Introducing TreeClimber, a test to compare microbial community structures - PubMed (original) (raw)

Comparative Study

Introducing TreeClimber, a test to compare microbial community structures

Patrick D Schloss et al. Appl Environ Microbiol. 2006 Apr.

Abstract

The phylogenetic and ecological complexity of microbial communities necessitates the development of new methods to determine whether two or more communities have the same structure even though it is not possible to sample the communities exhaustively. To address this need, we adapted a method used in population genetics, the parsimony test, to determine the relatedness of communities. Here we describe our implementation of the parsimony test, TreeClimber, in which we reanalyzed six previously published studies and compared the results of the analysis to those obtained using integral-LIBSHUFF.

PubMed Disclaimer

Figures

FIG. 1.

Examples of using Fitch's algorithm (11) to score a phylogenetic tree when samples are obtained from two communities. The letters represent treatments for the nodes, and the numbers represent the treatment label for each sequence considered. The parsimony scores (P) and treatment labels for each node as they aggregate through the nodes are indicated.

FIG. 2.

TreeClimber-generated probability distribution of MrBayes-generated and neighbor-joining (NJ) phylogenetic trees for the data of McCaig et al. (21). A Scottish soil data set was compared to the distribution of scores obtained from 10,000 random joining trees when there were 137 and 138 samples for each treatment. The asterisk at a parsimony score of 84 indicates the score at which the cumulative random probability was equal to 0.047. When MrBayes-generated trees were used, 98.2% of the trees had a P value less than 0.05 and the P value for the neighbor-joining tree was 0.004.

Similar articles

• Evaluating different approaches that test whether microbial communities have the same structure.
  Schloss PD. Schloss PD. ISME J. 2008 Mar;2(3):265-75. doi: 10.1038/ismej.2008.5. Epub 2008 Jan 31. ISME J. 2008. PMID: 18239608
• Microbial community succession and bacterial diversity in soils during 77,000 years of ecosystem development.
  Tarlera S, Jangid K, Ivester AH, Whitman WB, Williams MA. Tarlera S, et al. FEMS Microbiol Ecol. 2008 Apr;64(1):129-40. doi: 10.1111/j.1574-6941.2008.00444.x. Epub 2008 Mar 6. FEMS Microbiol Ecol. 2008. PMID: 18328082
• Use of multivariate statistics for 16S rRNA gene analysis of microbial communities.
  Rudi K, Zimonja M, Trosvik P, Naes T. Rudi K, et al. Int J Food Microbiol. 2007 Nov 30;120(1-2):95-9. doi: 10.1016/j.ijfoodmicro.2007.06.004. Epub 2007 Jun 12. Int J Food Microbiol. 2007. PMID: 17602772 Review.
• Phylogenetic approaches for describing and comparing the diversity of microbial communities.
  Martin AP. Martin AP. Appl Environ Microbiol. 2002 Aug;68(8):3673-82. doi: 10.1128/AEM.68.8.3673-3682.2002. Appl Environ Microbiol. 2002. PMID: 12147459 Free PMC article. Review. No abstract available.

Cited by

• Bacterial succession on the leaf surface: a novel system for studying successional dynamics.
  Redford AJ, Fierer N. Redford AJ, et al. Microb Ecol. 2009 Jul;58(1):189-98. doi: 10.1007/s00248-009-9495-y. Epub 2009 Feb 17. Microb Ecol. 2009. PMID: 19221834
• Bacterial communities associated with tuberculate ectomycorrhizae of Rhizopogon spp.
  Kretzer AM, King ZR, Bai S. Kretzer AM, et al. Mycorrhiza. 2009 Apr;19(4):277-282. doi: 10.1007/s00572-008-0213-2. Epub 2008 Dec 9. Mycorrhiza. 2009. PMID: 19066986
• Comparison of next-generation sequencing samples using compression-based distances and its application to phylogenetic reconstruction.
  Tran NH, Chen X. Tran NH, et al. BMC Res Notes. 2014 May 29;7:320. doi: 10.1186/1756-0500-7-320. BMC Res Notes. 2014. PMID: 24886411 Free PMC article.
• Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures.
  Schloss PD, Handelsman J. Schloss PD, et al. Appl Environ Microbiol. 2006 Oct;72(10):6773-9. doi: 10.1128/AEM.00474-06. Appl Environ Microbiol. 2006. PMID: 17021230 Free PMC article.
• K-shuff: A Novel Algorithm for Characterizing Structural and Compositional Diversity in Gene Libraries.
  Jangid K, Kao MH, Lahamge A, Williams MA, Rathbun SL, Whitman WB. Jangid K, et al. PLoS One. 2016 Dec 2;11(12):e0167634. doi: 10.1371/journal.pone.0167634. eCollection 2016. PLoS One. 2016. PMID: 27911946 Free PMC article.

References

1. 1. Begon, M., J. L. Harper, and C. R. Townsend. 1996. Ecology: individuals, populations, and communities, 3rd ed., p. 829-830. Blackwell Science, Malden, MA.
2. 1. Bond, P. L., P. Hugenholtz, J. Keller, and L. L. Blackall. 1995. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl. Environ. Microbiol. 61:1910-1916. - PMC - PubMed
3. 1. Breitbart, M., B. Felts, S. Kelley, J. M. Mahaffy, J. Nulton, P. Salamon, and F. Rohwer. 2004. Diversity and population structure of a near-shore marine-sediment viral community. Proc. R. Soc. Lond. B Biol. Sci. 271:565-574. - PMC - PubMed
4. 1. 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.
5. 1. Curtis, T. P., W. T. Sloan, and J. W. Scannell. 2002. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 99:10494-10499. - PMC - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Atypon
  • Europe PubMed Central
  • PubMed Central

• Medical

  • MedlinePlus Health Information