title: Fungi and inflammatory bowel diseases: Alterations of composition and diversity.
abstract: OBJECTIVE
  Altered bacterial diversity of the intestinal mucosa-associated microbiota may reflect the net influence of lifestyle factors associated with the development of chronic inflammatory bowel diseases (IBD). While a reduced bacterial diversity has been reported in IBD, little is known about the fungal microbiota. The aim of this study was to carry out a systematic analysis of intestinal fungal microbiota in IBD.
  
  
  METHODS
  The mucosa-associated fungal microbiota of 104 colonic biopsy tissues from 47 controls and 57 IBD patients was investigated using metagenomic 18S rDNA-based denaturing gradient gel electrophoresis (DGGE), clone libraries, sequencing, and in situ hybridization techniques.
  
  
  RESULTS
  Fungi-specific 18S rDNA signatures could be detected in all 104 patients, accounting for only a small proportion of the intestinal microbiota (0.02% of the mucosal and 0.03% of the fecal microbiota). An overall fungal biodiversity of 43 different operational taxonomic units (OTUs) was found in the clone libraries. The qualitative composition of fungal microbiota was different between patients with IBD and controls. The DGGE profiles showed a higher mean fungal diversity in patients with Crohn's disease (CD) in comparison with controls (10.8+/-3.1 versus 6.2+/-2.4 for CD, p <or= 0.001). No disease-specific fungal species were found in the CD and ulcerative colitis (UC) group.
  
  
  CONCLUSIONS
  Diverse fungal species are part of the normal enteric microbiota, but diversity is increased and composition of the fungal communities varies in IBD. Further work is needed to investigate whether the alteration of the fungal flora in IBD is secondary to an imbalanced bacterial microbiota or an independent etiologic factor.
authors.affiliation: Institute for Clinical Molecular Biology, Christian-Albrechts-University (CAU), Kiel, Germany. s.ott@mucosa.de
authors.forename: Stephan J
authors.initials: SJ
authors.lastname: Ott
authors.forename: Tanja
authors.initials: T
authors.lastname: Kühbacher
authors.forename: Meike
authors.initials: M
authors.lastname: Musfeldt
authors.forename: Philip
authors.initials: P
authors.lastname: Rosenstiel
authors.forename: Stephan
authors.initials: S
authors.lastname: Hellmig
authors.forename: Ateequr
authors.initials: A
authors.lastname: Rehman
authors.forename: Oliver
authors.initials: O
authors.lastname: Drews
authors.forename: Wilko
authors.initials: W
authors.lastname: Weichert
authors.forename: Kenneth N
authors.initials: KN
authors.lastname: Timmis
authors.forename: Stefan
authors.initials: S
authors.lastname: Schreiber
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001483:Base Sequence; D003093:Colitis, Ulcerative / Q000382:microbiology; D003424:Crohn Disease / Q000382:microbiology; D005243:Feces / Q000382:microbiology; D005260:Female; D005658:Fungi / Q000302:isolation & purification*; D006801:Humans; D017403:In Situ Hybridization; D017404:In Situ Hybridization, Fluorescence; D015212:Inflammatory Bowel Diseases / Q000382:microbiology*; D007413:Intestinal Mucosa / Q000382:microbiology*; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction