Perspective on the use of synthetic biology in rudimentary food fermentations

Abstract

Rudimentary food fermentation can be defined as a spontaneous process of conversion of food components through enzymatic action. A great variety of fermented foods are produced using spontaneous approaches; however, cocoa and coffee represent the most important agricultural commodities on international markets. As a manner to increase the efficiency of these processes, starter cultures have been developed and applied under field conditions. The selection process begins with the recovery of microbial strains from spontaneous fermentation through phenotypic and metabolic traits. Next, mutation-based breeding is used to develop and improve well-adapted starter cultures. With advances in synthetic biology, especially in the last decade, the development of robust cellular fabrications with high fermentative capacity has become easier—largely due to the development of genomic approaches, such as next-generation sequencing techniques, CRISPR-Cas system and bioinformatics tools. This review brings prospects on the use of synthetic biology to design new robust strains for use in cocoa and coffee fermentations, but which can be extended to other rudimentary foods. In addition, metabolic traits and target genes (e.g., UvrA, RecA, GPD1, and GPP2) are proposed as a starting point for the improvement of cocoa and coffee starters. Finally, the regulatory and safety requirements for these food crops are addressed. This review aims to stimulate research on the process of fermentation and the associated synthetic biology tools to produce fermented food efficiently and sustainably.