Lozupone Catherine, Knight Rob
Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
Appl Environ Microbiol. 2005 Dec;71(12):8228-35. doi: 10.1128/AEM.71.12.8228-8235.2005.
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.
我们在此介绍一种基于系统发育信息计算微生物群落差异的新方法。这种方法称为UniFrac，它将系统发育树中分类单元集合之间的系统发育距离衡量为树的分支长度中通向一种环境或另一种环境的后代（而非两者）的比例。UniFrac可用于确定群落是否存在显著差异，使用聚类和排序技术同时比较多个群落，并衡量不同因素（如化学和地理因素）对样本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、水和冰中培养菌株及环境克隆的细菌16S rRNA基因文库，来证明其效用。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，且与海冰中的环境克隆序列相似，但与沉积物和水中的环境克隆序列不同；（ii）地理位置与北极和南极的冰和沉积物中的细菌群落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）中的细菌群落与温暖的贫营养海水中的细菌群落不同，而单个海水样本中的细菌群落彼此之间并不比与沉积物或冰样本中的细菌群落更相似。这些结果表明，UniFrac利用丰富的环境rRNA序列提供了一种表征微生物群落的新方法，并允许对环境中谱系分布背后的因素进行定量洞察。
