title: Fungal Dysbiosis in Mucosa-associated Microbiota of Crohn's Disease Patients.
abstract: OBJECTIVE
  Gut microbiota is involved in many physiological functions and its imbalance is associated with several diseases, particularly with inflammatory bowel diseases. Mucosa-associated microbiota could have a key role in induction of host immunity and in inflammatory process. Although the role of fungi has been suggested in inflammatory disease pathogenesis, the fungal microbiota has not yet been deeply explored. Here we analysed the bacterial and fungal composition of the mucosa-associated microbiota of Crohn's disease patients and healthy subjects.
  
  
  METHODS
  Our prospective, observational study evaluated bacterial and fungal composition of mucosa-associated microbiota of 23 Crohn's disease patients [16 in flare, 7 in remission] and 10 healthy subjects, using 16S [MiSeq] and ITS2 [pyrosequencing] sequencing, respectively. Global fungal load was assessed by real time quantitative polymerase chain reaction.
  
  
  RESULTS
  Bacterial microbiota in Crohn's disease patients was characterised by a restriction in biodiversity. with an increase of Proteobacteria and Fusobacteria. Global fungus load was significantly increased in Crohn's disease flare compared with healthy subjects [p < 0.05]. In both groups, the colonic mucosa-associated fungal microbiota was dominated by Basidiomycota and Ascomycota phyla. Cystofilobasidiaceae family and Candida glabrata species were overrepresented in Crohn's disease. Saccharomyces cerevisiae and Filobasidium uniguttulatum species were associated with non-inflamed mucosa, whereas Xylariales order was associated with inflamed mucosa.
  
  
  CONCLUSIONS
  Our study confirms the alteration of the bacterial microbiota and is the first demonstration of the existence of an altered fungal microbiota in Crohn's disease patients, suggesting that fungi may play a role in pathogenesis.
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
authors.forename: Giuseppina
authors.initials: G
authors.lastname: Liguori
authors.affiliation: Equipe Avenir Gut Microbiota and Immunity, U1157/UMR7203, Faculté de Médecine Saint-Antoine, Université Pierre et Marie Curie, Paris, France Inflammation-Immunopathology-Biotherapy Département, Hospitalo-Universitaire, Paris, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Lamas
authors.affiliation: Inflammation-Immunopathology-Biotherapy Département, Hospitalo-Universitaire, Paris, France INRA, UMR1319 MICALIS, Jouy en Josas, France AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France.
authors.forename: Mathias L
authors.initials: ML
authors.lastname: Richard
authors.affiliation: Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Brandi
authors.affiliation: Inflammation-Immunopathology-Biotherapy Département, Hospitalo-Universitaire, Paris, France INRA, UMR1319 MICALIS, Jouy en Josas, France AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France.
authors.forename: Gregory
authors.initials: G
authors.lastname: da Costa
authors.affiliation: Inflammation-Immunopathology-Biotherapy Département, Hospitalo-Universitaire, Paris, France INRA, UMR1319 MICALIS, Jouy en Josas, France AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France.
authors.forename: Thomas W
authors.initials: TW
authors.lastname: Hoffmann
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
authors.forename: Massimo Pierluigi
authors.initials: MP
authors.lastname: Di Simone
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
authors.forename: Carlo
authors.initials: C
authors.lastname: Calabrese
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
authors.forename: Gilberto
authors.initials: G
authors.lastname: Poggioli
authors.affiliation: Inflammation-Immunopathology-Biotherapy Département, Hospitalo-Universitaire, Paris, France INRA, UMR1319 MICALIS, Jouy en Josas, France AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Langella
authors.affiliation: Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
authors.forename: Massimo
authors.initials: M
authors.lastname: Campieri
authors.affiliation: Equipe Avenir Gut Microbiota and Immunity, U1157/UMR7203, Faculté de Médecine Saint-Antoine, Université Pierre et Marie Curie, Paris, France Inflammation-Immunopathology-Biotherapy Département, Hospitalo-Universitaire, Paris, France INRA, UMR1319 MICALIS, Jouy en Josas, France AgroParisTech, UMR1319 MICALIS, Jouy en Josas, France Service de Gastroentérologie et Nutrition, Assistance Publique Hôpitaux de Paris et Université Paris6, Paris, France. harry.sokol@aphp.fr.
authors.forename: Harry
authors.initials: H
authors.lastname: Sokol
mesh_terms: D000328:Adult; D044822:Biodiversity; D016022:Case-Control Studies; D003106:Colon / Q000382:microbiology*; D003424:Crohn Disease / Q000382:microbiology*; D004271:DNA, Fungal / Q000032:analysis / Q000302:isolation & purification; D018450:Disease Progression; D064806:Dysbiosis / Q000175:diagnosis* / Q000382:microbiology; D005260:Female; D005658:Fungi / Q000235:genetics / Q000302:isolation & purification*; D000069196:Gastrointestinal Microbiome; D006801:Humans; D007413:Intestinal Mucosa / Q000382:microbiology*; D008297:Male; D008875:Middle Aged; D011446:Prospective Studies; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D004271:DNA, Fungal
keywords: Inflammatory bowel disease; fungal microbiota; mucosa-associated microbiota