BiomeHorizon: Visualizing Microbiome Time Series Data in R

Isaac Fink; Richard J Abdill; Ran Blekhman; Laura Grieneisen

doi:10.1128/msystems.01380-21

BiomeHorizon: Visualizing Microbiome Time Series Data in R

Isaac Fink, Richard J Abdill, Ran Blekhman, Laura Grieneisen

Genetics, Cell Biology and Development (CBS)

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

Abstract

Despite playing a key role in the health of their hosts, host-associated microbial communities demonstrate considerable variation over time. These communities comprise thousands of temporally dynamic taxa, which makes visualizing microbial time series data challenging. As such, a method to visualize both the proportional and absolute change in the relative abundance of multiple taxa across multiple subjects over time is needed. To address this gap, we developed BiomeHorizon, the first automated, open-source R package that visualizes longitudinal compositional microbiome data using horizon plots. BiomeHorizon is available at https://github.com/blekhmanlab/biomehorizon/ and a guide with step-by-step instructions for using the package is provided at https://blekhmanlab.github.io/biomehorizon/.

Original language	English (US)
Journal	mSystems
Volume	7
Issue number	3
DOIs	https://doi.org/10.1128/msystems.01380-21
State	Published - Jun 2022

Bibliographical note

Funding Information:
We thank members of the Blekhman Lab, especially Sambhawa Priya, for comments on the tutorial. We also thank Abigail Johnson and members of the Amboseli Baboon Research Project, especially Susan Alberts, Beth Archie, and Jenny Tung, for generating the publicly available data sets used in the package. This work was supported by the National Institute of Health (NIH R35-GM128716 to R.B.) and the University of Minnesota Grand Challenges in Biology Postdoctoral Fellowship to L.G.

Publisher Copyright:
© 2022 Fink et al.

Keywords

R package
microbiome
time series
Microbiota
Animals, Wild
Animals
Time Factors
Humans
Bacteria
Research Design

PubMed: MeSH publication types

Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

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10.1128/msystems.01380-21

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abstract = "Despite playing a key role in the health of their hosts, host-associated microbial communities demonstrate considerable variation over time. These communities comprise thousands of temporally dynamic taxa, which makes visualizing microbial time series data challenging. As such, a method to visualize both the proportional and absolute change in the relative abundance of multiple taxa across multiple subjects over time is needed. To address this gap, we developed BiomeHorizon, the first automated, open-source R package that visualizes longitudinal compositional microbiome data using horizon plots. BiomeHorizon is available at https://github.com/blekhmanlab/biomehorizon/ and a guide with step-by-step instructions for using the package is provided at https://blekhmanlab.github.io/biomehorizon/.",

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BiomeHorizon: Visualizing Microbiome Time Series Data in R

Abstract

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Keywords

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