Abstract
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. IMPORTANCE 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.
Original language | English (US) |
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Article number | e00219-18 |
Journal | mSystems |
Volume | 3 |
Issue number | 6 |
DOIs | |
State | Published - Dec 2018 |
Keywords
- Bioinformatics
- Linear mixed effects
- Longitudinal analysis
- Microbiome
ASJC Scopus subject areas
- Microbiology
- Ecology, Evolution, Behavior and Systematics
- Biochemistry
- Physiology
- Modeling and Simulation
- Molecular Biology
- Genetics
- Computer Science Applications