Dataset Information

Phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.

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, QIIME 2 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 and implementation

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

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Bradley PH

PROVIDER: S-EPMC7703751 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Publications

phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.

Bradley Patrick H PH Pollard Katherine S KS

Bioinformatics (Oxford, England) 20200201 4

<h4>Summary</h4>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, QIIME 2 and R interfaces that allows researchers to perform phylogenetic regression on 16S amplicon and shotgun se ...[more]

PMID: 31588499

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