Dynamics of microbial ecology during cocoa fermentation and drying: Towards the identification of molecular markers

This study aimed to evaluate molecular microbial markers associated with cocoa fermentation and drying steps. The dynamics of microbial populations were analyzed during postharvest processing (fermentation and sun drying) of cocoa from Ivory Coast. The variations in bacterial and yeast communities structure were monitored by a molecular technique (PCR-DGGE) using 16S rRNA and 26S rRNA profiles. Dominant microbial species were determined by sequencing. Our results showed that treatments of cocoa generated great variations in the microbial ecology in terms of number of species detected. The bacterial ecology quickly underwent dramatical changes during the fermentation step after two days. The dominance of Enterobacteria was first observed and then accompanied by Lactic acid bacteria and at the latest stages by acetic acid bacteria. Furthermore, Hanseniaspora opuntiae yeast species predominated during cocoa bean fermentation and drying processes. In addition, two bacterial species were only identified during the drying step of fermented cocoa beans and are potential candidates for biological markers of this process. •Microbial communities exhibited dynamic changes during cocoa fermentation & drying.•Bacterial ecology of cocoa beans is highly altered during post-harvest processing.•Gluconobacter xylinum and Clostridium sp were only detected in drying step.•G. xylinum and Clostridium sp could be molecular markers of quality.