Analyses of the microbial diversity across the human microbiome.
Analyses of the microbial diversity across the human microbiome.
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DOI：
10.1371/journal.pone.0032118
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Methé BA
中科院分区：
文献类型：
--
作者：
Li K;Bihan M;Yooseph S;Methé BA
人体微生物多样性分析是了解群落结构、生物学和生态学的基础。美国国立卫生研究院人类微生物组计划提供了一个前所未有的机会，通过对来自200多名健康人的口腔、皮肤、远端肠道和阴道身体区域的16个S rRNA基因序列(16个S)进行焦磷酸测序，从而提供了一个前所未有的机会来研究身体生境和个人之间的微生物多样性，从而使统计技术的应用成为可能。在这项研究中，两种方法被用来阐明人类微生物群落多样性的性质和程度。首先，对Bootstrap和参数曲线拟合技术进行评估，以估计个体间生境的最大独特分类群数量、Smax和分类群发现率。其次，我们的结果表明，低丰度类群的多样性在不同生境和个体之间的变化不能用标准的生态多样性指数来充分量化。低丰度分类群的这种影响促使我们引入了一种新的基于排名的多样性衡量标准--尾部统计量(“τ”)，它基于排名丰度曲线的标准差，如果通过围绕最丰富的分类群的反射使其对称的话。由于τ的S对低丰度类群的敏感性较高，将其应用于分类学依赖和独立方法对分类单元的多样性估计，揭示了个体与生境之间恢复的值较大的范围，以及生境内不同的多样性格局。在个体内和个体之间的τ值范围最大的是粪便，它也显示了最未发现的分类群。口腔和皮肤栖息地呈现出不同的多样性格局，而阴道栖息地始终是多样性最小的。总而言之，这些结果证明了几种专门针对下一代序列数据调整的可视化和分析方法的重要性，并推动了这些方法的引入，进一步揭示了低丰度类群是人类微生物组遗传多样性的重要储存库。
Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, Smax, and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, (“τ”), based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ’s greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for next-generation sequence data, further revealing that low abundant taxa serve as an important reservoir of genetic diversity in the human microbiome.
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