Statistical assessment of variability of terminal restriction fragment length polymorphism analysis applied to complex microbial communities

Applied and Environmental Microbiology

Volumn 75, Issue 22, 2009, Pages 7268-7270

  Rossi, Pierre ^a   Gillet, François ^a   Rohrbach, Emmanuelle ^a   Diaby, Nouhou ^a   Holliger, Christof ^a  

^a EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MICROORGANISMS;

MICROBIAL COMMUNITIES; POLYMORPHISM ANALYSIS; REPRODUCIBILITIES; STANDARDIZED PROCEDURE; STATISTICAL ASSESSMENT; TECHNOLOGICAL IMPROVEMENTS; TERMINAL RESTRICTION FRAGMENT LENGTH POLYMORPHISMS; TERMINAL RESTRICTION FRAGMENTS;

POLYMORPHISM;

MICROBIAL COMMUNITY; POLYMORPHISM; STATISTICAL ANALYSIS;

ARTICLE; DNA EXTRACTION; ELECTROPHORESIS; GENETIC VARIABILITY; MICROBIAL COMMUNITY; REPRODUCIBILITY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

EID: 70449361164     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00135-09     Document Type: Article

References (27)

1. Abdo, Z., U. M. E. Schuette, S. J. Bent, C. J. Williams, L. J. Forney, and P. Joyce. 2006. Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environ. Microbiol. 8:929-938.
2. Blackwood, C. B., T. Marsh, S. H. Kim, and E. A. Paul. 2003. Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities. Appl. Environ. Microbiol. 69:926-932.
3. Clement, B. G., L. E. Kehl, K. L. DeBord, and C. L. Kitts. 1998. Terminal restriction fragment patterns (TRFPs), a rapid, PCR-based method for the comparison of complex bacterial communities. J. Microbiol. Methods 31:135-142.
4. Culman, S. W., H. G. Gauch, C. B. Blackwood, and J. E. Thies. 2008. Analysis of T-RFLP data using analysis of variance and ordination methods: a comparative study. J. Microbiol. Methods 75:55-63.
5. Egert, M., and M. W. Friedrich. 2003. Formation of pseudo-terminal restriction fragments, a PCR-related bias affecting terminal restriction fragment length polymorphism analysis of microbial community structure. Appl. Environ. Microbiol. 69:2555-2562.
6. Engebretson, J. J., and C. L. Moyer. 2003. Fidelity of select restriction endonucleases in determining microbial diversity by terminal-restriction fragment length polymorphism. Appl. Environ. Microbiol. 69:4823-4829.
7. Fitzjohn, R. G., and I. A. Dickie. 2007. TRAMPR: an R package for analysis and matching of terminal-restriction fragment length polymorphism (TRFLP) profiles. Mol. Ecol. Notes 7:583-587.
8. Frey, J. C., E. R. Angert, and A. N. Pell. 2006. Assessment of biases associated with profiling simple, model communities using terminal-restriction fragment length polymorphism-based analyses. J. Microbiol. Methods 67:9-19.
9. Fromin, N., J. Hamelin, S. Tarnawski, D. Roesti, K. Jourdain-Miserez, N. Forestier, S. Teyssier-Cuvelle, F. Gillet, M. Aragno, and P. Rossi. 2002. Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ. Microbiol. 4:634-643.
10. Grant, A., and L. A. Ogilvie. 2003. Terminal restriction fragment length polymorphism data analysis. Appl. Environ. Microbiol. 69:6342-6343.
11. Hartmann, M., J. Enkerli, and F. Widmer. 2007. Residual polymerase activity-induced bias in terminal restriction fragment length polymorphism analysis. Environ. Microbiol. 9:555-559.
12. Hartmann, M., and F. Widmer. 2008. Reliability for detecting composition and changes of microbial communities by T-RFLP genetic profiling. FEMS Microbiol. Ecol. 63:249-260.
13. Hewson, I., and J. A. Fuhrman. 2006. Improved strategy for comparing microbial assemblage fingerprints. Microb. Ecol. 51:147-153.
14. Kaplan, C. W., and C. L. Kitts. 2003. Variation between observed and true terminal restriction fragment length is dependent on true TRF length and purine content. J. Microbiol. Methods 54:121-125.
15. Legendre, P., and L. Legendre. 1998. Numerical ecology, 2nd ed. Elsevier, Amsterdam, The Netherlands.
16. Lehman, R. M. 2007. Understanding of aquifer microbiology is tightly linked to sampling approaches. Geomicrobiol. J. 24:331-341.
17. Luna, G. M., A. Dell'Anno, and R. Danovaro. 2006. DNA extraction procedure: a critical issue for bacterial diversity assessment in marine sediments. Environ. Microbiol. 8:308-320.
18. Oksanen, J., R. Kindt, P. Legendre, B. O'Hara, G. L. Simpson, and M. H. H. Stevens. 2008. vegan: community ecology package. R package version 1.11-0 http://cran.r-project.org/; http://vegan.r-forge.r-project.org/.
19. Osborne, C. A., M. Galic, P. Sangwan, and P. H. Janssen. 2005. PCR-generated artefact from 16S rRNA gene-specific primers. FEMS Microbiol. Lett. 248:183-187.
20. Osborne, C. A., G. N. Rees, Y. Bernstein, and P. H. Janssen. 2006. New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities. Appl. Environ. Microbiol. 72:1270-1278.
21. Pandey, J., K. Ganesan, and R. K. Jain. 2007. Variations in T-RFLP profiles with differing chemistries of fluorescent dyes used for labeling the PCR primers. J. Microbiol. Methods 68:633-638. (Pubitemid 46329168)
22. Qiu, X. Y., L. Y. Wu, H. S. Huang, P. E. McDonel, A. V. Palumbo, J. M. Tiedje, and J. Z. Zhou. 2001. Evaluation of PCR-generated chimeras: mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl. Environ. Microbiol. 67:880-887.
23. Ramette, A. 2007. Multivariate analyses in microbial ecology. FEMS Microbiol. Ecol. 62:142-160.
24. Rudi, K., M. Zimonja, P. Trosvik, and T. Naes. 2007. Use of multivariate statistics for 16S rRNA gene analysis of microbial communities. Int. J. Food Microbiol. 120:95-99.
25. Schutte, U. M. E., Z. Abdo, S. J. Bent, C. Shyu, C. J. Williams, J. D. Pierson, and L. J. Forney. 2008. Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl. Microbiol. Biotechnol. 80:365-380.
26. Sipos, R., A. J. Szekely, M. Palatinszky, S. Revesz, K. Marialigeti, and M. Nikolausz. 2007. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targeting bacterial community analysis. FEMS Microbiol. Ecol. 60:341-350.
27. Trosvik, P., B. Skanseng, K. S. Jakobsen, N. C. Stenseth, T. Naes, and K. Rudi. 2007. Multivariate analysis of complex DNA sequence electropherograms for high-throughput quantitative analysis of mixed microbial populations. Appl. Environ. Microbiol. 73:4975-4983.