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Microbiome Monday: How Microbes Make Fermented Food

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Welcome to another Microbiome Monday! The Museum’s new special exhibition The Secret World Inside You is now open, and we're bringing you weekly primers on the human microbiome and the research surrounding it from Curators Rob DeSalle and Susan Perkins, as well as from other scientists who are working in this exciting field.

Microbes play key roles in human health, but that's not the only place humans encounter them. These invisible life forms are also key to producing some of our favorite foods, from the yogurt you had for breakfast to bread, cheese, and more. This week, Dr. DeSalle explains the role that microbial life plays in the making of a trio of fine foodstuffs that depend on fermentation: pickles, beer, and sourdough bread.

Cooking with Microbes

Just like any form of life, microbes need energy. To get it, they consume molecules they come into contact with for sustenance. No metabolism is perfect, though, and even the smallest meals produce waste products, a process known as fermentation. A microbe's trash can be a treasure to us, thoughthese waste molecules are key ingredients in the fermented foods and drinks that are cornerstones of cuisine around the world.

Fermentation works by feeding sugars to microbes like yeast, a fungus, or a bacteria such as Lactobacillus. The two types of microbes have different means of processing the carbohydrates they dine on. For bacteria, the end product of fermenting sugar is a simple molecule called lactic acid, a weak acid with a rather sour taste. Yeast, one the other hand, produces a molecule called ethanol, the inebriating agent in alcohol. Humans figured out early on that both of these waste products could create tasty dishes while also helping food keep longer, as demonstrated in the three recipes below.


Illustration showing steps and ingredients of pickle recipe including cucumbers, spices, water, dill, and ending with pickles in a jar.
Vegetables like cucumbers are pickled in the presence of microbes and a brine solution, and are commonly flavored with garlic, dill, and other ingredients.
© M. Fearon

Fermenting vegetable matter with bacteria (specifically strains of Lactobacillus) produces sour-flavored, long-lasting treats. Better known as "pickling," this process is used in cuisines all around the world to crafts foods from kosher dills to kimchi. The process is thought to have originated thousands of years ago in Egyptian society.  


The basic recipe for beer: hops, grain, water, malt, and yeast.
While beer has many different flavors and styles, the basic recipe includes water, hops, grain, malt, and yeast.
© M. Fearon

Fermenting grains or fruits with yeast is a tradition at least as old as pickling, and one that's also known around the world. Luckily for folks who enjoy a beer or glass of wine with dinner, yeast converts sugars into alcohol instead of lactic acid. While the two substances have similar chemical formulas (lactic acid consists of  six hydrogen molecules, teamed with three carbon and three oxygen atoms, while alcohol binds six hydrogen atoms to a pair of carbon atoms and a single oxygen atom) they do very different things when they come in contact with our bodies and communicate with our brains—hence the difference between sour-tasting pickles and inebriating beer.

Sourdough Bread

Sourdough Recipe
Yeast and bacteria are both involved in the fermentation process of sourdough bread.
© M. Fearon

But what happens when a concoction combines Lactobacillus and yeast? Sourdough bread is a good example of this forced symbiosis. Bakers have taken advantage of a wide array of Lactobacillus species and their close relatives to produce three kinds of sourdough bread. The lactic acid from the bacteria and carbon dioxide produced by the fermentation of yeast give this bread its distinctive tangy taste and fluffy texture. The fermentation process also converts the linoleic acid in bread flour into fatty acids that resist the growth of mold and help the loaf stay edible longer, a quality that made this food a favorite among gold surveyors in California. In addition, the presence of yeast means that sourdough freshly out of the oven will have some alcohol in it, although this content evaporates as time goes by.