UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Catherine A. Lozupone,Rob Knight +1 more
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The 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.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.read more
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phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
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Metagenomic biomarker discovery and explanation
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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
J. Gregory Caporaso,Christian L. Lauber,William A. Walters,Donna Berg-Lyons,Catherine A. Lozupone,Peter J. Turnbaugh,Noah Fierer,Rob Knight +7 more
TL;DR: This work sequences a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample to demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature.
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