Uncovering the Horseshoe Effect in Microbial Analyses.
Uncovering the Horseshoe Effect in Microbial Analyses.
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DOI：
10.1128/msystems.00166-16
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发表时间：
2017-01
期刊：
影响因子：
6.4
通讯作者：
Knight R
中科院分区：
文献类型：
--
作者：
Morton JT;Toran L;Edlund A;Metcalf JL;Lauber C;Knight R
马蹄形效应通常被认为是维数减少的产物。我们表明，这在微生物组数据的情况下是不正确的，事实上，马蹄铁可以帮助分析人员发现不同环境中的微生物生态位。马蹄形效应是一个长期以来引起生态学家兴趣的现象。这种效应通常被认为是维数降低的产物，并且开发了多种技术来解开这种现象并简化解释。在这里，我们提供的证据表明，马蹄铁的出现是距离指标饱和的结果——这是一个在其他领域熟悉的概念，但对微生物生态学来说是新的。这种饱和特性失去了关于群落差异的信息，仅仅是因为它不能区分没有任何共同特征的样本。这一现象说明了微生物群落的生态位分化，并表明了物种沿环境梯度的更替。在这里，我们从应用于模拟、土壤样本和死后小鼠样本的多维降维技术中提出了观察到的马蹄形效应的基本原理。对这一现象的深入了解可以从高层次的排序图中定位生态位分化模式，这可以指导传统的统计工具沿着环境梯度精确定位微生物生态位。重要性马蹄形效应通常被认为是维数降低的产物。我们表明，这在微生物组数据的情况下是不正确的，事实上，马蹄铁可以帮助分析人员发现不同环境中的微生物生态位。
The horseshoe effect is often considered an artifact of dimensionality reduction. We show that this is not true in the case for microbiome data and that, in fact, horseshoes can help analysts discover microbial niches across environments. The horseshoe effect is a phenomenon that has long intrigued ecologists. The effect was commonly thought to be an artifact of dimensionality reduction, and multiple techniques were developed to unravel this phenomenon and simplify interpretation. Here, we provide evidence that horseshoes arise as a consequence of distance metrics that saturate—a familiar concept in other fields but new to microbial ecology. This saturation property loses information about community dissimilarity, simply because it cannot discriminate between samples that do not share any common features. The phenomenon illuminates niche differentiation in microbial communities and indicates species turnover along environmental gradients. Here we propose a rationale for the observed horseshoe effect from multiple dimensionality reduction techniques applied to simulations, soil samples, and samples from postmortem mice. An in-depth understanding of this phenomenon allows targeting of niche differentiation patterns from high-level ordination plots, which can guide conventional statistical tools to pinpoint microbial niches along environmental gradients. IMPORTANCE The horseshoe effect is often considered an artifact of dimensionality reduction. We show that this is not true in the case for microbiome data and that, in fact, horseshoes can help analysts discover microbial niches across environments.