title: Bacteriophages in gut samples from pediatric Crohn's disease patients: metagenomic analysis using 454 pyrosequencing.
abstract: 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.
authors.affiliation: Enteric Virus Group, Murdoch Childrens Research Institute, Melbourne, Australia. josef.wagner@mcri.edu.au
authors.forename: Josef
authors.initials: J
authors.lastname: Wagner
authors.forename: Jovana
authors.initials: J
authors.lastname: Maksimovic
authors.forename: Gabriella
authors.initials: G
authors.lastname: Farries
authors.forename: Winnie H
authors.initials: WH
authors.lastname: Sim
authors.forename: Ruth F
authors.initials: RF
authors.lastname: Bishop
authors.forename: Donald J
authors.initials: DJ
authors.lastname: Cameron
authors.forename: Anthony G
authors.initials: AG
authors.lastname: Catto-Smith
authors.forename: Carl D
authors.initials: CD
authors.lastname: Kirkwood
mesh_terms: D001435:Bacteriophages / Q000502:physiology*; D016022:Case-Control Studies; D002648:Child; D003106:Colon / Q000821:virology*; D003424:Crohn Disease / Q000235:genetics / Q000821:virology*; D004279:DNA, Viral / Q000235:genetics; D005260:Female; D041981:Gastrointestinal Tract / Q000821:virology*; D006801:Humans; D007082:Ileum / Q000821:virology*; D008297:Male; D056186:Metagenomics; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D004279:DNA, Viral