Food Fermentation: How Microorganisms Make Food Delicious

By: Jesslyn Shields  | 
fermented foods
Fermented canned vegetables, such as marinated cabbage, carrots, cucumbers and sauerkraut can extend the life of foods from your garden, lasting for up to a year in a dark, cool location. Yulia Naumenko/Getty Images

You might think you generally try to avoid microorganisms in your food, because bacteria and yeast cause food to spoil. But the truth is we wouldn't have a lot of the world's most delicious foods and beverages — coffee, chocolate, vanilla, cheese, bread, beer and cured meats, just to name a few — without fermentation, which involves the intentional use of microorganisms to transform food. The line between spoiling and fermentation is a muddy one, but a distinction humans have been futzing with for millennia.

"What microbiology has illuminated is that all the plants and animal products that make up our food are inevitably populated by a diversity of microorganisms," emails Sandor Katz, self-described "fermentation revivalist," teacher and author of several books about fermentation, including "Wild Fermentation," "The Art of Fermentation," "Fermentation as Metaphor," and "Fermentation Journeys."


"Fermentation involves encouraging the growth of some microorganisms — ones that make our food more stable, more delicious, more nutritious, safer, less toxic or alcoholic — and thereby prevent the growth of the ones that can decompose our food or make us sick," says Katz. "Certain ferments, such as strong cheeses, are edgy in that some people find them compellingly delicious, while others think they are disgusting and are reminded of decomposition and death. Science offers us no sharp dividing line between fermentation and spoilage. In most cases it is obvious, but in certain cases it is culturally determined and subjective."

Humans and Fermentation

Pretty much every culinary tradition in the world uses fermentation in some way or another. Humans began using fermentation to brew beer, preserve food, make their food tasty and render toxic things edible millennia before Louis Pasteur proved that living cells were responsible for fermentation.

"The oldest examples of fermentation in the archeological record are from about 10,000 years ago in China, though I would argue that that tells us more about the history of pottery than the history of fermentation," says Katz. "Presumably the cultural practice of fermentation is older than that, using pits in the ground, gourds, animal membranes, wood or other biodegradable materials."


According to Katz, it's no surprise that fermentation can be traced back to around the same time as humans began developing communities around domesticating plants and animals. In order for it to make sense to invest all our time and energy into growing food, humans would have had to come up with a strategy for storing and preserving food so that the harvest of a few weeks could last the community many months.

Also, basically every culture in the world has figured out how to ferment sugars into alcohol. It's possible our primate ancestors understood the party-inducing effects of eating a bunch of fermented fruit they found on the ground. All humans had to do was figure out how to do it on purpose.

fermented foods
Sourdough starter is used to prepare homemade sourdough bread without the use of commercial yeast. The starter is made from a mixture of flour and water fermented for a few days until the mixture is ready for use.
Beachmite Photography/Getty Images


The Science of Fermentation

The word "ferment" comes from the Latin word for boiling or rising, which you'll understand if you've ever seen beer brewing or bread dough rising — both signs of fermentation in action. A biologist would probably say fermentation is the anaerobic production of energy, meaning that microorganisms that don't need oxygen to accomplish metabolization to fuel their bodies transform nutrients into energy in the absence of oxygen. This is true for some fermented foods — for instance, sauerkraut and alcohol are both products of the hard work of anaerobic bacteria. However, other foods and beverages that we consider "ferments" are made by aerobic microorganisms that use oxygen to do their business: kombucha, vinegars and miso are a few.

The applied science of zymology, or zymurgy, is the study of how microorganisms, whether they use oxygen to metabolize or not, ferment the stuff around us — what the biochemical processes are, which specific organisms are doing it, and how this works all over the world, including in our foods.


There are three basic types of fermentation that can happen in the foods and drinks we enjoy every day:

  • Alcoholic fermentation has been a fermentation fan favorite for millennia — it uses yeasts to convert sugars to ethanol, carbon dioxide and other byproducts.
  • Acetic acid fermentation happens after alcoholic fermentation ends, and the result is usually vinegar.
  • Lactic acid fermentation is the magic behind so many of our favorite foods, from sourdough bread to kimchi to cheese and yogurt. Lactic acid bacteria digest simple carbohydrates to produce lactic acid — a process that turns sweet things sour, which is what gives pickles their characteristic kick.


What Can Fermentation Do for You?

Not all fermented foods and beverages do the same things in our bodies, but according to Katz, they can help us out in a few important ways:

  • Predigestion: The microorganisms that ferment the food essentially break down things like carbohydrates, proteins and chemical bonds before we eat it, in some cases making it more easily digested and bioavailable. "Even nutrients which create problems for many people, such as lactose or gluten, can be broken down by fermentation," says Katz.
  • Detoxification: Some foods can only be made edible through fermentation. The microorganisms take potentially toxic (to us) compounds and digest them into harmless or even beneficial forms, rendering foods that could otherwise be poisonous or irritating safe to eat. One example of this can be found in cassava tubers grown in some regions of the world — they contain high levels of cyanide when they're harvested and require fermentation to make them safe to eat.
  • Nutrient enhancement: Fermentation generates additional B vitamins in most foods, K vitamins in some. Some metabolic byproducts we can think of as micronutrients are just beginning to be investigated.
  • Probiotics: "I think of the bacteria themselves as the most profound benefit of fermented foods, in that they exist in great diversity and can help to restore biodiversity in the gut that has diminished thanks to chemical exposure as well as modern diets high in overprocessing and low in fiber," says Katz. "The trillions of bacteria that live in and on our bodies are physiologically important, playing important roles in digestion, immune function, synthesizing nutrients and regulating chemicals that impact many different organs, including our brains. Eating live fermented foods, especially a variety of them, can help to restore biodiversity in the gut and potentially improve digestion, immune function and more."

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