UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context

We introduce UniFrac, a web application available at http://bmf.colorado.edu/unifrac webcite, that allows several phylogenetic tests for differences among communities to be easily applied and interpreted. We demonstrate the use of UniFrac to cluster multiple environments, and to test which environments are significantly different. We show that analysis of previously published sequences from the Columbia river, its estuary, and the adjacent coastal ocean using the UniFrac interface provided insights that were not apparent from the initial data analysis, which used other commonly employed techniques to compare the communities.UniFrac provides easy access to powerful multivariate techniques for comparing microbial communities in a phylogenetic context. We thus expect that it will provide a completely new picture of many microbial interactions and processes in both environmental and medical contexts.Sequencing microbial genes directly from the environment has uncovered a vast diversity of microbial lineages that had not been found by techniques that require cultivation [1,2]. The gene encoding the small subunit of ribosomal RNA (SSU rRNA) has been especially useful as a marker for phylogenetic diversity [1]. Although sequences are often used to catalogue the types of microorganisms present in a single environment, comparisons between sequences from multiple environments are increasingly important because they can test whether microbial community composition changes in response to specific environmental variables. Such applications include testing how disease affects oral or gut microbial communities [3-5], understanding industrial processes such as the different types of activated sludge in batch reactors [6], understanding how pollution affects natural ecosystems [7,8], and understanding the basic ecology and distribution of microbes [7,9,10].When comparing microbial communities, researchers often begin by determining whether each pair of communities is significantly d