The Fermentation Effect – 25 Magazine, Issue 10

The Fermentation Effect – 25 Magazine, Issue 10

TThe journey of coffee is complex and fascinating.

SOPHIA JIYUAN ZHANG and FLORAC DE BRUYN share research findings amassed during a four-year research collaboration focused on creating a better understanding of the impact of post-harvest coffee processing on coffee quality across different geographic locations.

As we walk along this path through the seeds, fruits, green coffee beans, roasted beans, and, finally, a brewed cup, we can appreciate the effort that goes into each single stage of the entire coffee value chain. Not surprisingly, each of these stages is interlinked and can be optimized to deliver coffee of ever-increasing quality. Coffee quality is commonly evaluated at the level of the green coffee beans and the brewed cup. As the green coffee beans have all the flavor precursors locked inside them, their quality bears a close relationship to the final cup quality.

But the role of post-harvest processing cannot be ignored when one thinks about improving coffee quality. The main goal of post-harvest processing is to remove the outer layers of the coffee cherries and transform their seeds into a dried and stable carrier of flavor precursors, i.e., green coffee. The common methods to achieve this are wet and dry processing, whose history can be traced back to the very birth of the coffee industry. Meanwhile, many hybrid or novel methods also have gained popularity in the coffee production regions, such as the well-known pulped honey process or the trendy anaerobic fermentation (i.e., with limiting or absence of oxygen during fermentation). In recent years, many producers have taken the lead in innovating coffee processing and have experimented with different methods across production regions. This provides a huge amount of empirical evidence regarding the influence of processing methods and specific processing parameters on coffee quality. However, rigorous scientific proof to back them up remains veiled, yet longs to be discovered.

For the past four years, we have been working with coffee through a bilateral industry-academia research collaboration between the Vrije Universiteit Brussel (Brussels, Belgium) and Nestlé Research (Vers-chez-les-Blanc, Switzerland), endeavoring to understand coffee post-harvest processing. Here, we’ll highlight some of our research findings with different coffee varieties in various geographical locations – we hope you’ll find it as insightful and thrilling as we did during our journey.

Microbes and Metabolism

Two main phenomena happen during coffee post-harvest processing, namely the microbial activities in the processing environment and the internal seed metabolism of the coffee beans. The dynamic character of the processing is highlighted in the continuous consumption of nutrients and production of substances by the microorganisms, as well as an ongoing re-shuffling of the seed’s own metabolomic profile (i.e., a concentration profile of many different substances in the beans). The complexity lies in the multiple steps within a single processing method and its dependency on various external factors, such as temperature, coffee variety, and processing equipment.

Microorganisms are present in virtually any environment and, therefore, also in the coffee processing ecosystem. As they play a crucial role in other fermented food productions (see “Fermenting Flavor”), it is perhaps not surprising that microorganisms also perform important functional roles during coffee processing. Microorganisms are already present on the coffee cherry’s surface before the processing even begins: as processing progresses, these microorganisms (especially the lactic acid bacteria) thrive on nutrient-rich plant material, such as pulp and/ or mucilage, that is released into the fermentation environment. While they grow, microorganisms produce metabolites from these plant nutrients and accumulate in the processing environment – this is called a fermentation by microbiologists. To our excitement, we found that fermentation happens in different parts of the coffee ecosystem during wet and dry processing. During wet processing, fermentation happens in the processing water, while during dry processing, fermentation happens in the drying outer layers of the cherries. Interestingly, some of the metabolites produced during fermentation remain on the surface of the beans, and can even survive the entire process. As such, they linger on the green coffee beans as a microbial signature. We called this phenomenon the fermentation effect.

Figure 1: Our multiphasic approach decoding the journey of coffee from cherry to cup, including metabolomic (top) and microbiological (bottom) approaches to unravel the coffee processing ecosystem, as well as the sensory evaluations of the brewed cup. For full results, see relevant research papers.

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.

Different Processes Accumulate Different Concentrations of Metabolites

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.

Coffee Variety as a Fermentation Variable

Different coffee varieties will show variability in metabolite composition of the mucilage and pulp of their fresh coffee cherries. As the main provider of nutrients for the microorganisms, the compositional differences in mucilage across different coffee varieties also impacts the extent of the fermentation effect. For example, we found that the Typica coffee cherries we used in Latin America had a juicy mesocarp layer that was richer in nutrients than that of Catimor ones in Asia. In combination with external factors, like the local ambient temperature, we found that this affected the pH profiles, the microbial community dynamics, and the metabolite compositions during fermentation. Therefore, it is important to take the coffee variety into account when evaluating the potential impacts of the processing practices.

Figure 2: Coffee post-harvest processing consists of several dynamic and intertwined activities, mainly microbial activities and endogenous bean metabolism (left). Switching the processing methods or changing the processing parameters could change the (green) coffee bean composition and the sensory profile of the brewed cup. The extent of their impacts on coffee quality depended on the parameter altered and the processing conditions (right).

We believe that this diversity is coffee’s strength, because it means that there is a vast amount of permutations of the factors above that remain to be explored and that this diversity in the coffee value chain interweaves craft and science. We remain convinced that some of the outcomes are bound to result in a damn fine cup of coffee.

SOPHIA JIYUAN ZHANG, a chemist and coffee enthusiast, has worked on multiple coffee plantations around the world to understand the links between processing and coffee quality. FLORAC DE BRUYN is a microbiologist with a keen interest for spontaneous food fermentations, focusing on the coffee fermentation microbial ecosystem during his PhD. Both now work for Nestlé Research in Switzerland.

Further Reading

Relevant research papers have been published in: De Bruyn, F*., Zhang, S.J.*, Pothakos, V.*, Torres, J., Lambot, C., Moroni, A.V., De Vuyst, L. (2017). Exploring the impacts of post-harvest processing on the microbiota and metabolite profiles during green coffee bean production. Applied and Environmental Microbiology 83, e02398-16.

Zhang, S.J.*, De Bruyn, F.*, Pothakos, V.*, Falconi, C., Torres, J., Moccand, C., Weckx, S., De Vuyst, L. (2019). Following coffee production from cherries to cup: microbiological and metabolomic analysis of wet processing of Coffea arabica. Applied and Environmental Microbiology 85, e02635-18.

* equal contribution

Fermenting Flavor

Microorganisms play a crucial role in the fermented food products we know and love.


Bacterial groups of leuconostocs and lactobacilli acidify white cabbage, giving its signature pleasant acidity and making it safe to consume.


Bacterial species of lactobacilli and streptococci play an important role in creating the creamy, smooth texture and refreshing acidity.


Yeasts produce alcohol and fruity/floral aromas, making beer enjoyable to consume.

Soft Ripened Cheese

Bacterial species of lactococcus will create a soft and creamy interior. On top of that, molds will create a white, bloomy rind on the surface.

Read more about cheese fermentation in “Fermenting a Farming System” by Bronwen Percival in Issue 2 of 25.

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