UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
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 desce...
Published in: | Applied and Environmental Microbiology |
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American Society for Microbiology
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Online Access: | http://dx.doi.org/10.1128/aem.71.12.8228-8235.2005 https://journals.asm.org/doi/pdf/10.1128/AEM.71.12.8228-8235.2005 |
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crasmicro:10.1128/aem.71.12.8228-8235.2005 2024-06-23T07:47:29+00:00 UniFrac: a New Phylogenetic Method for Comparing Microbial Communities Lozupone, Catherine Knight, Rob 2005 http://dx.doi.org/10.1128/aem.71.12.8228-8235.2005 https://journals.asm.org/doi/pdf/10.1128/AEM.71.12.8228-8235.2005 en eng American Society for Microbiology https://journals.asm.org/non-commercial-tdm-license Applied and Environmental Microbiology volume 71, issue 12, page 8228-8235 ISSN 0099-2240 1098-5336 journal-article 2005 crasmicro https://doi.org/10.1128/aem.71.12.8228-8235.2005 2024-06-10T04:07:17Z 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. Article in Journal/Newspaper Antarc* Antarctic Arctic Sea ice ASM Journals (American Society for Microbiology) Arctic Antarctic Applied and Environmental Microbiology 71 12 8228 8235 |
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ASM Journals (American Society for Microbiology) |
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crasmicro |
language |
English |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Lozupone, Catherine Knight, Rob |
spellingShingle |
Lozupone, Catherine Knight, Rob UniFrac: a New Phylogenetic Method for Comparing Microbial Communities |
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://dx.doi.org/10.1128/aem.71.12.8228-8235.2005 https://journals.asm.org/doi/pdf/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_source |
Applied and Environmental Microbiology volume 71, issue 12, page 8228-8235 ISSN 0099-2240 1098-5336 |
op_rights |
https://journals.asm.org/non-commercial-tdm-license |
op_doi |
https://doi.org/10.1128/aem.71.12.8228-8235.2005 |
container_title |
Applied and Environmental Microbiology |
container_volume |
71 |
container_issue |
12 |
container_start_page |
8228 |
op_container_end_page |
8235 |
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1802651593720463360 |