Cited by 8,227Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesPolar Research and Ecology

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UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

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Lozupone, Catherine, Knight, Rob·2005·Applied and Environmental Microbiology

DOI 10.1128/aem.71.12.8228-8235.2005PMC PMC1317376

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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.

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“…et al., 2010; Chang et al., 2011; Chen et al., 2012; Halko et al., 2011; Katoh & Standley, 2013; Legendre & Legendre, 2012; Lozupone et al., 2007; Lozupone & Knight, 2005; McDonald et al., 2012, 2018; McKinney, 2010; Price et al., 2010; Stackebrandt & Goodfellow, 1991; Vázquez-Baeza et al.,…”
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Self-citation

Authors: Lozupone, C., & Knight, R.
Affiliations: University of Colorado Boulder (US)
Corresponding author: Knight, Rob
ORCID: Lozupone, Catherine
Knight, Rob
Venue: Applied and Environmental Microbiology
Publisher: American Society for Microbiology
Published: 2005-12
Volume: 71
Issue: 12
Pages: 8228-8235
ISSN: 0099-2240 (ISSN-L)
1098-5336
DOI: 10.1128/aem.71.12.8228-8235.2005
PMC: PMC1317376
OpenAlex: W2170024099
Cited by: 8,227
References: 48
Citations by year: 2026: 311 · 2025: 420 · 2024: 500 · 2023: 564 · 2022: 681 · 2021: 832 · 2020: 766 · 2019: 654 · 2018: 676 · 2017: 607 · 2016: 508 · 2015: 401 · 2014: 363 · 2013: 281 · 2012: 210
FWCI: 31.33
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
Locations: Applied and Environmental Microbiology (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health
National Institute of General Medical Sciences (T32-GM08759, T32GM008759, T32GM142607)
Topics: Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Environmental Science › Ecology › Polar Research and Ecology
Keywords: UniFrac, phylogenetic distance, microbial community comparison, 16S rRNA gene library, bacterial communities, community clustering, ordination, sea ice bacteria, marine sediment bacteria, marine bacteria
MeSH terms: Bacteria, Genetic Techniques, Geography, Phylogeny, RNA, Ribosomal, 16S

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UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

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