PCR-DGGE for the profiling of cheese bacterial communities: strengths and weaknesses of a poorly explored combined approach

Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) represents a still valid molecular tool for the profiling of complex microbial ecosystems, including cheeses. In the present study, a double PCR-DGGE approach has been applied to the investigation of the bacterial diversity of seven cheese models to objectively assess strengths and weaknesses of such an approach. To that end, the bacterial DNA was extracted directly from both the cheese replicates and the bulks of colonies harvested from the serial dilution agar plates of selective solid media used for the enumeration of presumptive lactobacilli, lactococci and thermophilic cocci, respectively. The results overall collected allowed the main bacterial taxa to be identified and roughly quantified. Rough quantification of the main cultivable species represents a strength of the PCR-DGGE approach applied, whereas its main weaknesses were represented by the low degree of selectivity of the conventional growth media used for cultivation of lactic acid bacteria and the underestimation of the effective microbial diversity occurring in the seven cheese models.