Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities View Full Text


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Article Info

DATE

2008-07-22

AUTHORS

Ursel M. E. Schütte, Zaid Abdo, Stephen J. Bent, Conrad Shyu, Christopher J. Williams, Jacob D. Pierson, Larry J. Forney

ABSTRACT

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies. More... »

PAGES

365-380

References to SciGraph publications

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  • 2004-11. Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics in ANTONIE VAN LEEUWENHOEK
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  • 2005-04. Links between Geographic Location, Environmental Factors, and Microbial Community Composition in Sediments of the Eastern Mediterranean Sea in MICROBIAL ECOLOGY
  • 2001-12. Interpreting 16S rDNA T-RFLP Data: Application of Self-Organizing Maps and Principal Component Analysis to Describe Community Dynamics and Convergence in MICROBIAL ECOLOGY
  • 2007-04-04. MiCA: A Web-Based Tool for the Analysis of Microbial Communities Based on Terminal-Restriction Fragment Length Polymorphisms of 16S and 18S rRNA Genes in MICROBIAL ECOLOGY
  • 2004-12-22. Bacterial community profiles on feathers during composting as determined by terminal restriction fragment length polymorphism analysis of 16S rDNA genes in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
  • 2007-05-10. Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2006-07-27. Influence of plant diversity and elevated atmospheric carbon dioxide levels on belowground bacterial diversity in BMC MICROBIOLOGY
  • 2007-07-01. Dynamics of Nitrous Oxide Reductase Genes (nosZ) in Intertidal Rocky Biofilms and Sediments of the Douro River Estuary (Portugal), and their Relation to N-biogeochemistry in MICROBIAL ECOLOGY
  • 2005-10. Soil Bacterial and Fungal Community Structure Across a Range of Unimproved and Semi-Improved Upland Grasslands in MICROBIAL ECOLOGY
  • 2006-06-13. Bacterial diversity in permanently cold and alkaline ikaite columns from Greenland in EXTREMOPHILES
  • 2006-02-01. Improved Strategy for Comparing Microbial Assemblage Fingerprints in MICROBIAL ECOLOGY
  • 2001-10-01. Ecologically meaningful transformations for ordination of species data in OECOLOGIA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00253-008-1565-4

    DOI

    http://dx.doi.org/10.1007/s00253-008-1565-4

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/18648804


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