For centuries people have been using microbes to their advantage, turning grapes into wine, milk into cheese, and cabbage into sauerkraut. People benefit from what microbes do naturally: They eat. They digest organic compounds, changing the chemical makeup of one product and turning it into a completely different yet tasty food or drink.

Milk, for example, is turned into cottage cheese when the bacteria Leuconostoc break down the milk sugar (lactose) to produce lactic acid. The acid curdles the milk into cheese curds. Different types of bacteria or mold make different kinds of cheeses. Bacteria are used in the production of all kinds of foods. Before coffee beans are washed, dried, and roasted, they are first soaked in a tank of bacteria that break down bits of shell still stuck on the bean. And without microbes, there would be no chocolate. Cocoa beans must...