Microbial trend analysis for common dynamic trend, group comparison, and classification in longitudinal microbiome study.
Microbial trend analysis for common dynamic trend, group comparison, and classification in longitudinal microbiome study.
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DOI：
10.1186/s12864-021-07948-w
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发表时间：
2021-09-15
期刊：
影响因子：
4.4
通讯作者：
Li H
中科院分区：
文献类型：
--
作者：
Wang C;Hu J;Blaser MJ;Li H
人体微生物群是动态的，其动态特性在维持健康和驱动疾病方面起着关键作用。随着纵向微生物组研究的增加，科学家们渴望了解微生物动力学的全面表征及其对健康和疾病相关表型的影响。然而，由于纵向微生物组数据的结构具有挑战性，很少有分析方法可用于表征微生物动态随时间的变化。我们提出了一个微生物趋势分析（MTA）框架，用于高维和基于系统发育的纵向微生物组数据。MTA可以完成以下三个任务：1)在群落水平上捕捉一组生物的共同微生物动态趋势，并确定优势类群；2)各组间微生物总体动态趋势是否存在显著差异；3)根据纵向微生物谱对个体受试者进行分类。我们的大量模拟表明，所提出的MTA框架在假设检验、分类单元识别和主题分类方面具有强大的鲁棒性。我们的真实数据分析通过对小鼠的纵向研究进一步说明了MTA的效用。所提出的MTA框架是纵向微生物组研究动态微生物模式的有效工具。在线版本包含补充材料，可在（10.1186/s12864-021-07948-w）获得。
The human microbiome is inherently dynamic and its dynamic nature plays a critical role in maintaining health and driving disease. With an increasing number of longitudinal microbiome studies, scientists are eager to learn the comprehensive characterization of microbial dynamics and their implications to the health and disease-related phenotypes. However, due to the challenging structure of longitudinal microbiome data, few analytic methods are available to characterize the microbial dynamics over time. We propose a microbial trend analysis (MTA) framework for the high-dimensional and phylogenetically-based longitudinal microbiome data. In particular, MTA can perform three tasks: 1) capture the common microbial dynamic trends for a group of subjects at the community level and identify the dominant taxa; 2) examine whether or not the microbial overall dynamic trends are significantly different between groups; 3) classify an individual subject based on its longitudinal microbial profiling. Our extensive simulations demonstrate that the proposed MTA framework is robust and powerful in hypothesis testing, taxon identification, and subject classification. Our real data analyses further illustrate the utility of MTA through a longitudinal study in mice. The proposed MTA framework is an attractive and effective tool in investigating dynamic microbial pattern from longitudinal microbiome studies. The online version contains supplementary material available at (10.1186/s12864-021-07948-w).
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影响因子：
48
作者：
Callahan BJ;McMurdie PJ;Rosen MJ;Han AW;Johnson AJ;Holmes SP
通讯作者：
Holmes SP
影响因子：
2.1
作者：
Chen, Jun;Bushman, Frederic D.;Li, Hongzhe
通讯作者：
Li, Hongzhe
影响因子：
6.4
作者：
Bokulich NA;Dillon MR;Zhang Y;Rideout JR;Bolyen E;Li H;Albert PS;Caporaso JG
通讯作者：
Caporaso JG
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
1.5
作者：
Dmitrienko, Alex;Tamhane, Ajit C.
通讯作者：
Tamhane, Ajit C.