High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals
High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals
复制标题
高通量测序揭示了健康人粘膜和管腔壁龛内不同的微生物种群
DOI：
10.1080/19490976.2015.1044711
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发表时间：
2015-01-01
期刊：
影响因子：
12.2
通讯作者：
Carroll, Ian M.
中科院分区：
文献类型：
--
作者：
Ringel, Yehuda;Maharshak, Nitsan;Carroll, Ian M.
背景：肠道微生物群与人类健康和疾病相关。管腔微生物群（LM）和粘膜相关微生物群（MAM）是两个不同的生态系统，具有不同的代谢和免疫功能。目的：利用 16S rRNA 基因的高通量测序来表征人类肠道 LM 和 MAM。方法：在对未准备好的肠道进行柔性乙状结肠镜检查之前（粪便）和期间（粘膜），从 24 名健康受试者身上收集新鲜粪便样本和远端结肠粘膜活检组织。 16S rRNA 基因的高通量测序用于表征细菌群落。使用 QIIME 管道处理序列。结果：LM 和 MAM 群体存在显着差异（ANOSIM：R = 0.49，P = 0.001）。与 MAM 相比，LM 显示出更紧密的聚类（平均加权 UniFrac 距离分别为 0.27 +/- 0.05 与 0.43 +/- 0.09，P < 0.001），并显示出更高的多样性（香农多样性指数：分别为 4.96 +/- 0.37 与 4.14 +/- 0.56，P < 0.001）。 LM 和 MAM 中的优势门存在显着差异：厚壁菌门（分别为 41.4% vs. 29.1%，FDR < 0.0001）、拟杆菌门（分别为 20.2% vs. 26.3%，FDR < 0.05）、放线菌门（分别为 22% vs. 12.6%，FDR < 0.0001）和变形菌门（9.3% 对比 19.3%， FDR < 0.0001，分别）。 2 个生态位之间 56 个属的丰度存在显着差异 (FDR < 0.1)。粪便微生物群中的所有属均存在于 MAM 中，同时发现 10 个属是 MAM 所独有的。结论：LM 和 MAM 是不同的微生物生态系统，它们在微生物多样性和组成方面存在显着差异。应独立研究这两个微生物生态位，以更好地了解肠道微生物群在健康和疾病中的作用。
Background: The intestinal microbiota is associated with human health and diseases. The luminal microbiota (LM) and the mucosal-associated microbiota (MAM) are 2 distinct ecosystems with different metabolic and immunological functions. Aim: To characterize the intestinal LM and MAM in humans using high throughput sequencing of the 16S rRNA gene. Methods: Fresh fecal samples and distal colonic mucosal biopsies collected from 24 healthy subjects before (fecal) and during (mucosa) a flexible sigmoidoscopy of an un-prepared bowel. High throughput sequencing of the 16S rRNA gene was used to characterize bacterial communities. Sequences were processed using the QIIME pipeline. Results: LM and MAM populations were significantly different (ANOSIM: R = 0.49, P = 0.001). The LM displayed tighter clustering compared to the MAM (average weighted UniFrac distances 0.27 +/- 0.05 vs. 0.43 +/- 0.09, P < 0.001, respectively), and showed higher diversity (Shannon diversity index: 4.96 +/- 0.37 vs 4.14 +/- 0.56, respectively, P < 0.001). The dominant phyla in the LM and MAM were significantly different: Firmicutes (41.4% vs. 29.1%, FDR < 0.0001, respectively), Bacteroidetes (20.2% vs. 26.3%, FDR < 0.05, respectively), Actinobacteria (22% vs. 12.6%, FDR < 0.0001, respectively) and Proteobacteria (9.3% vs. 19.3%, FDR < 0.0001, respectively). The abundance of 56 genera differed significantly (FDR < 0.1) between the 2 niches. All of the genera in the fecal microbiota were present in the MAM while 10 genera were found to be unique to the MAM. Conclusion: The LM and MAM are distinct microbial ecosystems that differ significantly from each other in microbial diversity and composition. These two microbial niches should be investigated independently to better understand the role of the intestinal microbiota in health and disease.