The best master chocolatiers are... microscopic

The characteristic flavor and aroma of chocolate and its quality are the result of the natural fermentation of cocoa beans by communities of natural fungi and bacteria.

Chocolate
16/01/2026
3 min

Chocolate derives from chocolate, a word that the Spanish colonizers went imported at the end of the 16th century as a phonetic derivative of a Nahuatl term (Aztec language) of uncertain etymology, which was the name given to a new drink that mixed cocoa with chocoatl (bitter water). The scientific name of the cacao plant leaves no room for doubt, Theobroma cacao It means "cacao, the food of the gods," and certainly, few people can resist the allure of a good piece of chocolate, dark or milk, but always smooth thanks to the quality of the cocoa fats and its unmistakable spicy flavor.

In fact, cocoa was so highly valued by the Aztecs that during their empire, Cocoa beans were used as a form of paymentAlthough we associate the use of cacao with Mesoamerica, the genus of plants Theobroma It originated in the Amazon rainforest, between Ecuador, Brazil, Peru, and Colombia, since The headwaters of the Amazon River are where we find the greatest variety of wild cacao speciesThese are the areas from which the domesticated subspecies cultivated worldwide are derived. It is also where the earliest archaeological remains of pottery containing traces of bean powder and cacao husk are found.

'Sweet' microorganisms

The cacao fruit is large, and when opened, it contains a gelatinous pulp with rows of cacao beans. These beans are extremely bitter. To enjoy chocolate, traditional techniques involve extracting the cacao beans along with the sugar-rich gelatinous pulp; these are first fermented for about seven days in special wooden boxes and then sun-dried. They are then evaluated for quality and sent for processing. Although there is evidence that cacao has been harvested and consumed for over 5,000 years, The fermentation process hasn't changed much.This fermentation, which generates the metabolites responsible for the characteristic flavor and aroma, is produced by local communities of natural microorganisms that grow on the nutrient-rich gelatin and cocoa beans. These microorganisms generate heat, acidify the environment, and cause the cell walls to break down. Therefore, since the fermentation occurs entirely naturally, without the addition of external microorganisms, it depends on biotic (fungi and bacteria) and abiotic (temperature, humidity) factors specific to the geographical location where the beans are harvested.

Cocoa beans are first dried and then ground to obtain cocoa powder.

It's curious to think that humans control the vast majority of fermentation processes crucial to high-consumption foods and beverages, such as cheese, beer, and wine (with patents protecting the composition of the yeast or fungal strain mixtures necessary for their production), yet we still don't control fermentation itself. That's why a recent scientific article analyzing, using the latest genome sequencing and analysis technology, the different communities of microorganisms that occur during the fermentation of cocoa beans from three producing regions of Colombia, some of them considered producers of the highest valued cocoa, with the aim of finding out what relevance microorganisms have in the quality of the resulting cocoa.

The results are exceptionally interesting. Researchers identified up to 24 species of bacteria and 20 of fungi involved in cacao fermentation and were able to link them to the production of specific metabolites—such as pyrazines (compounds that give a nutty flavor) or aldehydes (associated with fruity and floral aromas). The proportion of microorganisms differed in the Antioquia region, for example, compared to the other regions studied, as did the metabolite composition of the fermentation product and the quality of the resulting cacao "liquor." By studying the contribution of each microorganism and the succession of communities during the fermentation process, the researchers concluded that they could reduce the original great diversity of microorganisms to a main common denominator: 5 bacterial species and 4 fungi (mostly yeasts), which generate the main components. If we add these strains synthetically in the correct proportion, externally and under controlled conditions, to initiate fermentation in any type of cultivated cocoa beans, we obtain excellent cocoa of consistent quality, according to expert tasters. The addition of this "perfect" blend of fermentation-initiating microorganisms eliminates dependence on external factors related to the geographical production region while ensuring good yields across all cocoa subspecies and regions.

Little girl enjoying churros with chocolate.

The results of this research, therefore, allow chocolate production to fully enter the world of modern biotechnology, where the production of excellent quality cocoa can be controlled, similarly to how we do with beer or sparkling wine. Looking further ahead, in the future, we will be able to explore diverse compositions of microorganisms to produce high-quality cocoa with different organoleptic properties of flavor and aroma, properties we may not even be able to imagine now. The microorganisms involved in cocoa fermentation will be the best master chocolatiers.

stats