Cocoa (Theobroma cacao) bean fermentation is a spontaneous process involving interactions between various factors that contribute to the final flavors of premium chocolate. Understanding these underlying interactions could enable desired flavor profiles to be reproduced under controlled conditions. Using bean fermentation samples from Colombian farms, researchers established that pH, temperature and microbiota composition, including both bacteria and fungi, influence key flavor attributes of premium chocolate. The findings provide the basis for the design of fermentation starters to robustly reproduce fine chocolate characteristics.
Gopaulchan et al. established the previously suggested role of pH and temperature changes as robust predictors of chocolate flavor characteristics. Image credit: Sci.News.
The production of fermented foods, such as chocolate, relies on the metabolic activities of microbial communities.
Members of these communities transform the raw substrate, cocoa beans, into the precursor for chocolate production.
Although after harvest, cocoa beans undergo several processing steps to produce the final chocolate, the fermentation step, however, is a spontaneous process.
“The unique flavor of chocolate is determined by the fermentation of cocoa beans,” said Dr. Gabriel Castrillo from the University of Nottingham and his colleagues.
“However, unlike the fermentation of wine, cheese, or dough — in which specific microorganisms are introduced during the process to refine flavor — cocoa beans ferment naturally, and little is known about the microorganisms involved.”
“The flavor profile of the beans is closely tied to the location of the farm where they are produced, leading to variability in quality and flavor of chocolate.”
In the study, Dr. Castrillo and co-authors performed a DNA sequencing-based analysis of fermenting cocoa beans from three different cocoa farms in Colombia.
They found that a unique microbial community drives a characteristic fermentation process at a farm in Antioquia, which resulted in a finer flavor, as verified by professional food tasters.
Using the sequencing data, the authors determined the inter-microbial interactions and metabolic pathways involved in the fermentation process.
This allowed them to design a defined microbial community of bacteria and fungi that could reproduce the fine flavor of chocolate under laboratory conditions, which was verified by the same professional tasters and analyses of the chocolate metabolites.
Further research could guide the design of industrial fermentation starters, uncoupling the chocolate flavor from geographical constraints.
“The results of this work expand our understanding of how the microbial community composition present in fermentation is a key determinant of chocolate flavor characteristics,” the scientists said.
“We developed a robust pipeline enabling the design of fermentation starters that will contribute to the domestication of spontaneous and unpredictable microbial fermentation of cocoa occurring on farms.”
“This sets the stage for the emergence of a modern chocolate industry akin to the beer or cheese industry, based on controlled cocoa fermentations, driven by synthetic microbial starters capable of robustly reproducing unique flavor attributes in cocoa beans and chocolate.”
The team’s paper was published this week in the journal Nature Microbiology.
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D. Gopaulchan et al. A defined microbial community reproduces attributes of fine flavour chocolate fermentation. Nat Microbiol, published online August 18, 2025; doi: 10.1038/s41564-025-02077-6
