A phylogenetic transform enhances analysis of compositional microbiota data
A phylogenetic transform enhances analysis of compositional microbiota data
复制标题
DOI：
10.7554/elife.21887
复制
发表时间：
2017-02-15
期刊：
影响因子：
7.7
通讯作者：
David, Lawrence A.
中科院分区：
文献类型：
--
作者：
Silverman, Justin D.;Washburne, Alex D.;David, Lawrence A.
微生物群落（微生物群）的调查通常以物种的相对丰度来衡量，说明了这些群落对人类健康和疾病的重要性。然而，统计假象通常困扰着相对丰度数据的分析。在这里，我们介绍 PhILR 变换，它将微生物进化模型与等距对数比变换相结合，使现成的统计工具能够安全地应用于微生物群调查。我们证明，社区层面结构的分析可以应用于 PhILR 转换数据，其基准性能可与标准工具相媲美或超越。此外，通过分解 PhILR 变换空间中的距离，我们确定了可能适应不同人体部位的邻近进化枝。分解方差表明，人体部位内细菌进化枝的共变随着系统发育相关性的增加而增加。这些发现共同说明了 PhILR 转换如何结合统计和系统发育模型来克服组成数据挑战并实现与微生物群落相关的进化见解。
Surveys of microbial communities (microbiota), typically measured as relative abundance of species, have illustrated the importance of these communities in human health and disease. Yet, statistical artifacts commonly plague the analysis of relative abundance data. Here, we introduce the PhILR transform, which incorporates microbial evolutionary models with the isometric log-ratio transform to allow off-the-shelf statistical tools to be safely applied to microbiota surveys. We demonstrate that analyses of community-level structure can be applied to PhILR transformed data with performance on benchmarks rivaling or surpassing standard tools. Additionally, by decomposing distance in the PhILR transformed space, we identified neighboring clades that may have adapted to distinct human body sites. Decomposing variance revealed that covariation of bacterial clades within human body sites increases with phylogenetic relatedness. Together, these findings illustrate how the PhILR transform combines statistical and phylogenetic models to overcome compositional data challenges and enable evolutionary insights relevant to microbial communities.