Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures

Applied and Environmental Microbiology

Volumn 72, Issue 10, 2006, Pages 6773-6779

  Schloss, Patrick D ^a,b   Handelsman, Jo ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; ECOLOGY; MOLECULAR STRUCTURE; PROBABILITY; STATISTICAL METHODS;

MICROBIAL COMMUNITY; OPERATIONAL TAXONOMIC UNIT (OTU); PHYLOGENETIC TREES;

MICROBIOLOGY;

BIODIVERSITY; COMMUNITY STRUCTURE; MICROBIAL COMMUNITY; SOFTWARE; TAXONOMY;

ARTICLE; COMMUNITY STRUCTURE; COMPUTER PROGRAM; ECOLOGY; HUMAN; MICROBIAL DIVERSITY; MICROFLORA; MOUSE; NONHUMAN; NONPARAMETRIC TEST; OPERATIONAL TAXONOMIC UNIT; PHYLOGENETIC TREE; PROBABILITY; SPECIES DISTRIBUTION; SPECIES RICHNESS; STATISTICAL ANALYSIS; TAXONOMY;

BIODIVERSITY; CLASSIFICATION; ECOLOGY; ECOSYSTEM; ENVIRONMENTAL MICROBIOLOGY; NUCLEAR FAMILY; SOFTWARE;

OTUS;

EID: 33750078701     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.00474-06     Document Type: Article

References (27)

1. Anderson, M. J. 2001. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 26:32-46.
2. Burnham, K. P., and W. S. Overton. 1979. Robust estimation of population size when capture probabilities vary among animals. Ecology 60:927-936.
3. Chao, A. 1984. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 11:265-270.
4. Chao, A., R. L. Chazdon, R. K. Colwell, and T.-J. Shen. 2006. Abundance-based similarity indices and their estimation when there are unseen species in samples. Biometrics 62:361-371.
5. Chao, A., R. L. Chazdon, R. K. Colwell, and T. J. Shen. 2005. A new statistical approach for assessing similarity of species composition with incidence and abundance data. Ecol. Lett. 8:148-159.
6. Chao, A., W.-H. Hwang, Y.-C. Chen, and C.-Y. Kuo. 2000. Estimating the number of shared species in two communities. Stat. Sinica 10:227-246.
7. Chao, A., and S. M. Lee. 1992. Estimating the number of classes via sample coverage. J. Am. Stat. Assoc. 87:210-217.
8. Chao, A., T. J. Shen, and W. H. Hwang. 2006. The applications of Laplace's boundary-mode approximations to estimate species richness and shared species richness. Aust. N. Z. J. Stat. 48:117-128.
9. Eckburg, P. B., E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E. Nelson, and D. A. Relman. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638.
10. Excoffier, L., P. E. Smouse, and J. M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491.
11. Horner-Devine, M. C., M. Lage, J. B. Hughes, and B. J. Bohannan. 2004. A taxa-area relationship for bacteria. Nature 432:750-753.
12. Hughes, J. B., J. J. Hellmann, T. H. Ricketts, and B. J. M. Bohannan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:4399-4406.
13. 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.
14. Lozupone, C., and R. Knight. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl. Environ. Microbiol. 71:8228-8235.
15. Ludwig, W., O. Strunk, R. Westram, L. Richter, H. Meier, Yadhukumar, A. Buchner, T. Lai, S. Steppi, G. Jobb, et al. 2004. ARB: a software environment for sequence data. Nucleic Acids Res. 32:1363-1371.
16. Maddison, W. P., and M. Slatkin. 1991. Null models for the number of evolutionary steps in a character on a phylogenetic tree. Evolution 45:1184-1197.
17. Mai, V., O. C. Stine, and J. G. M. J. Morris. 2005. Timing in collection of stool samples. Science 310:1118.
18. Martin, A. P. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68:3673-3682.
19. Pei, Z., E. J. Bini, L. Yang, M. Zhou, F. Francois, and M. J. Blaser. 2004. Bacterial biota in the human distal esophagus. Proc. Natl. Acad. Sci. USA 101:4250-4255.
20. Schloss, P. D., and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71:1501-1506.
21. Schloss, P. D., and J. Handelsman. 2006. Introducing TreeClimber, a test to compare microbial community structures. Appl. Environ. Microbiol. 72:2379-2384.
22. Schloss, P. D., B. R. Larget, and J. Handelsman. 2004. Integration of microbial ecology and statistics: a test to compare gene libraries. Appl. Environ. Microbiol. 70:5485-5492.
23. Seguritan, V., and F. Rohwer. 2001. FastGroup: a program to dereplicate libraries of 16S rDNA sequences. BMC Bioinformatics 2:9.
24. Singleton, D. R., M. A. Furlong, S. L. Rathbun, and W. B. Whitman. 2001. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67:4374-4376.
25. Smith, W., A. R. Solow, and P. E. Preston. 1996. An estimator of species overlap using a modified beta-binomial model. Biometrics 52:1472-1477.
26. Yue, J. C., and M. K. Clayton. 2005. A similarity measure based on species proportions. Commun. Stat. Theor. Methods 34:2123-2131.
27. Yue, J. C., M. K. Clayton, and F. C. Lin. 2001. A nonparametric estimator of species overlap. Biometrics 57:743-749.