Nine species of fungi and bacteria have been found in cocoa beans that produce fine chocolate, and this knowledge could help producers develop better flavours
By Carissa Wong
18 August 2025
Chocolate is made by fermenting cocoa beans, which come from the fruit of cacao trees
Mimi Chu Leung
We could soon taste new kinds of chocolate after the discovery of fungi and bacteria that produce fruity and caramel notes from cocoa beans.
Chocolate is typically made by fermenting cocoa beans from the fruit of cacao trees, drying them, roasting them and then grinding them up into a paste that is separated into cocoa butter and cocoa solids. These are then mixed in varying amounts with other ingredients to produce dark, milk or white chocolate.
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During the fermentation step, microbes that come from the surrounding environment digest parts of the cocoa fruit and produce various molecules that contribute to chocolate’s flavour. In most cases, this brings dark, woody flavours, says David Salt at the University of Nottingham, UK. But finer chocolate also has fruity flavours, often found in products sold by boutique chocolate makers, he says.
To find out which microbes may produce such flavours, Salt and his colleagues collected samples of fermenting beans from cocoa farms in Colombia. By analysing genetic material in the samples, they identified five bacteria and four fungi that were consistently found in batches of beans that produced fine-flavoured chocolate.
The team then took cocoa beans that were sterilised to carry no other microbes and used the nine microbes to ferment them, before grinding the beans into a liquid, known as a cocoa liquor. A handful of chocolate-tasting experts then assessed the liquor and found it had various fruity notes that weren’t present in liquors made from beans that lacked these microbes. “Adding those microbes gave it citrusy flavours, berry flavours, flowery flavours, tropical fruit and caramel flavours,” says Salt.