A Method for Determining Taxonomical Contributions to Group Differences in Microbiomic Investigations

Alexa Pragman, Richard Issacson, Christine Wendt, Cavan Reilly

Research output: Contribution to journalArticlepeer-review

Abstract

Here we show how one can decompose the contribution of different levels of taxonomic classification in terms of their impact on differences in the microbiota when comparing two groups. First we demonstrate a difficulty in trying to estimate taxonomic effects at multiple levels simultaneously and demonstrate an approach to determining which taxa have differences in means that are identified. We then develop a model based on an approach that is popular in the RNA-Seq analysis literature and apply it to the problem of determining which taxa differ between two patient groups. This model provides a more powerful method than simpler alternatives. A Bayesian computational strategy is used to obtain exact inference. Simulation studies indicate that the procedure works as intended, and an application to the study of COPD demonstrates the method's practical utility. Software is provided for implementing the method.

Original languageEnglish (US)
Pages (from-to)930-939
Number of pages10
JournalJournal of Computational Biology
Volume22
Issue number10
DOIs
StatePublished - Oct 1 2015

Bibliographical note

Publisher Copyright:
© Copyright 2015, Mary Ann Liebert, Inc.

Keywords

  • Bayesian modeling
  • COPD
  • microbiota
  • overdispersed counts

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