Expanding the UniFrac Toolbox

PLoS One. 2016 Sep 15;11(9):e0161196. doi: 10.1371/journal.pone.0161196. eCollection 2016.

Abstract

The UniFrac distance metric is often used to separate groups in microbiome analysis, but requires a constant sequencing depth to work properly. Here we demonstrate that unweighted UniFrac is highly sensitive to rarefaction instance and to sequencing depth in uniform data sets with no clear structure or separation between groups. We show that this arises because of subcompositional effects. We introduce information UniFrac and ratio UniFrac, two new weightings that are not as sensitive to rarefaction and allow greater separation of outliers than classic unweighted and weighted UniFrac. With this expansion of the UniFrac toolbox, we hope to empower researchers to extract more varied information from their data.

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics
  • Humans
  • Microbiota*
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics

Substances

  • RNA, Ribosomal, 16S

Grants and funding

This work was supported by a Discovery Grant from the National Research Council of Canada RGPIN-2015-03878 and Canadian Institutes of Health Research, http://www.cihr-irsc.gc.ca, MOP123459. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.