA
  1. Correspondence to Dr Harry Sokol, Service de Gastroentérologie et Nutrition, Hôpital Saint-Antoine, 184 rue du faubourg St Antoine, Paris 75571, cedex 12, France; harry.sokol{at}


Objective The bacterial intestinal microbiota plays major roles in human physiology and IBDs. Although some data suggest a role of the fungal microbiota in IBD pathogenesis, the available data are scarce. The aim of our study was to characterise the faecal fungal microbiota in patients with IBD.

Design Bacterial and fungal composition of the faecal microbiota of 235 patients with IBD and 38 healthy subjects (HS) was determined using 16S and ITS2 sequencing, respectively. The obtained sequences were analysed using the Qiime pipeline to assess composition and diversity. Bacterial and fungal taxa associated with clinical parameters were identified using multivariate association with linear models. Correlation between bacterial and fungal microbiota was investigated using Spearman's test and distance correlation.

Results We observed that fungal microbiota is skewed in IBD, with an increased Basidiomycota/Ascomycota ratio, a decreased proportion of Saccharomyces cerevisiae and an increased proportion of Candida albicans compared with HS. We also identified disease-specific alterations in diversity, indicating that a Crohn's disease-specific gut environment may favour fungi at the expense of bacteria. The concomitant analysis of bacterial and fungal microbiota showed a dense and homogenous correlation network in HS but a dramatically unbalanced network in IBD, suggesting the existence of disease-specific inter-kingdom alterations.

Conclusions Besides bacterial dysbiosis, our study identifies a distinct fungal microbiota dysbiosis in IBD characterised by alterations in biodiversity and composition. Moreover, we unravel here disease-specific inter-kingdom network alterations in IBD, suggesting that, beyond bacteria, fungi might also play a role in IBD pathogenesis.


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