Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities
Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities
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DOI：
10.1128/aem.01996-06
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发表时间：
2007-03-01
影响因子：
4.4
通讯作者：
Knight, Rob
中科院分区：
文献类型：
--
作者：
Lozupone, Catherine A.;Hamady, Micah;Knight, Rob
微生物多样性和分布的评估是环境微生物学的主要关注点。衡量群落多样性的一般方法有两种：使用每个分类单元的丰度的定量措施和仅使用有/无数据的定性措施。定量测量非常适合于揭示由于相对分类单元丰度的变化而引起的群落差异（例如，当一组特定的分类群因为有限的营养源变得丰富而繁荣时）。当社区的差异主要在于哪些人可以生活在其中时，定性措施提供的信息最多（例如，在高温下），部分原因是丰度信息可能掩盖分类群存在的重要变异模式。我们使用两个基于16 S rRNA的微生物种群调查和两个群落β多样性的系统发育测量来说明这些原则：未加权的UniFrac，一种定性测量，和加权的UniFrac，一种新的定量测量，我们已经将其添加到UniFrac网站（http：//bmf.colorado.edu/unifrac）。这些研究考虑了矿物化学、温度和地理对黄石国家公园酸性温泉中微生物群落组成的相对影响，以及肥胖和亲属关系对小鼠肠道微生物群落组成的影响。我们表明，将定性和定量措施应用于相同的数据集，可以导致显着不同的结论结构微生物多样性的主要因素，并可以提供洞察社区差异的性质。我们还证明，加权和未加权的UniFrac测量是强大的方法来建立潜在的遗传学。
The assessment of microbial diversity and distribution is a major concern in environmental microbiology. There are two general approaches for measuring community diversity: quantitative measures, which use the abundance of each taxon, and qualitative measures, which use only the presence/absence of data. Quantitative measures are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present. We illustrate these principles using two 16S rRNA-based surveys of microbial populations and two phylogenetic measures of community beta diversity: unweighted UniFrac, a qualitative measure, and weighted UniFrac, a new quantitative measure, which we have added to the UniFrac website (http://bmf.colorado.edu/unifrac). These studies considered the relative influences of mineral chemistry, temperature, and geography on microbial community composition in acidic thermal springs in Yellowstone National Park and the influences of obesity and kinship on microbial community composition in the mouse gut. We show that applying qualitative and quantitative measures to the same data set can lead to dramatically different conclusions about the main factors that structure microbial diversity and can provide insight into the nature of community differences. We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny.