Reprint of “Nucleic acid techniques in bacterial systematics and identification" [Int. J. Food Microbiol., 120 (2007) 225–236]

Systematics and identification play central roles in any discipline of microbiology. The current prokaryotic taxonomic framework as proposed in Bergey's Manual of Systematic Bacteriology is mainly based on small subunit rRNA data. Alternative markers representing the conserved core of the prokaryotic genomes roughly support rRNA based phylogenetic inference. Consequently, many of the nucleic acid based techniques for identification target these molecules: i.e. comparative sequencing, specific probing, diagnostic PCR, and pattern techniques. For studies at species and lower taxonomic ranks, however, alternative less conserved targets have to be chosen. An overview of commonly used targets and methods for identification or differentiation is given below.