Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

Washburne, Alex D.; Silverman, Justin D.; Leff, Jonathan W.; Bennett, Dominic J.; Darcy, John L.; Mukherjee, Sayan; Fierer, Noah; David, Lawrence A.

doi:10.7717/peerj.2969

i

Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets

2017
By Washburne, Alex D. ; Silverman, Justin D. ; Leff, Jonathan W. ; ...

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Journal Title:

PeerJ
Personal Author:

Washburne, Alex D. ; Silverman, Justin D. ; Leff, Jonathan W. ; Bennett, Dominic J. ; Darcy, John L. ; Mukherjee, Sayan ; Fierer, Noah ; David, Lawrence A.
NOAA Program & Office:

CIRES (Cooperative Institute for Research in Environmental Sciences)
Description:

Marker gene sequencing of microbial communities has generated big datasets of microbial relative abundances varying across environmental conditions, sample sites and treatments. These data often come with putative phylogenies, providing unique opportunities to investigate how shared evolutionary history affects microbial abundance patterns. Here, we present a method to identify the phylogenetic factors driving patterns in microbial community composition. We use the method, “phylofactorization,” to re-analyze datasets from the human body and soil microbial communities, demonstrating how phylofactorization is a dimensionality-reducing tool, an ordination-visualization tool, and an inferential tool for identifying edges in the phylogeny along which putative functional ecological traits may have arisen.
Source:

PeerJ, 5, e2969
DOI:

https://doi.org/10.7717/peerj.2969
ISSN:

2167-8359
Format:

pdf
Publisher:

PeerJ
Document Type:

Journal Article
License:

https://creativecommons.org/licenses/by/4.0/
Rights Information:

CC BY
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Library
Main Document Checksum:

urn:sha-512:4d1b8821815a586fe3a791594fc842cde566ee36e0ac81b605eab11afd5aac70a73acfd6d1cfeca8880066027743812b2e34f84e0e5433023b070725de1f69e3
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https://repository.library.noaa.gov/view/noaa/69870/noaa_69870_DS1.pdf
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[PDF - 1.38 MB ]

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