Metagenomic prospection of bacteria linked to quorum sensing during spontaneous cocoa fermentation

Abstract

The process of fermentation of cocoa beans is not well standardized since it is carried out by microorganisms that are autochthonous from cocoa beans. It is a highly complex process because there is a microbial succession that starts with yeasts and it is maintained and finished by lactic acid and acetic acid bacteria. In this way, many authors tried to achieve a bacterial well-defined starter culture to guarantee the standardization in the characteristic chocolate flavor, that is dependent on microbial metabolites released during this process. Nevertheless, it is not described yet in literature a starter culture that may be applied successfully in the fermentative process. Moreover, some authors mentioned the quality of chocolate might be related to the presence of genes related to Quorum Sensing (QS) or Quorum Quenching (QQ) classic pathways. In that context, it is important to understand the dynamics of the fermentation process under bacterial communication view, isolating strains that dominate in a process to develop, after phenotypic characterization, a starter well-defined culture. In conclusion, our goals are: (I) study the microbiota of cocoa beans fermentation during specific times; (II) To sequence genomic DNA extracted from fermentation samples and to analyze with Illumina HiSeq 2500 platforms;(III) do bioinformatic analysis to identify bacterial strains that express genes related to QS and QQ; (IV) Enumerate, isolate and perform phenotypic analysis in QS bioassays to measure QSexpression genes in vitro; (V) Use HPLC-MS/MS to quantify the autoinducer molecules present in isolated bacterial cultures; (VI) Propose a starter culture with well-defined bacterial populations for cocoa fermentation. The results of this project should contribute to improvement and selection of flavors during cocoa beans fermentation. (AU)