Fungi and inflammatory bowel diseases: Alterations of composition and diversity.
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.
Ott
Stephan J
SJ
Institute for Clinical Molecular Biology, Christian-Albrechts-University (CAU), Kiel, Germany. s.ott@mucosa.de
Kühbacher
Tanja
T
Musfeldt
Meike
M
Rosenstiel
Philip
P
Hellmig
Stephan
S
Rehman
Ateequr
A
Drews
Oliver
O
Weichert
Wilko
W
Timmis
Kenneth N
KN
Schreiber
Stefan
S
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