DNA fingerprinting techniques applied to the identification, taxonomy and community analysis of prokaryotes

Abstract

The characterization of bacteria or microbial communities at the genotypic level is of crucial importance to medical, industrial and environmental microbiology, as well as microbial ecology and taxonomy. Compared to phenotypic testing, molecular methods based on the investigation of total DNA or segments of DNA are superior because the analysis is independent of possible variations in cultures due to growth and media conditions (e.g. temperature, pH, composition of media). Furthermore, other methods such as serotyping have been shown to be an excellent method for typing certain strains, e.g. Salmonella. However, the discriminatory power of serotyoing may be low for other groups of strains. For example, most strains of Staphylococcus aureus (Karakawa et al. 1985) express a single serotype only. During recent years, a broad spectrum of DNA-fingerprinting techniques have been developed, covering all ranks between phylum and strains, including those taxa that have not yet been cultured in the laboratory. At the beginning of the molecular era, pulsed-field gel electrophoresis was applied to the discrimination of yeast strains (Schwartz and Cantor 1984). In the following decade, the resolution power of genes coding ribosomal RNA for the identification and taxonomy of species (Pace et al. 1986; Woese 1987) was investigated. Researchers can now choose from a wide spectrum of techniques, spanning applications such as the identification and authentification of strains, phylogenetic analysis and the elucidation of microbial epidemiology and population structures. © 2006 Springer-Verlag Berlin Heidelberg.