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Applied and Environmental Microbiology, December 2005, p. 8228-8235, Vol. 71, No. 12
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.12.8228-8235.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

Catherine Lozupone1 and Rob Knight2*

Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309,1 Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 803092

Received 3 May 2005/ Accepted 26 August 2005

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.

* Corresponding author. Mailing address: Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309. Phone: (303) 492-1984. Fax: (303) 492-7744. E-mail: rob{at}spot.colorado.edu.

Applied and Environmental Microbiology, December 2005, p. 8228-8235, Vol. 71, No. 12
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.12.8228-8235.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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