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Bacteriophages in gut samples from pediatric Crohn's disease patients: metagenomic analysis using 454 pyrosequencing
Josef Wagner1, Jovana Maksimovic, Gabriella Farries
1Enteric Virus Group, Murdoch Childrens Research Institute, Melbourne, Australia. josef.wagner@mcri.edu.au
Insights
Bacteriophage (phages) are more abundant in the gut of pediatric Crohn's disease (CD) patients, suggesting a potential role in disease development. Further research is needed to understand phage dysbiosis in CD.
Area of Science:
- Gastroenterology
- Microbiology
- Virology
Background:
- The role of bacteriophage (phages) in Crohn's disease (CD) pathogenesis remains largely unknown.
- This study aimed to investigate phage abundance in the gastrointestinal tract of pediatric CD patients.
Purpose of the Study:
- To determine the abundance and diversity of bacteriophage in ileal and colonic samples from pediatric Crohn's disease patients.
- To compare phage communities between CD patients and healthy controls.
Main Methods:
- Analysis of ileal and colonic biopsies and gut wash samples from CD patients and controls.
- Utilized 454 high-throughput pyrosequencing and a sequence-independent single-primer amplification method to identify viral sequences.
Main Results:
- A total of 186,143 high-quality reads were analyzed.
- Phage abundance was significantly higher in CD gut wash (n=691) and ileal samples (n=52) compared to controls (n=20).
- Caudovirales phage were the most abundant viral sequences identified.
Conclusions:
- Characterized a diverse phage community in the gut of CD patients, with distinct differences from controls.
- Increased phage abundance in CD ileum and gut wash samples suggests a potential role in CD development.
- The role of phage dysbiosis in Crohn's disease warrants further investigation.
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.
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