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

Publication ,  Journal Article
Washburne, AD; Silverman, JD; Leff, JW; Bennett, DJ; Darcy, JL; Mukherjee, S; Fierer, N; David, LA
Published in: PeerJ
2017

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.

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Published In

PeerJ

DOI

ISSN

2167-8359

Publication Date

2017

Volume

5

Start / End Page

e2969

Location

United States

Related Subject Headings

  • 11 Medical and Health Sciences
  • 06 Biological Sciences
 

Citation

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Washburne, A. D., Silverman, J. D., Leff, J. W., Bennett, D. J., Darcy, J. L., Mukherjee, S., … David, L. A. (2017). Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets. PeerJ, 5, e2969. https://doi.org/10.7717/peerj.2969
Washburne, Alex D., Justin D. Silverman, Jonathan W. Leff, Dominic J. Bennett, John L. Darcy, Sayan Mukherjee, Noah Fierer, and Lawrence A. David. “Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets.PeerJ 5 (2017): e2969. https://doi.org/10.7717/peerj.2969.
Washburne AD, Silverman JD, Leff JW, Bennett DJ, Darcy JL, Mukherjee S, et al. Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets. PeerJ. 2017;5:e2969.
Washburne, Alex D., et al. “Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets.PeerJ, vol. 5, 2017, p. e2969. Pubmed, doi:10.7717/peerj.2969.
Washburne AD, Silverman JD, Leff JW, Bennett DJ, Darcy JL, Mukherjee S, Fierer N, David LA. Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets. PeerJ. 2017;5:e2969.

Published In

PeerJ

DOI

ISSN

2167-8359

Publication Date

2017

Volume

5

Start / End Page

e2969

Location

United States

Related Subject Headings

  • 11 Medical and Health Sciences
  • 06 Biological Sciences