Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2014

Debugging Crohn's disease (#410)

Claire L O'Brien 1 2 3 , David M Gordon , Gwen E Allison 3 , Paul Pavli 1 2
  1. Gastroenterology and Hepatology Unit, Canberra Hospital, Canberra, ACT, Australia
  2. Medical School, Australian National University, Canberra, ACT, Australia
  3. Research School of Biology, Australian National University, Canberra, ACT, Australia

Introduction: Putative pathogens, shifts in microbiota composition (the dysbiosis hypothesis), excessive bacterial translocation, and reduced mucosal microbial diversity have all been implicated in Crohn’s disease (CD).  The aim of this study was to characterise and compare the microbiota of early- and late-stage CD tissues, and to seek evidence for a number of putative pathogens, dysbiosis, and reduced diversity.

Methods: We used pyrosequencing of V1-V3 regions of the universal bacterial 16S rRNA gene, and species specific primers targeting Escherichia coli, Yersinia, and Mycobacterium avium subspecies paratuberculosis, to examine the microbial composition of late-stage CD tissues (surgically resected affected and unaffected mucosa [n=58: 29 CD; 8 other-IBD; 21 non-IBD] and lymph nodes [n=20: 8 CD; 2 other-IBD; 10 non-IBD]).  Tissues from early-stage CD (aphthous ulcers [n=11] and adjacent mucosal biopsies [n=11]) underwent 16S rRNA gene pyrosequencing only.  The microbial communities were analysed using Mothur and JMP, V.9.

Results: Dysbiosis was a feature of late-, not early-stage CD.  Reduced bacterial diversity was observed for both early- and late-stage CD, relative to non-IBD (p = <0.0001, p = 0.003, respectively).  Three bacterial genera (Bacteroides, and two Unclassified) were present in all aphthous ulcer samples.  No genus was common to all late-stage CD tissues, but E. coli was increased relative to non-IBD (p = <0.0001).  We found no evidence for other putative pathogens in late-stage CD, including Yersinia and Mycobacterium.

Conclusion: The intestinal microbiome differs with respect to the stage of CD: dysbiosis occurs late and may be the consequence of disease, rather than a predisposing factor.  Reduced diversity was observed in early and late-stage CD, not non-IBD.  Reduced diversity may affect the ecology of the bacterial communities making them less functionally redundant and correspondingly less resilient to perturbations.  Further studies are warranted to understand the role, if any, of bacteria found in common to all aphthous ulcers.