DNA sequencing and the Chocolate Factory

It's been exciting to see the progress in getting the Theobroma cacao genome sequenced and off to the databases. But.... I've toured the Theo chocolate factory twice now, and there's a crucial piece in the story that appears to be missing. You see, chocolate is like wine. We don't get the chocolate we love from eating the fruit. We get the so-called "food of the gods" by eating the fruit after it's been fermented. And, just like wine, microorganisms are the ones doing the fermenting. I learned this from attending two separate tours at Theo chocolates, our local chocolate factory. One tour was sponsored by the Puget Sound chapter of the American Chemical Society. The other was just a Saturday morning in the summer. Both were delicious. Before the tours, I was a virgin in the world of chocolate. Now, I'm a snob. Apparently, some of the most important steps in making good chocolate happen long before the beans arrive at the factory door. Before chocolate beans travel to the US, the fruit from the Cacao plant needs to ferment. This step happens on the farm. Cacao fruit are put in funny-looking boxes and bacteria break down substances in the beans. To really know about making good chocolate, we need to know who works on the fermentation. We need to know about the bacteria and yeast that participate in this most important step. Fermenting cacao is a sweet area and ripe for a good metagenomics sequencing project. We do know the bacteria in the fermentation mix are important because they produce the volatile compounds and polyphenols that give chocolate it's flavor and antioxidant properties. That's right, if chocolate is properly treated, it has antioxidants and is healthy. The metagenome is also important for the "terre noire," a phrase that I think means something like "taste of the place." [correction from Vicki - the word is "terroir"] When I toured Theo Chocolate with the chemists, we were treated to a lecture by Andy McShea, the chemist at Theo. Theo has done interesting work measuring the volatile compounds from different chocolate beans and characterizing the distinctive profiles from each type of bean. Apparently, if the fermentation goes bad, the beans will never be good. I liked that. Chocolate factories make better chocolate by doing good science.