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

By Catherine A. Lozupone, Micah Hamady, Rob Knight. BMC Bioinformatics, 2006

1,489 citations recorded by the source corpus.

BackgroundMoving beyond pairwise significance tests to compare many microbial communities simultaneously is critical for understanding large-scale trends in microbial ecology and community assembly. Techniques that allow microbial communities to be compared in a phylogenetic context are rapidly gaining acceptance, but the widespread application of these techniques has been hindered by the difficulty of performing the analyses.ResultsWe introduce UniFrac, a web application available at http://bmf.colorado.edu/unifrac, 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.ConclusionUniFrac 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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/07cea93a5c8bf18312ebf2191bd7c115cf055d41

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Citations in the corpus

Soil bacterial and fungal communities across a pH gradient in an arable soil (2010, methodology): “The differences in overall community composition between each pair of samples was determined using the unweighted UniFrac metric (Lozupone and Knight, 2005; Lozupone et al., 2006), which calculates the distance between any pair of communities based on the fraction of unique (nonoverlapping) branch l”
Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer (2012, methodology): “Unweighted UniFrac distance metrics analysis was performed using OTUs for each sample [21,22], and principal Table 1.”
Environmental and ecological factors that shape the gut bacterial communities of fish: a meta‐analysis (2012, methodology): “This web application calculated the UniFrac distance based on the percentage of unique phylogenetic branch length among all pairs of gut communities, thus inferring the extent of phylogenetic overlap between communities from each host (Lozupone & Knight 2005; Lozupone et al. 2006).”
A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses (2009, methodology): “As a final means to characterize Acidobacteria communities, we used UniFrac to cluster soils based on the unique fraction of phylodiversity contained in each soil based on pairwise comparisons between all samples (Lozupone et al., 2006; Lozupone and Knight, 2005).”
Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities (2007, methodology): “edu /unifrac by selecting the “Use Abundance Weights” option, allowing researchers to run both weighted and unweighted analyses in the context of a convenient Web interface (12).”
A diversity profile of the human skin microbiota. (2008, methodology): “The UniFrac package was used to compare unique branch length between communities (Lozupone and Knight 2005; Lozupone et al. 2006).”
Indirect host effect on ectomycorrhizal fungi: Leaf fall and litter quality explain changes in fungal communities on the roots of co-occurring Mediterranean oaks (2010, methodology): “The phylogenetic structure of the ECM communities was statistically assessed using UNIFRAC (Lozupone et al., 2006).”
Testing the functional significance of microbial community composition. (2009, methodology): “We used the weighted UniFrac algorithm (Lozupone et al. 2006) to determine whether soil inocula affected the composition of the microbial communities on each litter type.”
Diversity of Bifidobacteria within the Infant Gut Microbiota (2012, background): “It has been postulated that bacterial transmission may take place from the mother to the newborn/infant through direct contact with maternal microbiota during birth and through breast milk during lactation [16,19,41].”
The Human Microbiome Project (2007, neutral): “Science 315, 1126–1130 (2007). 30.”
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. (2009, background): “…of many improved computational methods for comparing large numbers of microbial communities including UniFrac (Lozupone and Knight 2005; Lozupone et al. 2006), SONS (Schloss and Handelsman 2006), and network-based comparisons (Ley et al. 2008a) will allow very rapid progress to be made.”
Human oral, gut, and plaque microbiota in patients with atherosclerosis (2010, methodology): “To compare diversity between samples, we used the weighted and unweighted UniFrac distance metrics (55, 56) using a random sample of 1,700 sequences per sample (one atherosclerotic plaque sample had fewer than 1,500 sequences and was omitted from the analysis).”