UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

TLDR

The authors introduce UniFrac, a phylogeny‑based method for quantifying differences between microbial communities. UniFrac measures the fraction of branch length unique to each environment in a phylogenetic tree, enabling significance testing, clustering, ordination, and factor contribution analysis across multiple communities. Applying UniFrac to 16S rRNA libraries revealed that ice, water, and sediment isolates cluster together, geographic location has little effect in polar sediments, and bacterial communities differ between impacted and oligotrophic seawater, demonstrating UniFrac’s utility for characterizing microbial community structure.

Abstract

ABSTRACT We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.