title: Fungal microbiota dysbiosis in IBD.
abstract: 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.
  
  
  
  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.
  
  
  
  We observed that fungal microbiota is skewed in IBD, with an increased Basidiomycota/Ascomycota ratio, a decreased proportion ofSaccharomyces cerevisiaeand an increased proportion ofCandida albicanscompared 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.
  
  
  
  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.
authors: Sorbonne 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.|Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.|Department of Gastroenterology, Saint Antoine Hospital, Paris, France.|Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
authors: Harry
authors: H
authors: Sokol
authors: Sorbonne 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.|Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
authors: Valentin
authors: V
authors: Leducq
authors: Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA.
authors: Hugues
authors: H
authors: Aschard
authors: ILTOO Pharma, iPEPS ICM, Hôpital Pitié Salpêtrière, Paris, France.
authors: Hang-Phuong
authors: HP
authors: Pham
authors: Sorbonne 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.|Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
authors: Sarah
authors: S
authors: Jegou
authors: Department of Gastroenterology, Saint Antoine Hospital, Paris, France.|Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
authors: Cecilia
authors: C
authors: Landman
authors: Sorbonne 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.|Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.
authors: David
authors: D
authors: Cohen
authors: Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
authors: Giuseppina
authors: G
authors: Liguori
authors: Department of Gastroenterology, Saint Antoine Hospital, Paris, France.|Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
authors: Anne
authors: A
authors: Bourrier
authors: Department of Gastroenterology, Saint Antoine Hospital, Paris, France.|Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
authors: Isabelle
authors: I
authors: Nion-Larmurier
authors: Department of Gastroenterology, Saint Antoine Hospital, Paris, France.|Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
authors: Jacques
authors: J
authors: Cosnes
authors: Department of Gastroenterology, Saint Antoine Hospital, Paris, France.|Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
authors: Philippe
authors: P
authors: Seksik
authors: Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.|Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
authors: Philippe
authors: P
authors: Langella
authors: Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.|Massachusetts Technology and Analytics, Brookline, Massachusetts, USA.
authors: David
authors: D
authors: Skurnik
authors: Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.|Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
authors: Mathias L
authors: ML
authors: Richard
authors: Department of Gastroenterology, Saint Antoine Hospital, Paris, France.|Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Paris, France.
authors: Laurent
authors: L
authors: Beaugerie
mesh_terms: D001203:Ascomycota / Q000302:isolation & purification*; D001419:Bacteria / Q000302:isolation & purification; D001487:Basidiomycota / Q000302:isolation & purification*; D002176:Candida albicans / Q000302:isolation & purification*; D016022:Case-Control Studies; D003093:Colitis, Ulcerative / Q000235:genetics / Q000382:microbiology*; D003424:Crohn Disease / Q000235:genetics / Q000382:microbiology*; D064806:Dysbiosis / Q000382:microbiology*; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012336:RNA, Ribosomal, 16S / Q000032:analysis*; D012441:Saccharomyces cerevisiae / Q000302:isolation & purification
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: INFLAMMATORY BOWEL DISEASE