Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.
Oligotyping: Differentiating between closely related microbial taxa using 16S rRNA gene data.
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DOI：
10.1111/2041-210x.12114
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发表时间：
2013-12-01
影响因子：
6.6
通讯作者：
Sogin ML
中科院分区：
文献类型：
--
作者：
Eren AM;Maignien L;Sul WJ;Murphy LG;Grim SL;Morrison HG;Sogin ML
细菌构成了地球上最多样化的生命领域，它们几乎占据了每一个可能的生态位，在生物和化学过程中发挥着关键作用。研究细菌生态系统的组成和生态，了解其功能是至关重要的。高通量测序技术可以通过16S核糖体RNA基因扩增子对细菌多样性进行几乎全面的描述。这些群落的分析通常依赖于通过参考数据库或使用事实上的序列相似性阈值的聚类方法来确定可操作的分类单元的分类分配。然而，这些方法往往不能解决在复杂的微生物数据集中密切相关的生物之间有意义的生态差异。在本文中，我们描述了寡分型，这是一种新的监督计算方法，允许研究人员通过规范方法通过16S核糖体RNA基因数据在环境数据集中确定的最终操作分类单元中调查密切相关但不同的细菌有机体的多样性。我们对来自两种不同环境的两个数据集的分析表明，寡分型在区分具有生态重要性的不同微生物种群方面的能力。寡分型可以解决密切相关的生物体在不同环境中的分布，揭示以前被忽视的微生物群落的生态模式。URL http://oligotyping.org提供了一个用于寡类型的开源软件管道。
Bacteria comprise the most diverse domain of life on Earth, where they occupy nearly every possible ecological niche and play key roles in biological and chemical processes. Studying the composition and ecology of bacterial ecosystems and understanding their function are of prime importance. High-throughput sequencing technologies enable nearly comprehensive descriptions of bacterial diversity through 16S ribosomal RNA gene amplicons. Analyses of these communities generally rely upon taxonomic assignments through reference data bases or clustering approaches using de facto sequence similarity thresholds to identify operational taxonomic units. However, these methods often fail to resolve ecologically meaningful differences between closely related organisms in complex microbial data sets. In this paper, we describe oligotyping, a novel supervised computational method that allows researchers to investigate the diversity of closely related but distinct bacterial organisms in final operational taxonomic units identified in environmental data sets through 16S ribosomal RNA gene data by the canonical approaches. Our analysis of two data sets from two different environments demonstrates the capacity of oligotyping at discriminating distinct microbial populations of ecological importance. Oligotyping can resolve the distribution of closely related organisms across environments and unveil previously overlooked ecological patterns for microbial communities. The URL http://oligotyping.org offers an open-source software pipeline for oligotyping.