Diversity, dynamics and activity of bacterial populations in 'Registered Designation of Origin' Salers cheese by single-strand conformation polymorphism analysis of 16S rRNA genes

Abstract

The aim of this work was to measure the dynamic global metabolic activities of the microbial community during ripening of RDO Salers cheese by using a direct molecular approach. A culture-independent approach including PCR, reverse transcriptase PCR (RT-PCR) and single strand conformation polymorphism (SSCP) analysis of 16S rRNA genes was applied on 'Registered Designation of Origin' Salers cheese samples collected in three farms. The evolution of the global structure of the microbial community in terms of structure or global activities was assessed using ecological indices. The diversity of the global population was higher on RNA patterns than on DNA patterns, because of less dominance and greater richness. Comparison of the SSCP patterns derived from RNA and DNA analysis indicated that the dominant population was not necessarily the most active. The metabolic activities of each bacterial group changed significantly during ripening. Besides lactic acid bacteria that were dominant on both DNA and RNA patterns, the dynamics of the presence and activity of microbial groups rarely studied in the core of cheese, such as corynebacteria, or of unidentified peaks were reported. By using SSCP RNA analysis, we were able to obtain information about the activity of bacterial population in cheese, which varied a lot between cheeses and was changing perpetually during ripening. Double DNA-RNA SSCP analysis opens up future prospects in the microbial ecology of cheeses. It will have many applications for controlling of microbial community during cheese processing.