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...
Main Authors: | , |
---|---|
Other Authors: | |
Format: | Text |
Language: | English |
Published: |
2005
|
Subjects: | |
Online Access: | http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.540.3312 http://webpages.math.luc.edu/~tobrien/Lonzopone2005.pdf |
id |
ftciteseerx:oai:CiteSeerX.psu:10.1.1.540.3312 |
---|---|
record_format |
openpolar |
spelling |
ftciteseerx:oai:CiteSeerX.psu:10.1.1.540.3312 2023-05-15T13:50:57+02:00 Unifrac: a new phylogenetic method for comparing microbial communities Catherine Lozupone Rob Knight The Pennsylvania State University CiteSeerX Archives 2005 application/pdf http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.540.3312 http://webpages.math.luc.edu/~tobrien/Lonzopone2005.pdf en eng http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.540.3312 http://webpages.math.luc.edu/~tobrien/Lonzopone2005.pdf Metadata may be used without restrictions as long as the oai identifier remains attached to it. http://webpages.math.luc.edu/~tobrien/Lonzopone2005.pdf text 2005 ftciteseerx 2016-01-08T11:02:20Z 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 signifi-cantly 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 Text Antarc* Antarctic Arctic Sea ice Unknown Antarctic Arctic |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
ftciteseerx |
language |
English |
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 signifi-cantly 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 |
author2 |
The Pennsylvania State University CiteSeerX Archives |
format |
Text |
author |
Catherine Lozupone Rob Knight |
spellingShingle |
Catherine Lozupone Rob Knight Unifrac: a new phylogenetic method for comparing microbial communities |
author_facet |
Catherine Lozupone Rob Knight |
author_sort |
Catherine Lozupone |
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 |
publishDate |
2005 |
url |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.540.3312 http://webpages.math.luc.edu/~tobrien/Lonzopone2005.pdf |
geographic |
Antarctic Arctic |
geographic_facet |
Antarctic Arctic |
genre |
Antarc* Antarctic Arctic Sea ice |
genre_facet |
Antarc* Antarctic Arctic Sea ice |
op_source |
http://webpages.math.luc.edu/~tobrien/Lonzopone2005.pdf |
op_relation |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.540.3312 http://webpages.math.luc.edu/~tobrien/Lonzopone2005.pdf |
op_rights |
Metadata may be used without restrictions as long as the oai identifier remains attached to it. |
_version_ |
1766254418171265024 |