Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities

Applied and Environmental Microbiology

Volumn 73, Issue 5, 2007, Pages 1576-1585

  Lozupone, Catherine A ^a   Hamady, Micah ^b   Kelley, Scott T ^c   Knight, Rob ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UCB 450   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; CLASSIFICATION (OF INFORMATION); DATA ACQUISITION; GEOTHERMAL SPRINGS; PARKS; RNA; WEBSITES;

MICROBIAL DIVERSITY; PHYLOGENY; TAXON; UNIFRAC;

BACTERIA;

RNA 16S;

ABUNDANCE; COMMENSAL; COMMUNITY STRUCTURE; KINSHIP; MICROBIAL COMMUNITY; OBESITY; PHLOGOPITE; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; RNA; RODENT; SPECIES DIVERSITY; THERMAL SPRING;

CHEMISTRY; GEOGRAPHY; INTESTINE FLORA; MEASUREMENT; MICROBIAL DIVERSITY; MICROFLORA; MOUSE; NONHUMAN; OBESITY; PHYLOGENY; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REVIEW; TAXON; TEMPERATURE SENSITIVITY; THERMAL SPRING; UNITED STATES;

ANIMALS; BACTERIA; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DIGESTIVE SYSTEM; DNA, RIBOSOMAL; ECOSYSTEM; GENES, RRNA; GEOLOGIC SEDIMENTS; HOT SPRINGS; MICE; PHYLOGENY; RNA, RIBOSOMAL, 16S; VARIATION (GENETICS);

NORTH AMERICA; UNITED STATES; YELLOWSTONE NATIONAL PARK;

EID: 33947269742     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.01996-06     Document Type: Review

References (34)

1. Badano, E. I., and L. A. Cavieres. 2006. Impacts of ecosystem engineers on community attributes: effects of cushion plants at different elevations of the Chilean Andes. Divers. Distrib. 12:388-396.
2. Bluis, J., and D. Shin. 2003. Nodal distance algorithm: calculating a phylogenetic tree comparison metric, p. 87-94. In Proceedings of the Third IEEE Symposium on BioInformatics and BioEngincering. IEEE. Los Alamitos, CA.
3. Breitbart, M., P. Salamon, B. Andresen, J. M. Mahaffy, A. M. Segall, D. Mead, F. Azam, and F. Rohwer. 2002. Genomic analysis of uncultured marine viral communities. Proc. Natl. Acad. Sci. USA 99:14250-14255.
4. De Benedictis, P. A. 1973. On the correlations between certain diversity indices. Am. Nat. 107:295-302.
5. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Inc., Sunderland, MA.
6. Felsenstein, J. 1989. PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:164-166.
7. Gower, J. C. 1966. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53:325-338.
8. Hill, M. O. 1973. Diversity and evenness: a unifying notion and its consequences. Ecology 54:427-432.
9. Hugenholtz, P. 2002. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3:REV1EWS0003.
10. Ingalls, A. M., M. M. Dickie, and G. D. Snell. 1950. Obese, a new mutation in the house mouse. J. Hered. 41:317-318.
11. Ley, R. E., F. Backhed, P. Turnbaugh, C. A. Lozupone, R. D. Knight, and J. I. Gordon. 2005. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA 102:11070-11075.
12. Lozupone, C., M. Hamady, and R. Knight. 2006. UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371-384.
13. Lozupone, C., and R. Knight. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235.
14. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, W. Forster, I. Brettske, S. Gerber, A. W. Ginhart, O. Gross, S. Grumann, S. Hermann, R. Jost, A. Konig, T. Liss, R. Lussmann, M. May, B. Nonhoff, B. Reichel, R. Strehlow, A. Stamatakis, N. Stuckmann, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, and K. H. Schleifer. 2004. ARB: a Software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
15. Ma, M. 2005. Species richness vs. evenness: independent relationship and different responses to edaphic factors. OIKOS 111:192-198.
16. Magurran, A. E. 2004. Measuring biological diversity. Blackwell, Oxford, United Kingdom.
17. Manier, D. J., and N. T. Hohhs. 2006. Large herbivores influence the composition and diversity of shrub-stepped communities in the Rocky Mountains, USA. Oecologica 146:641-651.
18. Martin, A. P. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68:3673-3682.
19. 18a. Mathur, J., R. W. Bizzocn, D. G. Ellis, D. A. Lipson, A. W. Poole, R. Levine, and S. T. Kelley. 12 January 2007. Effects of abiotic factors on phylogenetic diversity of bacterial communities in acidic thermal springs. Appl. Environ. Microbiol. doi:10.1128/AEM.02567-06.
20. May, R. M. 1975. Patterns of species abundance and diversity, p. 81-120. In M. L. Cody and J. L. Diamond (ed.), Ecology and evolution of communities. Harvard University Press, Cambridge, MA.
21. Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734-740.
22. Pace, N. R., D. A. Stahl, D. J. Lane, and G. J. Olsen. 1985. Analyzing natural microbial populations by rRNA sequences. ASM News 51:4-12.
23. Penny, D., and M. D. Hendy. 1985. The use of tree comparison metrics. Syst. Zool. 34:75-82.
24. Pulley, H. W., J. D. Derner, and B. J. Wilsey. 2005. Patterns of plant species diversity in remnant and restored tallgrass prairies. Restor. Ecol. 13:480-487.
25. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
26. Sneath, P. H. A., and K. R. Sokal. 1973. Numerical taxonomy-the principles and practice of numerical classification. W. H. Freeman, San Francisco, CA.
27. Stamatakis, A., T. Ludwig, and H. Meier. 2005. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21:456-463.
28. Stirling, G., and B. Wilsey. 2001. Empirical relationships between species richness, evenness, and proportional diversity. Am. Nat. 158:286-299.
29. Toti, D. S., F. A. Coyle, and J. A. Miller. 2000. A structured inventory of Appalachian grass bald and heath bald spider assemblages and a test of species richness estimator performance. J. Arachnol. 28:329-345.
30. Wehh, C. O. 2000. Exploring the phylogenetic structure of ecological communities: an example for rain forest trees. Am. Nat. 156:145-155.
31. Wehh, C. O., D. D. Ackerley, M. A. McPeek, and M. J. Donoghue. 2002. Phylogenics and community ecology. Annu. Rev. Ecol. Syst. 33:475-505.
32. Whittaker, R. H. 1972. Evolution and measurement of species diversity. Taxon 21:213-251.
33. Xenopolous, M. A., and P. C. Frost. 2003. UV radiation, phosphorus, and their combined effects on the taxonomic composition of phytoplankton in a boreal lake. J. Phycol. 39:291-302.
34. Zhang, Y., R. Proenca, M. Maffei, M. Barone, L. Leopold, and J. M. Friedman. 1994. Positional cloning of the mouse obese gene and its human homologue. Nature 372:425-432.