Use of the rpoB gene as an alternative to the V3 gene for the identification of spoilage and pathogenic bacteria species in milk and milk products

Aim: To evaluate the rpoB gene as an alternative to the V3 gene for the identification of bacterial species in milk and milk products. Methods and Results: DNA obtained from different bacterial species strains was amplified by PCR using rpoB primers. PCR products of each bacterial species were then separated on a DGGE gel. The molecular fingerprints of the bacterial species tested were integrated into a database. The DGGE analysis shows a single band for the rpoB gene amplicons per each bacterial species. Comparison of electrophoretic profiles obtained from V3 16S rDNA amplification with those from this study obtained with rpoB showed that for some bacterial species that co‐migrated after amplification of the V3 region, distinct bands were observed on the gel with the amplification products of the rpoB region. Conclusions: The results obtained in this study show the discriminatory power of the rpoB gene, indicating that it can be used as an alternative to the V3 16S rRNA gene for the identification of bacterial species in milk and milk products. Significance and Impact of the Study: PCR‐DGGE targeting the rpoB gene is a way of discriminating the bacterial species that co‐migrated with the amplification of the V3 gene and so avoids the sequencing of the co‐migrating bands.