Oligotyping analysis of the human oral microbiome
Oligotyping analysis of the human oral microbiome
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DOI：
10.1073/pnas.1409644111
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发表时间：
2014-07-15
影响因子：
11.1
通讯作者：
Welch, Jessica L. Mark
中科院分区：
文献类型：
--
作者：
Eren, A. Murat;Borisy, Gary G.;Welch, Jessica L. Mark
人类微生物组计划对健康个体中的细菌种群进行了普查，但由于分类学分辨率有限，阻碍了对该普查的生物医学意义的理解。一种称为寡聚型的高分辨率方法通过使用香农熵评估单个核苷酸位置来识别信息最丰富的核苷酸位置，然后定义寡聚型，从而克服了这一限制。我们应用这种方法来全面分析口腔微生物组。使用人类微生物组计划口腔九个位点的 16S rRNA 基因序列数据，我们从 V1-V3 数据中识别出 493 个寡型，从 V3-V5 数据中识别出 360 个寡型。通过与人类口腔微生物组数据库进行比较，我们将这些寡型与物种级分类单元名称相关联。我们发现了密切相关的寡型，有时差异只有一个核苷酸，在口腔部位和个体之间表现出显着不同的分布。我们还在个别样本中检测到高丰度的潜在致病类群。许多寡型优先位于牙菌斑中，其他寡型位于角化牙龈或颊粘膜中，并且一些寡型是栖息地分组的特征，例如喉咙、扁桃体、舌背、硬腭和唾液。密切相关的寡型的不同栖息地分布表明了以前未认识到的生态和功能生物多样性水平。我们的结论是，寡分型的香农熵方法能够分析整个微生物组，区分密切相关但不同的分类单元，并结合栖息地分析，提供对健康和疾病微生物群落的深入了解。
The Human Microbiome Project provided a census of bacterial populations in healthy individuals, but an understanding of the biomedical significance of this census has been hindered by limited taxonomic resolution. A high-resolution method termed oligotyping overcomes this limitation by evaluating individual nucleotide positions using Shannon entropy to identify the most information-rich nucleotide positions, which then define oligotypes. We have applied this method to comprehensively analyze the oral microbiome. Using Human Microbiome Project 16S rRNA gene sequence data for the nine sites in the oral cavity, we identified 493 oligotypes from the V1-V3 data and 360 oligotypes from the V3-V5 data. We associated these oligotypes with species-level taxon names by comparison with the Human Oral Microbiome Database. We discovered closely related oligotypes, differing sometimes by as little as a single nucleotide, that showed dramatically different distributions among oral sites and among individuals. We also detected potentially pathogenic taxa in high abundance in individual samples. Numerous oligotypes were preferentially located in plaque, others in keratinized gingiva or buccal mucosa, and some oligotypes were characteristic of habitat groupings such as throat, tonsils, tongue dorsum, hard palate, and saliva. The differing habitat distributions of closely related oligotypes suggest a level of ecological and functional biodiversity not previously recognized. We conclude that the Shannon entropy approach of oligotyping has the capacity to analyze entire microbiomes, discriminate between closely related but distinct taxa and, in combination with habitat analysis, provide deep insight into the microbial communities in health and disease.