The DOI matches its Crossref record; 96 of the 96 references it cites were found in a registry or an index.
A phylogenetic transform enhances analysis of compositional microbiota data
Open accessPublished version of a preprint
Abstract
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.
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Cites
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Cited by
Microbiome Datasets Are Compositional: And This Is Not Optional
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Metadata
- Authors
- Silverman, J. D., Washburne, A. D., Mukherjee, S., & David, L. A.
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2017-02-15
- Volume
- 6
- ISSN
- 2050-084X (ISSN-L)
- OpenAlex
- W2510675082
- Cited by
- 319
- References
- 96
- FWCI
- 9.41
- Type
- journal article
- Language
- en
- Open access
- gold
- Licence
- creativecommons.org/licenses/by/4.0/ (vor)
- creativecommons.org/licenses/by/4.0/ (am)
- creativecommons.org/licenses/by/4.0/ (tdm)
- Funders
- National Science Foundation (IIS 1546331, IIS 1418261)
- Global Probiotics Council (Young Investigator Grant for Probiotics Research)
- Searle Scholars Program (15-SSP-184 Research Agreement)
- Alfred P. Sloan Foundation (BR2014-003)
- Duke University (Medical Scientist Training Program GM007171)
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- Silverman, J. D., Washburne, A. D., Mukherjee, S., & David, L. A. (2017). A phylogenetic transform enhances analysis of compositional microbiota data. eLife. https://doi.org/10.7554/elife.21887
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