Concurrently, the coffee bean is also a living entity that interacts with and reacts to its environment. As any living organism, it will thus be metabolically active throughout processing. The coffee beans are considered intermediate seeds, which allows them to react to different external environmental stress factors even under low moisture content and change their metabolite composition accordingly (made up of the dynamic sum of all carbohydrates, amino acids, and organic acids inside the seed). The two dominant stress factors along the processing chain are hypoxia, or lack of oxygen, during the underwater submersion and “drought stress” (lack of water) during drying. During wet processing, the beans experience both hypoxia and drought stress, while during dry processing, the beans are under prolonged drought stress. These are also the differences that contribute to the distinction between a washed and a natural coffee. Therefore, when we talk about the impact of coffee processing on flavor, we’re not just talking about the creation of “fermented flavors” that exist on the outside of the processed beans – we’re also talking about fundamental changes to the metabolic composition of the coffee bean itself.

Under different processing conditions, both microbiology and seed metabolism affect the metabolomic profiles of the coffee beans and thus ultimately the cup quality. Here, we briefly consider the impact of three specific wet processing parameters that we studied extensively: how long fermentation took place, if the cherries were mechanically demucilaged, and whether or not the beans were soaked after fermentation and washing. However, before we start, it’s helpful to clearly define some terms used around processing.

During basic wet processing, fresh coffee cherries have their pulp removed (depulping) and submerged under water (fermentation). Afterwards, the fermentation tank is drained, and the fermented beans are cleaned with water to remove any remnant mucilage (washing). Sometimes, these washed beans are then soaked in the tank or separate buckets with clean water again (soaking). After washing or soaking, the beans are dried during a drying step. One variation on classical fermentation is to remove the mucilage mechanically through the demucilager (where two rotating drums squeeze the beans to scrape off a large portion of the mucilage mechanically), which is what we’ll define here as the demucilaging process.

The length of fermentation exhibits a significant impact on the coffee quality. We found that whereas a long fermentation is commonly believed to downgrade coffee quality, leading to stinkers or acid beans, it can also have positive and even desirable effects, provided carefully controlled farm practices are maintained. Under hygienic processing conditions (in particular for the fermentation tank and washing channel), a longer fermentation allowed more time for the desirable microbial activities to deploy and resulted in a greater fermentation effect on the fermenting beans. This fermentation effect lingered on the green coffee beans, as reflected in the higher concentrations of microbial metabolites (e.g., lactic acid and mannitol) and the higher intensities of the floral or fruity volatile organic compounds. On the flip side of microbiology, a long fermentation duration reinforced the role of hypoxia through endogenous bean metabolism, affecting concentrations of simple carbohydrates (e.g., glucose and fructose), amino acids (e.g., aspartic acid and alanine), and organic acids (e.g., succinic acid). These compounds listed can act as main precursors in a series of chemical reactions during roasting, especially the Maillard Reaction, and generating signature coffee flavor. With the modification of the abundance of these flavor precursors on the green beans, longer fermentation resulted in an enhancement of the fruity notes in-cup.

The use of demucilaged rather than depulped beans as the starting material for fermentation during wet coffee processing has been controversial. As a more ecological alternative to classical fermentation, the use of a demucilager can save on the fresh water used during fermentation and reduces processing time, yet its impact on the sensory quality remains elusive. Our work showed that the presence of mucilage on depulped beans increased the nutrient density in the fermentation water for the microbes to work on. That’s why the fermentation effect in the water and on the beans was more intensive compared to a demucilaged fermentation process. This resulted in the green coffee beans from the depulped process retaining more microbial metabolites and differing in amino acid and phenolic profiles compared to the demucilaged process. As a result, the cup quality derived from these two processes showed subtle differences in their floral and fruity intensities.

In contrast to the factors mentioned above, the application of washing and soaking reduced the fermentation effect. With the absence of soaking or even a reduced amount of washing, the precious metabolites accumulated during fermentation were retained on the green coffee beans to a higher degree and improved the cupping score. However, if for whatever reason fermentation does not turn out well, soaking could help to get rid of some of the undesirable metabolites built up during fermentation and provide a means of controlling off-flavors in coffee.