PCR-DGGE markers for qualitative profiling of microbiota in raw milk and ripened cheeses

•PCR-DGGE markers of twenty four reference strains were developed.•These reference strains represented: starter-, non-starter-, fecal-, spore-forming- and pathogenic bacteria.•PCR-DGGE markers were applied to study microbial biodiversity of raw milk and ripening cheeses.

The aim of the study was to develop a reference markers for the qualitative evaluation of microbiota in raw milk and ripened cheeses with the use of the PCR-DGGE method. A total of 73 reference strains were used, and 24 strains representing 5 bacterial groups were selected to develop reference markers: starter bacteria, non-starter bacteria, fecal bacteria, spore-forming bacteria and pathogenic bacteria. The developed ladders were used to analyze samples of raw milk, cheeses and cheeses cultured on MRS, M17 and ML growth media. The presence of Leuconostoc spp., L. brevis and L. plantarum was determined in raw milk. A direct analysis of cheese samples revealed the prevalence of starter bacteria (P. freudenreichii, L. lactis and Leuconostoc spp.) and non-starter bacteria (L. fermentum and L. plantarum). E. coli, C. perfringens and S. aureus were identified in cheeses cultured on MRS, M17 and ML media. The developed markers are a useful tool for analyzing the microbiota of raw milk and cheese samples, which does not require band isolation, reamplification, sequencing or sequence identification, thus reducing the time and cost of analysis.