Omics approaches to explore the coffee fermentation microecosystem and its effects on cup quality

The cultivation and postharvest processing of coffee constitute the basis of the subsistence and traditional culture for rural family-owned farms, as well as for the economic success of commercial enterprises in many coffee-producing countries worldwide. The quality of the final beverage is determined by a multitude of variables. A key post-harvest factor is the spontaneous fermentation of the coffee beans, conducted directly on the farm, to remove the mucilage that firmly adheres to the beans. The effect of this fermentation step on the aromatic profile of the coffee is not yet sufficiently understood. All of the above have drawn the attention of researchers on the application of various omics approaches to elucidate fermentation processes in more detail. These approaches have been used to study the fermentation of Arabica (Coffea arabica) beans, as this species is economically most important worldwide. It is known that Arabica mild coffee is obtained through the wet method, which involves fermenting depulped coffee beans using various strategies and then washing the fermented coffee with clean water. In contrast, the fermentation of Canephora coffee beans has been much less studied using omics technologies. This review highlights the trends and future research in coffee fermentation based on a scientometric analysis, supplemented by a traditional systematic literature review. It highlights the composition of the coffee fermentation microbiome, as elucidated by metagenomics applications, in light of several factors that can influence its structure. Additionally, it considers the metabolites associated with microbial metabolism that can influence the chemical composition of coffee beans and, consequently, the cup quality. In this way, this review evidences the promising path in understanding microbial functions in coffee fermentation and in particular in the development of microbial inocula and in the refinement of fermentation processes to improve coffee quality.