The flavor of chocolate can vary a lot from piece to piece. Some chocolate treats may have a slight fruity tang. Others may carry hints of floral or even nutty flavors. Scientists knew that soil, rainfall and other conditions on cocoa bean farms shaped chocolate’s taste. But new research now shows that the flavor of chocolate depends mostly on the wild microbes that ferment the cocoa beans.

One might think cocoa plants’ DNA would determine the taste of chocolate. But “fermentation also is driving the flavor,” says David Gopaulchan. “I would even argue, [it] has an even bigger impact on the flavor.” Gopaulchan studies plant genetics at the University of Nottingham in England. He and his colleagues shared the new findings in the September Nature Microbiology.

Past studies have identified microbes involved in cocoa fermentation. But this work “pulled out all the stops to try to understand the process,” says Rachel Dutton. This microbiologist wasn’t involved in the work. But her company Microcosm Foods in Berkeley, Calif., studies fermented foods.

A microbial feast

Gopaulchan’s team worked with three women-owned farms in Colombia. All grow similar strains of cocoa. Two of the farms produced fine chocolate while the third made bulk chocolate. (Fine chocolates’ floral, fruity and other subtle flavors set them apart from plain bulk chocolate.)

The researchers tracked the temperature and pH in fermenting beans from each farm. They also tracked the microbes at each stage of the process.

Yeasts were some of the first microbes to belly up to the chocolate bar. They broke down sugars in the beans, turning them to alcohol. This process created heat within 24 hours of fermentation. That heat killed the beans and kept them from sprouting.

After 48 hours, some types of bacteria began to multiply. Those bacteria turned the alcohol made by the yeasts into acids. That increased the pH of the bean batch. The bacteria also further broke down the beans and the pulp that surrounded them. Other yeasts and bacteria soon joined the party. They turned the compounds made by earlier microbes into tasty molecules.

The timing and speed of the temperature and pH changes are key for making flavors, says Aimee Dudley. So are the transitions between microbes, she adds. Dudley studies yeast genetics but was not involved in the new study. She works at the Pacific Northwest Research Institute in Seattle, Wash.

Lab versus wild microbes

Gopaulchan and colleagues wondered if they could put together microbe teams to mimic what they’d seen. To find out, they looked at the DNA of the microbes involved in fermenting the beans. That allowed them to pick out microbes linked to certain flavor compounds. They could then predict a combo of microbes that should produce the two farms’ fine chocolate flavors.

The researchers put together bacteria-yeast mixes and fermented small batches of beans in the lab. A panel of expert tasters tested the lab-fermented beans. They confirmed that the flavors did match the two farms’ chocolates. Some of those flavors included notes of orange blossom, citrus and tropical fruit.

The lab mix wasn’t perfect, though. It lacked caramel, nut and light wood flavors from the farm-made chocolates. It also had more grassy notes than the fine chocolates did.

Still, the study shows that microbes that ferment cocoa form predictable communities, says Dutton. She has found similar predictable bunches of fungi and bacteria in cheese. In cheese and chocolate, different strains of local microbes bring their own flavors.

Designer microbes

In the future, lab-made microbe mixes could be used to produce designer flavors, Gopaulchan says. They could create flavors that don’t exist. Or ones that are hard to find in natural fermentation.

But some chocolate makers aren’t on board with that idea. Take Luisa Bedi and Martyn O’Dare. They make chocolate at Luisa’s Vegan Chocolates in Nottingham, England. Lab-made microbe mixes “would be very much rejected by the craft chocolate producers and market,” they say. Using pre-mixed microbes could reduce the variety of chocolate flavors. And there’s no need for those mixes when “good farming practices already produce great tasting chocolate.”

Lab-based microbes might also make too much of some compounds that flavor fine chocolates, Dudley says. “Humans have a very sharp boundary for what tastes really good and what tastes awful,” she says. “Yeast make the amount of those compounds at exactly that boundary of what humans think is palatable.” Messing with the mixes could cross the line. And that could turn chocolate from delicious to disgusting.