Food of the...Microbes??

—by Roxy Bergeron

Snap off a piece of your favorite chocolate bar. Pop it into your mouth and close your eyes. Tune in with patience and presence as it begins to slowly melt away. Be patient. Resist any temptation to apply dental pressure. Just—sit with it a while. Focus on the change in shape, the way the sides fall away and the bottom gets slippery....

True chocolate lovers share a cosmic affection for that supreme flavor, which has comforted and fascinated human beings for some 4000 years.

Chocolate begins its sublime alchemical journey toward becoming your Valentine truffle in a narrow band of planetary real estate on the equator. Central America and northern South America are the supposed ancestral home of the cacao tree, dubbed Theobroma cacao—“food of the gods”—by Carl Linnaeus in the 18th century. This divine tree now inhabits plantations and small farms in areas such as the Ivory Coast, Ghana, Indonesia, Brazil, Nigeria, Cameroon, Malaysia, and Ecuador.

Anatomy of a chocolate tree

The tree bears drooping clusters of tiny white flowers that sprout directly from the trunk. A set of peculiar stamens jut downward out of the blossoms. The fertilized flower produces a large oblong pod some five to 12 inches long, shaped more or less like a football (that’s an American football, just to be clear) attached to the trunk on a thick, stumpy stem. The fruit starts out light green, then turns yellow (or ruby-red, or other colors).

Inside this bumpy, segmented pod, 20 to 60 bitter cacao beans are set inside a thick, sticky pulp of pectin. It is within this sweet pectinaceous placenta—a nutritious paste laced with a sugary trinity of fructose, glucose, and sucrose, with a pinch of pentosans, citric acid, and a smattering of proteins, amino acids, vitamins, and minerals—that the critical fermentation process takes place through which Nature bestows upon the human world the food of the gods.

The transformation begins

The raw cacao beans begin their transformation into chocolate right there on the farm, where the harvested pods are knocked open—a machete, sharp knife, or a good whack with a hammer or wooden implement will do. The pulp cradling the seeds is scooped out and gathered up into heaps or placed in covered boxes, which are then covered with banana leaves.

In this warm and cozy place, an array of microbes, which arrived on the implements, baskets, and hands of the farmers, begin to work in shifts—an ecological or microbial succession, with one species following another through a complex biochemical fermentation process.

Yeasties and other beasties

The first shift starts breaking down the pulp surrounding the beans. All that tasty sugar feeds 11 different species of yeast, the two most abundant species being Candida rugosa and Kluyveromyces marxianus. These yeasties release ethanol and carbon dioxide as they feed on the lip-smackin’ sweet pulp, which, unfortunately leads to their own demise, as well as contributing to the demise of the tiny cotyledon (embryonic leaf), which had stirred to life but eventually succumbs to the rising temperature and changes within the pile. Flavor precursors then develop inside the bean.

Into this ever-warming pile enters the second shift—lactic-acid bacteria in the form of Lactobacillus and Streptococcus. A good stir of the pulpy mash at this point aerates and drains the pile, pulling down the pH. This is the third-shift whistle summoning acetic-acid bacteria from the Acetobacter and Gluconobacter camps.

By this time, the pile is really rocking with heat and oxygen, and a swarm of Bacillus clamber on board to complete the final transformation of the bean’s rarefied essence into chocolate flavor.

From bean to nib

The heaps are then dried carefully to prevent the growth of less-than-friendly microbes, either by the traditional method of spreading the beans out or using machines. Either way, the goal is to drop the water content to about 7 to 10 percent.

The dried beans then take a nice shower before enjoying a toasty roasting, where their flavor and fragrance are completely borne out and they bid a final farewell to any microbes that have overstayed their welcome (and any party-crashers). Then they undergo a luxurious squeezing (okay, they are ground up). All ground up and grown up into nibs, they are ready to be transformed into chocolate nirvana—baking bars, confections, syrups—for the ecstatic pleasure a bite or sip of chocolate can bring.

Then and now

Credit the ancient head-carving Olmec civilization from Mesoamerica for being the first humans ever to drink hot chocolate. Lost to the ages is the secret of how they came to ferment and process the beans, but a grateful world bows to their accomplishment. An obviously generous people, they shared their secret with the Mayans, who practically exploded with affection and celebration over the “food of the gods” and traded it forward to their buddies up north in the American Southwest.

The Aztecs really liked it, too, so much so that they demanded taxes be paid with cacao beans, offered the beans to the gods, and gave a calming chocolate snack to those about to be sacrificed. And all that in the first 3,000 years, from 1500 B.C. to 1500 A.D.

Food of the gods or Matina 1–6?

But that story is so last millennium. Here in the 21st century, 92% of cacao’s genome has been identified. The name “Matina 1–6” lacks the ethereal nature of the plant’s Linnaean counterpart, and its 35,000 gene count is puny compared to the billions of microbes that work in concert to transmute the bean into a cocoa nib.

Modern science has also suggested that five species total, drawn from each of the three main fermenting microbial groups— the yeasts, lactic-acid bacteria, and acetic-acid bacteria—could be whipped up into a biochemical cocktail of sorts and used to mimic the actions of Team Nature, the fermentation aggregation that has been working its alchemy beneath a blanket of banana leaves for millennia.


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Additional Reading

1. Go to for the nitty-gritty details of the biochemical process.
2. A great reference for the history of chocolate:
3. A peek into the kitchens and heads of some world-class Parisian chocolatiers:

[Roxy Bergeron is a volunteer cashier and dedicated chocolate lover. She is currently working on her first novel.]