Editor’s note: This article was first published by Roast Magazine‘s September/October 2023 issue, and is reprinted here with permission.

Technically Speaking: How Microbiome Activity During Post-Harvest Processing Affects Volatile Compounds in Coffee

By Isabella Vitaliano

Coffee is a highly complex compound. With roughly 200 volatile compounds in green coffee and roasted expressing upwards of 1,000, there are so many factors at play that can alter the sensory experience of the final cup. The consumer-facing side of the coffee industry may roll its eyes at flavor notes like apricot, sweet pear and lemon, but these flavor notes are in fact not entirely subjective. Flavors are correlated to the sensory experience associated with certain molecules: tartaric acid to berries, citric acid to lemons, esters to florals and so on.  

 Florals are highly sought after in the coffee industry, which is one of the reasons cultivars like Gesha hit such high price points. There is an incentive across the board to understand how these flavor compounds are produced, and the question at hand is, how do different processing methods and their microbiome activity alter these aromatic and flavor profiles? 

 Microbiome feels like such a buzz word these days, used to promote anything seemingly healthy for you. But our biomes do in fact play an important role in our lives and in the lives of our coffees. The diverse population of bacteria and yeast contributes in different ways in each step of coffee processing and, ultimately, this is reflected in the flavor profile of our cup. To understand the biochemical component of these processing methods, we have to review some of the basics around processing.

Washed versus Natural 

 Washed or “wet-processed” coffees are washed after the cherry is picked, as the name implies. Processing typically happens in a 24-hour period because the cherries rot quickly. After picking, the fruit around the seed is removed via depulping with either mechanically or with a hand crank. The depulped cherry is moved to a tank where it undergoes a number of microbial digestive processes, known as fermentation. According to Chris Kornman, the director of education at The Crown, “Up until 20 years ago, this microbial activity was purely functional in order to remove the skin from the seed. It can now act as an additional quality step to create more flavor in the coffee.” This stage of microbial activity can be done using either dry or wet fermentation. The coffee is typically left in the tank overnight, and the seeds are checked by hand because producers can feel if the mucilage has broken down or not. Once fermentation is complete, the seeds are washed and then dried on raised beds. 

In natural or “dry” processing, the fruit skin and pulp are left on the seed and the coffee is dried on a patio or raised drying beds. Raised beds allow for consistency and airflow, and the cherries are left to dry for up to 48 at least a week and in some cases more than a month. During this time, fermentation occurs, usually uncontrolled and unmonitored until they cherries are to dried to support yeast and bacteria. After this stage, both processes follow up at a dry mill to get the coffee ready for export by husking, sorting, checking for defects and bagging the coffee.  

 As I dive deeper into the world of post-harvest processing and microbiology, the term fermentation seems to be a loaded word. Microbial activity in the context of industry terms is often used interchangeably with fermentation. In washed processing, this microbial activity is used to break down the mucilage so that there is little to no fruit left on the seed during drying. In dry processing, the microbes on the surface of the seeds begin to metabolize the mucilage and create the flavor profiles that coffee buyers desire. When the microbes begin digesting the seed itself, it’s called a fermentation defect. 

Figure 1: Simplified Schematic of Aromatic Compound Formation

Microbial Activity

These microbes do not get a free ride from the origin to the roastery. If they did, you would have moldy or fermented-tasting coffee. Microbial activity produces a byproduct called metabolites, which are precursors to the flavors responsible for different aromatics. Metabolites then diffuse into seeds and transform during roasting via the magic of the Maillard Reaction. Essentially, we are benefiting from the waste products of these microbes.

In a 2019 article titled, “Exploring the impacts of postharvest processing on the aroma formation of coffee beans,” published in the journal Food Chemistry, researchers who conducted a thorough review of related scientific literature found that during processing bacteria and yeast metabolize their food source (sugar) differently and create different byproducts. If one type of processing encourages a certain type of microbe population, producers have the ability to intentionally produce different aromatics. A 2016 review cited in the article reveals that different levels of microbial population are in fact shown in different steps of processing as well as in the type of processing (washed vs natural).

Bacteria consume mucilage as a food source and spit out metabolites such as ethanol, lactic acid, and acetic acid, to name a few (see Figure 1, page XX). The pectin in the coffee pulp is a major source of energy for bacteria populations as well as yeast. The environment in different types of post-harvest processing can encourage the growth of certain species over others. A study detailed in an article titled, “Following Coffee Production from Cherries to Cup: Microbiological and Metabolomic Analysis of Wet Processing of Coffea arabica,” published in Applied and Environmental Microbiology in 2019, confirmed that microbial communities’ structures vary significantly between different types of processing. The relative abundance of bacteria in mucilage, endosperm, hull, and pulp were measured and the researchers found that populations of lactobacilli and yeast were much higher in dry over wet-processed coffees. Lactobacillus is also referred to as lactic acid bacteria because they produce the end metabolite lactic acid. This species is tolerant to acid, which allows it to survive in more acidic conditions that are encouraged during the uncontrolled fermentation in the early drying period that occurs after harvesting in natural processed coffees.

Yeast utilizes sugar to generate aroma-influencing molecules through two pathways, central carbon and nitrogen metabolism. (See Figure 1, page XX.) Pectin present in mucilage is broken down through the facilitation of water via hydrolysis which is then consumed by yeast. In turn, this releases simple sugars that act as an additional carbon source for yeast metabolism and aromatic formation. Yeast produces primary metabolites (alcohol) and secondary metabolites, which are the desired aromatics (esters, etc.). The microbial activity step in post-harvest natural processing allows glucose and fructose to be pulled out of the seed and provides even more nutrients for bacteria and yeast to feed on. It has been found that wet processing had higher concentrations of Lactococcus, which is a typical bacterium of milk and fermented dairy products. In another article published in Applied and Environmental Microbiology, this one titled “Exploring the Impacts of Postharvest Processing on the Microbiota and Metabolite Profiles during Green Coffee Bean Production” and published in 2016, glucose and fructose were confirmed to be lower in wet-processed coffees, suggesting that this type of post-harvest processing reduces the microbes’ sugar metabolism and alters the aromatics. Citric acid, which presents as bright and sharp (orange and lemons), is typically found to be higher in washed coffees. Candida, a type of bacteria that produces citric acid is found in higher concentrations during the soaking stage. This aligns with the general agreement that wet-processed coffees are found to have higher acidity. These are just a few highlights of the abundantly diverse microbial community structure.

Certain esters have been shown to contribute to the development of highly sought-after exotic sensory notes such as apricot and rose. Lactic acids discussed earlier as being more prevalent in dry processed coffees, can also be utilized for ester fermentation. According to the literature review published in Food Chemistry in 2019, cited previously, “Aldehydes are also generated during mucilage removal and serve an important purpose in aromatic compounds like higher alcohols and esters.” Table 1 (page XX) displays a brief list of volatile compounds and their associated aroma perceptions in green and roasted coffee. This is a long list, but it just scratches the surface of the compounds responsible for the sensory experience of coffee.

Table 1: Brief List of Volatile Composition of Coffee


Our perception of sugar is an interesting addition to the complicated web between cupping, microbes, and aromatics. If the sugars are pulled out from the seed and the yeast and bacteria consume more fructose and glucose, would this theoretically lower the sweetness? Not exactly. The sweetness we taste in the cup is not actual sugar. The percentage of sugar in a coffee bean is too low for human perception. During roasting, two chemical reactions—caramelization and the Maillard reaction—use up most of the sugars in green coffee. More than 99 percent of the sugars in green coffee have been shown to be degraded during roasting. The brain is a fickle thing, and the sensation of sweetness comes from association. The fruity and caramel-like aromatics of compounds like esters, aldehydes, and furans give the sensory impression of sweetness. Even if the processing method is technically lowering the amount of sugar in the seed, if molecules of these compounds are present it will increase the perceived sweetness of the coffee.

Bridging the Gap

The intention of this piece is to ultimately connect scientific papers with the industry so that they feel more cohesive and applicable to everyday work life. Education is such a powerful tool and one that often goes under the radar. It is the bridge between customers understanding (and tasting) the difference between a good coffee and a really great coffee. In the same way, it allows for people along the supply chain to make a good coffee into something really great. As producers become more innovative and experimental in their processing methods, it is important to understand how these methods affect the volatile compounds that create coffee’s flavor. By taking the time to understand a seemingly myopic topic we can broaden the landscape of our understanding and utilize this information as a tool to intentionally express an idea in the final cup.

Isabella is the Lab & Education coordinator at The Crown: Royal Coffee Lab and Tasting Room in Oakland, California. She graduated from the University of Central Florida with a degree in biomedical sciences and enjoys merging science and coffee in any way she can.