While rRNA gene analysis has fostered a monumental advance in wine microbiology
by enabling rapid speciation of isolates, the tools for differentiating between different
strains of the same species have advanced as well. This, in turn, has enabled a
much more exquisite dissection of individual constituents at the strain level within
the winery and local environs. Two general approaches have been taken to differentiate
subspecies and strains of wine-related bacteria or yeast. The first employs
whole or sub-genomic analysis through pulse field gel electrophoresis (PFGE),
various genomic RFLP methods or newer array approaches to directly examine the
isolate genomic makeup. The second approach employs whole genome PCR
sampling techniques that result in strain-specific fingerprints from which differentiation
of strains is possible.