UniFrac: a new phylogenetic method for comparing microbial communities
UniFrac: a new phylogenetic method for comparing microbial communities
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DOI：
10.1128/aem.71.12.8228-8235.2005
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发表时间：
2005-12-01
影响因子：
4.4
通讯作者：
Knight, R
中科院分区：
文献类型：
--
作者：
Lozupone, C;Knight, R
我们在这里介绍了一种基于系统发育信息计算微生物群落差异的新方法。这种名为UniFrac的方法测量了系统发育树中分类群组之间的系统发育距离，作为从一个环境或另一个环境产生后代的树的分支长度的部分，但不是两个都有。UniFrac可用于确定群落是否显著不同，使用聚类和排序技术同时比较多个群落，并衡量不同因素(如化学和地理)对样本之间相似性的相对贡献。我们通过将UniFrac应用于已发表的来自海洋沉积物、水和冰中细菌的培养分离物和环境克隆的16S rRNA基因库，证明了UniFrac的实用性。我们的结果表明：(I)来自冰、水和沉积物的培养菌株彼此相似，来自海冰的环境克隆序列相似，而来自沉积物和水的环境克隆序列相似；(Ii)地理位置与北极和南极冰和沉积物中细菌群落的差异没有很强的相关性；(Iii)受陆地影响的海水(无论是极地还是温带)和温暖的贫营养海水中的细菌群落存在差异，而单个海水样品中的细菌群落并不比沉积物或冰样中的细菌群落更相似。这些结果表明，UniFrac提供了一种利用丰富的环境rRNA序列来表征微生物群落的新方法，并允许对环境中谱系分布的基础因素进行定量了解。
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.