The UniFrac significance test is sensitive to tree topology.

Catherine A Lozupone,Rob Knight

doi:10.1186/s12859-015-0640-y

Abstract

Long et al. (BMC Bioinformatics 2014, 15(1):278) describe a “discrepancy” in using UniFrac to assess statistical significance of community differences. Specifically, they find that weighted UniFrac results differ between input trees where (a) replicate sequences each have their own tip, or (b) all replicates are assigned to one tip with an associated count. We argue that these are two distinct cases that differ in the probability distribution on which the statistical test is based, because of the differences in tree topology. Further study is needed to understand which randomization procedure best detects different aspects of community dissimilarities.

Highlights

Long et al (BMC Bioinformatics 2014, 15(1):278) describe a “discrepancy” in using UniFrac to assess statistical significance of community differences
In a recent paper [2], Long et al show that the results of weighted UniFrac significance tests differ when applied to input trees in two different formats: first a tree in which replicate tips each with a count of 1 are added when the sequence is found multiple times, or second a tree in which each tip has a count related to its abundance
Long et al assert that users of the UniFrac significance test should use the tool with caution, because the results can vary depending on the “arbitrary choice of input format.”

Summary

Introduction

Long et al (BMC Bioinformatics 2014, 15(1):278) describe a “discrepancy” in using UniFrac to assess statistical significance of community differences. Body UniFrac significance tests can be used to determine whether the types of sequences (e.g. representing bacterial 16S ribosomal RNA genes) in two different biological samples differ significantly between the samples. * Correspondence: Catherine.Lozupone@ucdenver.edu 1Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA Full list of author information is available at the end of the article (Fig. 1).

Results

Conclusion