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Bacteriophages in Gut Samples From Pediatric Crohn’s Disease Patients: Metagenomic Analysis Using 454 Pyrosequencing

Wagner, Josef PhD*,†; Maksimovic, Jovana PhD; Farries, Gabriella BSc(Hons)*; Sim, Winnie H. PhD*; Bishop, Ruth F. PhD, DSc, AO*,†; Cameron, Donald J. MBBS§; Catto-Smith, Anthony G. MBBS, MD†,§; Kirkwood, Carl D. PhD*,†,‖

doi: 10.1097/MIB.0b013e318292477c
Original Basic Science Articles

Background: The role of bacteriophage in Crohn’s disease (CD) is unknown. This study investigated the abundance of phages in ileal and colonic samples from pediatric CD patients and controls.

Methods: Ileal and colonic biopsies from 6 CD patients, gut wash samples from 3 CD patients, and ileal biopsies from 6 noninflammatory bowel disease patients (controls) were analyzed for the presence of bacteriophage using 454 high-throughput pyrosequencing. A sequence-independent single-primer amplification method was used to amplify viral sequences.

Results: A total of 186,143 high quality reads were obtained from the 4 sample populations. Contigs and sequence clusters (generated from unassembled singletons) were aligned with sequences from the National Center for Biotechnology Information viral reference database and analyzed by MEGAN. The largest number of viral hits was obtained from the CD gut wash samples (n = 691), followed by CD ileal samples (n = 52), control ileum samples (n = 20), and CD colonic samples (n = 1). The most abundant virus sequences identified belonged to the Caudovirales phage.

Conclusions: Our study characterized a diverse phage community in the gut of CD patients. In this study, we have identified differences in phage composition between CD patients and control individuals. The large abundance of phages in CD ileum tissue and CD gut wash sample suggests a role of phage in CD development. The role of phage dysbiosis in CD is currently unknown but opens up a new area of research.

Article first published online 6 June 2013

*Enteric Virus Group, Murdoch Childrens Research Institute, Melbourne, Australia;

Department of Paediatrics, University of Melbourne, Melbourne, Australia;

Bioinformatics Group, Murdoch Childrens Research Institute, Melbourne, Australia;

§Department of Gastroenterology & Clinical Nutrition, Royal Children’s Hospital, Melbourne, Australia; and

Department of Microbiology, Latrobe University, Bundoora, Australia.

Reprints: Josef Wagner, PhD, Enteric Virus Group, Murdoch Childrens Research Institute, Royal Children's Hospital, Melbourne, Flemington Road, 3052 VIC, Australia (e-mail:

Supported by (1) National Health and Medical Research Council (NHMRC) research grants (607382), (2) Theme Funding from the Murdoch Childrens Research Insitute, (3) Victorian Government’s Operational Infrastructure Support Program, and (4) Dr C.D. Kirkwood is supported by an NHMRC RD Wright Research Fellowship (607347).

The authors have no conflicts of interest to disclose.

Received February 25, 2013

Accepted March 14, 2013

© Crohn's & Colitis Foundation of America, Inc.
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