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Applied and Environmental Microbiology, March 2007, p. 1576-1585, Vol. 73, No. 5
0099-2240/07/$08.00+0     doi:10.1128/AEM.01996-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Quantitative and Qualitative ß Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities{triangledown}

Catherine A. Lozupone,1 Micah Hamady,2 Scott T. Kelley,3 and Rob Knight4*

Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309,1 Department of Computer Science, University of Colorado, Boulder, Colorado 80309,2 Department of Biology, San Diego State University, San Diego, California 92182-4614,3 Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 803094

Received 23 August 2006/ Accepted 20 December 2006

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 ß 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.

* Corresponding author. Mailing address: Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309. Phone: (303) 492-1984. Fax: (303) 492-7744. E-mail: rob{at}spot.colorado.edu.

{triangledown} Published ahead of print on 12 January 2007.

Applied and Environmental Microbiology, March 2007, p. 1576-1585, Vol. 73, No. 5
0099-2240/07/$08.00+0     doi:10.1128/AEM.01996-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



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