Wet Coffee Fermentation: From ecosystem analysis to starter culture development

Coffee is one of the most commonly consumed beverages in the world. Yet, a cup of coffee is the end-point of a complex chain of events. This chain includes post-harvest processing, roasting, and brewing. Post-harvest processing is performed on-plantation after the coffee fruits have been harvested and it yields the green coffee beans that can be roasted. During this post-harvest processing, a fermentation stage is implemented. This fermentation process entails an interplay between microbial activities and endogenous bean metabolism, which results in structural and compositional changes in the green coffee beans and affects cup quality. Since virtually all coffee in the world is fermented spontaneously, the microorganism-mediated functionalities of these processes are performed by wild bacteria and yeasts that originate from the environment. However, since there is no control over which microorganisms are present, it is possible that these functionalities are performed suboptimally. Moreover, undesired microbial communities can perform adverse functionalities, such as off-flavor or mycotoxin production. It is, therefore, crucial to understand the microbial dynamics of coffee processing and find ways of gaining control over this spontaneous food fermentation ecosystem. To remediate this knowledge gap about how and why microorganisms are essential for the production of coffee, field experiments were carried out to study the spontaneous coffee post-harvest processing in different geographical locations. Both standard and extended fermentation durations were included in the post-harvest processing chain. In all of these processes, lactic acid bacteria emerged as the predominant microbial group, in particular leuconostocs and lactobacilli, as unravelled through both culture-dependent and culture-independent microbiological methods. However, their growth dynamics depended on environmental factors and the coffee variety used. The source of these lactic acid bacteria was traced to the plantation environment. All this knowledge was implemented to develop a starter culture that could serve to control coffee fermentations and enhance green coffee bean quality and the coffee brewed thereof. Therefore, multiple coffee-autochthonous strains were selected, screened in a novel coffee mucilage simulation medium and studied with respect to their growth and metabolic activities on laboratory scale, and implemented in small- and large-scale coffee processing trials to validate their potential as starter cultures. The study cumulated in two lactic acid bacteria starter culture formulations that could potentially be used for improvement of coffee quality and enhancement of specific sensory notes in-cup.