Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach
Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach
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DOI：
10.1136/gut.2005.073817
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发表时间：
2006-02-01
期刊：
影响因子：
24.5
通讯作者：
Dore, J
中科院分区：
文献类型：
--
作者：
Manichanh, C;Rigottier-Gois, L;Dore, J
背景和目的：人们强烈怀疑肠道微生物群落（微生物群）在克罗恩病（CD）的发病和慢性化中的作用。然而，即使采用独立于培养物的分子方法，研究如此复杂的生态系统也是困难的。方法：我们首次使用综合宏基因组方法来研究全方位的肠道微生物多样性。我们使用 fosmid 载体构建了两个基因组 DNA 文库，这些基因组 DNA 直接从六名健康捐赠者和六名 CD 患者的粪便样本中分离出来。通过 DNA 杂交筛选两个 DNA 文库（每个文库由 25 000 个克隆组成）的 16S rRNA 基因来分析细菌多样性。结果：在 1190 个筛选的克隆中，我们鉴定了 125 个非冗余核糖型，主要以拟杆菌门和厚壁菌门为代表。在厚壁菌门中，在健康的微生物群中发现了 43 种不同的核糖型，而 CD 中只有 13 种（p < 0.025）。荧光原位杂交直接针对单独分析的粪便样本中的 16S rRNA (n = 12) 证实，CD 患者中属于该门的细菌比例显着减少 (p < 0.02)。 结论：宏基因组方法使我们能够检测到细菌门厚壁菌门复杂性的降低，作为 CD 患者粪便微生物群的特征。它还表明新细菌物种的存在。
Background and aim: A role for the intestinal microbial community (microbiota) in the onset and chronicity of Crohn's disease (CD) is strongly suspected. However, investigation of such a complex ecosystem is difficult, even with culture independent molecular approaches.Methods: We used, for the first time, a comprehensive metagenomic approach to investigate the full range of intestinal microbial diversity. We used a fosmid vector to construct two libraries of genomic DNA isolated directly from faecal samples of six healthy donors and six patients with CD. Bacterial diversity was analysed by screening the two DNA libraries, each composed of 25 000 clones, for the 16S rRNA gene by DNA hybridisation.Results: Among 1190 selected clones, we identified 125 non-redundant ribotypes mainly represented by the phyla Bacteroidetes and Firmicutes. Among the Firmicutes, 43 distinct ribotypes were identified in the kealthy microbiota, compared with only 13 in CD (p < 0.025). Fluorescent in situ hybridisation directly targeting 16S rRNA in faecal samples analysed individually (n = 12) confirmed the significant reduction in the proportion of bacteria belonging to this phylum in CD patients (p < 0.02).Conclusion: The metagenomic approach allowed us to detect a reduced complexity of the bacterial phylum Firmicutes as a signature of the faecal microbiota in patients with CD. It also indicated the presence of new bacterial species.