Evaluation of denaturing gradient gel electrophoresis (DGGE) used to describe structure of bacterial communities in Istrian cheese

Abstract

Denaturing gradient gel electrophoresis (DGGE) is a powerful method used to study structure of bacterial communities, without cultivation, based on the diversity of the genes coding for ribosomal RNA. However, the results are strongly dependent on the respective target region of the used primer systems. Therefore, three primer pairs that amplify different variable regions of the 16S rRNA gene (V1, V3 and V6 to V8) were tested in order to investigate the bacterial diversity existent in Istrian cheese. We found that primer set extremely influenced DGGE analysis. V3 primers were most efficient when 15 cheese associated isolates were resolved by DGGE. However, for Istrian cheese analysis, the best separation and highest number of bands in DGGE patterns were noticed for V6 to V8 primer pairs.

Key words: Denaturing gradient gel electrophoresis, bacterial communities, Istrian cheese.