Bokulich Nicholas A, Dillon Matthew R, Zhang Yilong, Rideout Jai Ram, Bolyen Evan, Li Huilin, Albert Paul S, Caporaso J Gregory
The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA.
Merck & Co., Inc., Kenilworth, New Jersey, USA.
mSystems. 2018 Nov 20;3(6). doi: 10.1128/mSystems.00219-18. eCollection 2018 Nov-Dec.
Studies of host-associated and environmental microbiomes often incorporate longitudinal sampling or paired samples in their experimental design. Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity, offering advantages over cross-sectional and pre-post study designs. To support the needs of microbiome researchers performing longitudinal studies, we developed q2-longitudinal, a software plugin for the QIIME 2 microbiome analysis platform (https://qiime2.org). The q2-longitudinal plugin incorporates multiple methods for analysis of longitudinal and paired-sample data, including interactive plotting, linear mixed-effects models, paired differences and distances, microbial interdependence testing, first differencing, longitudinal feature selection, and volatility analyses. The q2-longitudinal package (https://github.com/qiime2/q2-longitudinal) is open-source software released under a 3-clause Berkeley Software Distribution (BSD) license and is freely available, including for commercial use. Longitudinal sampling provides valuable information about temporal trends and subject/population heterogeneity. We describe q2-longitudinal, a software plugin for longitudinal analysis of microbiome data sets in QIIME 2. The availability of longitudinal statistics and visualizations in the QIIME 2 framework will make the analysis of longitudinal data more accessible to microbiome researchers.
对宿主相关微生物组和环境微生物组的研究在实验设计中通常纳入纵向采样或配对样本。纵向采样提供了有关时间趋势以及个体/群体异质性的宝贵信息，相较于横断面研究设计和前后对照研究设计具有优势。为了满足进行纵向研究的微生物组研究人员的需求，我们开发了q2-longitudinal，这是一款用于QIIME 2微生物组分析平台（https://qiime2.org）的软件插件。q2-longitudinal插件纳入了多种分析纵向和配对样本数据的方法，包括交互式绘图、线性混合效应模型、配对差异和距离、微生物相互依存性测试、一阶差分、纵向特征选择以及波动性分析。q2-longitudinal软件包（https://github.com/qiime2/q2-longitudinal）是根据三条款伯克利软件发行版（BSD）许可发布的开源软件，可免费获取，包括用于商业用途。纵向采样提供了有关时间趋势以及个体/群体异质性的宝贵信息。我们描述了q2-longitudinal，这是一款用于在QIIME 2中对微生物组数据集进行纵向分析的软件插件。QIIME 2框架中纵向统计和可视化功能的可用性将使微生物组研究人员更容易进行纵向数据分析。
