Scientists Have Unlocked the Secret of Great Chocolate --- Using the right microbes to ferment cocoa beans is the key to flavor.

“What's the secret to the best-tasting chocolate?

 

It is using the right microbes, and for the first time scientists have isolated a collection of those bugs and made a superior-tasting chocolate in a laboratory.

 

Chocolate, like sourdough or yogurt, begins with fermentation. Farmers stash cocoa beans scooped out of ripe cocoa pods in wooden boxes outdoors, cover them with leaves and leave them alone for a week. Fermentation is kicked off by bacteria and yeasts that live in the boxes or the soil.

 

If things go well, the beans and slimy white pulp that surrounds them will transform into brown beans that can be dried, roasted and cracked open. The flavorful nibs within are turned into chocolate liquor, the foundation for confections and baking chocolate.

 

Working with three farms in Colombia, researchers at the University of Nottingham collected samples of farm-fermented beans multiple times during the weeklong process. The South American nation is a major exporter of fine-flavor cocoa -- the kind used in more expensive chocolate.

 

Through a genetic analysis, the scientists zeroed in on microbes that were present throughout fermentation. They narrowed the list to those able to produce chemicals found in fully-fermented chocolate, and used a starter culture made of nine species to ferment beans in the lab.

 

"Lo and behold, they tasted like fine-flavor cocoa," said David Salt, a plant molecular biologist and emeritus professor at the University of Nottingham who was part of the research team.

 

Fine-flavor cocoa has fruity, caramel and floral notes that taste more complex than "bulk cocoa" grown in countries such as Ghana, according to the International Cocoa Organization.

 

A panel of taste experts at the Cocoa Research Center in Trinidad and Tobago scored the chocolate liquor made with the lab-fermented beans and determined that the cultures from two farms had floral and fruity flavors similar to fine-flavor varieties found in Madagascar.

 

Chocolate owes its taste in part to its terroir -- the particular natural environment it is grown in, such as its soil -- and other labs have shown how cocoa products from different locations have different collections of microbes on them. But this is the first time key microbes have been isolated and had their role reproduced.

 

"No one has so far reverse engineered it and gotten a successful starter culture," said Pablo Cruz-Morales, a biochemical engineer at the Novo Nordisk Foundation Center for Biosustainability at the Technical University of Denmark, who wasn't involved with the work.

 

The breakthrough, which the researchers described in the journal Nature Microbiology this month, could help farmers standardize the natural fermentation process.

 

But Cruz-Morales would just like to taste the chocolate. "I wish they had sent a little sample," he said.” [1]

 

1. REVIEW --- Science Shorts: Scientists Have Unlocked the Secret of Great Chocolate --- Using the right microbes to ferment cocoa beans is the key to flavor. Subbaraman, Nidhi.  Wall Street Journal, Eastern edition; New York, N.Y.. 30 Aug 2025: C4.