Microbial population changes during sourdough fermentation monitored by DGGE analysis of 16S and 26S rRNA gene fragments.

In this study, the microbial population dynamics were monitored during a traditional sourdough fermentation process using an integrated approach, including PCR-DGGE and conventional culturing procedures. Total DNA was extracted directly from samples taken at intervals during 24 h of fermentation using a rapid protocol. Partial 16S and 26S rDNA sequences from bacteria and yeasts, respectively, were amplified using two new pairs of primers and the products obtained were separated using denaturing gradient gel electrophoresis (DGGE). DGGE profiles indicated changes in the lactic acid bacteria (LAB) population structure. Sequencing of purified rDNA amplicons revealed that Lactobacillus sanfranciscensis, Lactobacillus brevis, Lactobacillus arizonensis-Lactobacillus plantarum group and Lactobacillus kimchii- Lactobacillus paralimentarius prevailed throughout fermentation. A close relative of the strain CS1, proposed to be a new species associated with Italian sourdoughs, was also detected. The yeast population was represented only by Saccharomyces cerevisiae species. Conventional culture-dependent methods partially reflected PCR-DGGE results, as a lower diversity in LAB species was detected. The present approach proved to be effective in giving a reliable overview of the microbial components of sourdough in a short time.