UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Open accessAbstract
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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The multiple sequence alignment obtained from BLS enables improved UniFrac effect size estimation for many variables known to be important to human digestive health.
“Our results show that the multiple sequence alignment (MSA) obtained from BLS (Fig. 1b and Methods) improves microbial phylogeny inference compared to other alignment methods and enables improved UniFrac26 effect size estimation for many variables known to be important to human digestive health.”
From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [26]
Principal Coordinates Unweighted UniFrac analysis separated ileum and colon samples along the first component and the two rooms along PC2 on Food A.
“Principal Coordinates Unweighted UniFrac analysis 20 showed separation of ileum and colon samples along the first component, whereas the two rooms clearly separated along PC2 on Food A (Fig1A and B).”
From The composition of the gut microbiota shapes the colon mucus barrier (2015) · cites this paper as [20]
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- Authors
- Lozupone, C., & Knight, R.
- Affiliations
- University of Colorado Boulder (US)
- Corresponding author
- 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
- 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
- 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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