The rpoB gene as a target for PCR-DGGE analysis to follow lactic acid bacteria dynamics during food fermentations

Culture-independent molecular techniques offer a valuable tool in the study and understanding of population dynamics in food fermentations. PCR-DGGE protocols have been developed based on the 16S rDNA gene; however, its heterogeneity complicates interpretation of the results. The rpoB gene, encoding the RNA polymerase beta subunit, usually exists in a single copy and offers a valuable alternative for PCR-DGGE analysis. In this study, PCR products generated from the rpoB gene of several strains of lactic acid bacteria (LAB), responsible for various fermentations, were analysed by DGGE, and a database of rpoB partial sequences was created. Unique DGGE profiles were obtained for rpoB sequences from the Lactobacillus, Lactococcus, Enterococcus, Streptococcus, Leuconostoc and Weisella strains tested, allowing their identification and differentiation in complex ecosystems, such as fermented food products. The application of rpoB targeted PCR-DGGE to tracking ecological changes in food systems during maturation was validated in fermented sausage and cheese.