Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution
Article first published online: 4 FEB 2009
© 2009 The Authors. Journal compilation © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd
Volume 11, Issue 4, pages 733–740, April 2009
How to Cite
Ishii, S. and Sadowsky, M. J. (2009), Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution. Environmental Microbiology, 11: 733–740. doi: 10.1111/j.1462-2920.2008.01856.x
- Issue published online: 1 APR 2009
- Article first published online: 4 FEB 2009
- Received 14 October, 2008; accepted 27 November, 2008.
A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or ‘fingerprints’ of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.