UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
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 fr...
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ftpubmed:oai:pubmedcentral.nih.gov:1317376 2023-05-15T13:44:10+02:00 UniFrac: a New Phylogenetic Method for Comparing Microbial Communities Lozupone, Catherine Knight, Rob 2005-12 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317376 http://www.ncbi.nlm.nih.gov/pubmed/16332807 https://doi.org/10.1128/AEM.71.12.8228-8235.2005 en eng American Society for Microbiology http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317376 http://www.ncbi.nlm.nih.gov/pubmed/16332807 http://dx.doi.org/10.1128/AEM.71.12.8228-8235.2005 Copyright © 2005, American Society for Microbiology Methods Text 2005 ftpubmed https://doi.org/10.1128/AEM.71.12.8228-8235.2005 2013-08-30T18:45:43Z 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. Text Antarc* Antarctic Arctic Sea ice PubMed Central (PMC) Arctic Antarctic Applied and Environmental Microbiology 71 12 8228 8235 |
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Methods Lozupone, Catherine Knight, Rob UniFrac: a New Phylogenetic Method for Comparing Microbial Communities |
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Methods |
description |
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. |
format |
Text |
author |
Lozupone, Catherine Knight, Rob |
author_facet |
Lozupone, Catherine Knight, Rob |
author_sort |
Lozupone, Catherine |
title |
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities |
title_short |
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities |
title_full |
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities |
title_fullStr |
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities |
title_full_unstemmed |
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities |
title_sort |
unifrac: a new phylogenetic method for comparing microbial communities |
publisher |
American Society for Microbiology |
publishDate |
2005 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317376 http://www.ncbi.nlm.nih.gov/pubmed/16332807 https://doi.org/10.1128/AEM.71.12.8228-8235.2005 |
geographic |
Arctic Antarctic |
geographic_facet |
Arctic Antarctic |
genre |
Antarc* Antarctic Arctic Sea ice |
genre_facet |
Antarc* Antarctic Arctic Sea ice |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317376 http://www.ncbi.nlm.nih.gov/pubmed/16332807 http://dx.doi.org/10.1128/AEM.71.12.8228-8235.2005 |
op_rights |
Copyright © 2005, American Society for Microbiology |
op_doi |
https://doi.org/10.1128/AEM.71.12.8228-8235.2005 |
container_title |
Applied and Environmental Microbiology |
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71 |
container_issue |
12 |
container_start_page |
8228 |
op_container_end_page |
8235 |
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1766198306219753472 |