儿童克罗恩病患者肠道样本中的噬菌体：454 焦磷酸测序的宏基因组分析。

Bacteriophages in gut samples from pediatric Crohn's disease patients: metagenomic analysis using 454 pyrosequencing.

机构信息

Enteric Virus Group, Murdoch Childrens Research Institute, Melbourne, Australia.

出版信息

Inflamm Bowel Dis. 2013 Jul;19(8):1598-608. doi: 10.1097/MIB.0b013e318292477c.

DOI:10.1097/MIB.0b013e318292477c

PMID:23749273

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.

摘要

背景

噬菌体在克罗恩病（CD）中的作用尚不清楚。本研究调查了儿科 CD 患者和对照者回肠和结肠样本中噬菌体的丰度。

方法

使用 454 高通量焦磷酸测序分析 6 例 CD 患者的回肠和结肠活检、3 例 CD 患者的肠道冲洗样本和 6 例非炎症性肠病患者（对照）的回肠活检中噬菌体的存在情况。使用无序列依赖性单引物扩增方法扩增病毒序列。

结果

从 4 个样本群体中获得了 186143 个高质量读数。将 Contigs 和序列簇（由未组装的单峰生成）与来自国家生物技术信息中心病毒参考数据库的序列对齐，并通过 MEGAN 进行分析。从 CD 肠道冲洗样本中获得了最多的病毒命中数（n = 691），其次是 CD 回肠样本（n = 52）、对照回肠样本（n = 20）和 CD 结肠样本（n = 1）。鉴定出的最丰富的病毒序列属于长尾病毒目噬菌体。