Bread, alcohol, dill pickles or cheese might come to mind when you think of foods that ferment, but one food that doesn’t usually make the list? Chocolate. Now, however, scientists and producers are discovering that microbes may be even more important to giving chocolate the taste we love than they are in flavoring wine.
For a new study in Current Biology, a lab team at the Pacific Northwest Diabetes Research Institute in Seattle tested unroasted coffee and cacao beans from around the world forSaccharomyces cerevisiae, the yeast used in baking, brewing and winemaking.
“The first really interesting thing we noticed was that they were all very different from each other,” says lab director and study co-author Aimée Dudley. “So a coffee strain from Colombian coffee was very similar to other Colombian strains, but it was really different from Yemeni coffee.”
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The variations are so obvious that the team can tell the origin of a bean based only on the DNA of its resident S. cerevisiae. That’s surprising because the varieties of the same species found on wine grapes are very similar, whether they come from California, Australia or anywhere else.
“Wine production was perfected and developed very early in human history, and as humans migrated across the planet they brought not only those grape vines but the strains of yeast with them,” says Dudley. The S. cerevisiae strains her team uncovered on the coffee and cacao, on the other hand, have a mix of wine yeast DNA and local wild yeasts.
Despite their strong similarities, different wine yeasts produce varied flavors out of the same grapes. If coffee and chocolate yeasts show so much more genetic diversity, says Dudley, they may be responsible for even more of the flavor in those foods: “How much of that terroir—how much of the taste and flavor and aroma and acidity properties—are associated with those fermentation steps and may be conferred by the microbes themselves?”
Coffee fermentation is not well understood, and according to the International Coffee Organization, it’s not clear whether the process even influences the flavor of the final product. Dudley says that before her lab’s study, there was little evidence S. cerevisiae was even involved.
Chocolate consultant Clay Gordon says that in his business, “the influence of fermentation is huge.” He works with the Nicaraguan company Ingemann, which contracts with farmers to collect their fresh cacao pods, then breaks the fruit open and ferments its sweet pulp and seeds (called beans) at a central plant. This setup lets Ingemann control the process—unusual for the chocolate industry, where the majority of farmers do their own processing. Gordon helps them run Cocoa Academy, a weeklong training for chocolatiers with a heavy focus on teaching processing techniques. “Ingemann can reliably get six different flavor profiles from the same variety of bean by varying fermentation and drying,” says Gordon. “You can get flavors that are fruity and bright or leathery and tobaccoy just by controlling the postharvest processing.”
Most commercial winemakers add controlled doses of known lab-grown S. cerevisiae to their grapes to ensure they get the flavors they want. Cacao fermentation is much more freeform: It depends on multiple kinds of yeast and bacteria, and in most cases all of them are naturally present on the plants—no inoculations added. They break down the fruit pulp and then turn the sugars inside the beans into what food scientists call “flavor precursors.”
“When you roast the bean, these are what generate the flavors we talk about in chocolate,” says Gordon. Now that Dudley’s lab has shown that S. cerevisiae differs so much from place to place, it’s easy to imagine that the other microbes on the beans are just as varied in their genes—and in the flavors they make.
“Right now, the way cacao is fermented is like wild fermentation in wine,” Gordon says. That is, it’s an older, less controlled approach. And it’s not likely to change soon for most chocolate producers. The Federation of Cocoa Commerce estimates that there are over 4 million smallholders growing the crop. Teaching all of them new fermentation methods would be a challenge. “Where wine became interesting is when people really gained control over microbes and chemistry,” says Gordon. “We’re just starting to get to that point with chocolate.”
For Dudley, however, chocolate is more likely to be the subject of an afternoon snack than a future study. Her lab wanted new strains of S. cerevisiae for medical research, and the beans were a convenient way to collect them from tropical parts of the world that hadn’t been well sampled. Researchers use the easy-to-handle yeast as a model to study the behavior of related, more dangerous fungi such as molds and Candida albicans, which causes thrush in people with weak immune systems. But the standard strains bred for lab experiments don’t offer a lot of variety.
“Wild yeasts actually have some really interesting properties that lab yeasts don’t have,” explains Dudley. “It’s kind of the difference between a domesticated dog and a wolf, if you want to think about it that way.”
The same could be said for the difference between the yeasts that make wine and the microbes that give us that rich and nuanced chocolate.