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phylogenize: correcting for phylogeny reveals genes associated with microbial distributions

Patrick H. Bradley, View ORCID ProfileKatherine S. Pollard
doi: https://doi.org/10.1101/425231
Patrick H. Bradley
1Gladstone Institute of Data Science and Biotechnology, San Francisco, CA USA
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Katherine S. Pollard
1Gladstone Institute of Data Science and Biotechnology, San Francisco, CA USA
2Department of Epidemiology & Biostatistics, University of California–San Francisco, CA USA
3Chan–Zuckerberg Biohub, San Francisco, CA USA
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  • ORCID record for Katherine S. Pollard
  • For correspondence: kpollard@gladstone.ucsf.edu
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Abstract

Summary Phylogenetic comparative methods are powerful but presently under-utilized ways to identify microbial genes underlying differences in community composition. These methods help to identify functionally important genes because they test for associations beyond those expected when related microbes occupy similar environments. We present phylogenize, a pipeline with web, QIIME2, and R interfaces that allows researchers to perform phylogenetic regression on 16S amplicon and shotgun sequencing data and to visualize results. phylogenize applies broadly to both host-associated and environmental microbiomes. Using Human Microbiome Project and Earth Microbiome Project data, we show that phylogenize draws similar conclusions from 16S versus shotgun sequencing and reveals both known and candidate pathways associated with host colonization.

Availability phylogenize is available at https://phylogenize.org and https://bitbucket.org/pbradz/phylogenize.

Contact kpollard{at}gladstone.ucsf.edu

Footnotes

  • Rewritten to emphasize differences from previous approaches, to reflect changes in the codebase (now available as an R package and through a QIIME2 plugin as well as through the website) and to add a new analysis of plant rhizosphere-associated microbes; Figure 1 revised; Supplemental file added.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 30, 2019.
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phylogenize: correcting for phylogeny reveals genes associated with microbial distributions
Patrick H. Bradley, Katherine S. Pollard
bioRxiv 425231; doi: https://doi.org/10.1101/425231
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phylogenize: correcting for phylogeny reveals genes associated with microbial distributions
Patrick H. Bradley, Katherine S. Pollard
bioRxiv 425231; doi: https://doi.org/10.1101/425231

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