by Mary May
figures by Aparna Nathan

People have been eating and drinking fermented foods since long before we understood how to cultivate the yeast and bacteria that make them. As anyone who’s cultivated a sourdough starter can attest, the microorganisms that make bread rise, ferment juice into alcohol, take the bitterness out of raw olives, and turn cabbage into kimchi are everywhere and all around us. These wild microorganisms form complex communities that help preserve food, making it inhospitable to harmful bacteria and molds. Much of the mass-produced, fermented foods we eat in the U.S. today use domesticated microbes. Wild fermented foods are making a comeback, however, gaining fans outside of the communities that have traditionally relied on them.

Cultures love culture

Evidence of wine fermentation goes back to 6,000 years ago in Sicily. Researchers found 13,000-year-old beer residue in Israel, yeast-leavened bread has been around since at least the ancient Egyptians, and fermented milk, like yogurt and kefir, emerged as animals like sheep and goats were domesticated. All of these early fermented foods developed far before we understood microbiology and had the tools to isolate any of these microbes. From Chinese soy sauce to French cheese, Ethiopian injera to Indonesian tempeh, Korean kimchi to German sauerkraut, fermented foods are fundamental parts of nearly every cuisine on Earth and have shaped the way people eat for thousands of years.

Figure 1: Fermented foods have shaped the cuisines of cultures all over the world and are common ingredients and foods everywhere.

The microbes that we have harnessed to keep our food fresh longer and taste better come from the environment, the food itself, and even the chefs. While yeast are well known as prolific fermenters, bacteria are also deeply involved in most wild fermentations; in a sourdough starter, for example, bacteria outnumber yeast 100 to 1 and are essential to its development and survival. 

Now, when commercial yogurt is made or beer is brewed at a large brewery, the microorganisms added are specially chosen to make consistent and predictable products. However, before Louis Pasteur invented pasteurization to stop bacterial contamination in milk and wine, the microbes responsible for fermentation were whatever organisms were already in the food or the kitchens of the people cooking.

Cheese and yogurt historically were dependent on the bacteria that made it into raw milk from the cow’s skin and the yeast used to ferment wine came from the grape skin. Traditionally, many fermented foods would start with a little bit of a previous batch, a technique called backslopping, helping to maintain the flavors and textures that the makers liked. Some families still pass down yogurt starters that contain undefined and complex bacterial communities that have been making yogurt for generations.

Microbial cultures survive through mutually beneficial relationships

Many different species of yeast and bacteria coexist in wild fermentations; the most common group of bacteria are lactic acid bacteria, which are characterized by their ability to produce lactic acid, one of the acids that gives sourdough its tang and lacto-fermented vegetables, like kimchi, their pickling power. The yeast that brewers and bakers add to their ferments is a strain that doesn’t produce any unexpected flavors and is optimized to produce alcohol or make bread rise. Wild ferments on the other hand, can have a variety of yeasts which produce many different flavors and they may grow and ferment more slowly.

In both sourdough starters and kombucha’s Symbiotic Community Of Bacteria and Yeast (SCOBY), the bacteria and yeast work together in a mutually beneficial arrangement. Because the starters are potential food sources for any microbes nearby, the yeast and bacteria in the starters not only eat the available food but also produce chemicals that are toxic to other microbes in a kind of microbial warfare. In a starter like a SCOBY, the ferment also creates a physical barrier that supports the community.

The yeasts eat sugars like fructose and glucose in the starter to produce ethanol and carbon dioxide (the gas that makes bread rise and some kombucha bubbly). Ethanol (i.e. alcohol) is toxic to many bacteria, but lactic acid bacteria don’t mind the ethanol – some survive even better than yeast in high levels of ethanol. The bacteria prefer to eat maltose, meaning the yeast and bacteria don’t have to compete for the same food. The acid produced by the bacteria prevents other bacteria that can’t tolerate acidic environments from growing. The yeast, which thrive in acidic environments, in turn break down starches into simpler sugars that the bacteria and yeast can eat more easily. Together, bacteria and yeasts make an inhospitable environment for microbes that might outcompete and kill the starter cultures and help make food for each other. 

Diagram, shape

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Figure 2: The yeast and bacteria in wild fermentations work together to prevent other microbes from growing. The yeast help breakdown starch into easy-to-eat sugars while producing ethanol and the bacteria produce acids. The ethanol and acids prevent other microbes from growing in the fermenting food.

Similarly, heirloom yogurt starters contain complex, unique bacterial communities that work together to keep out outside microbes that might kill them off. A home cook can make yogurt using a little bit of store-bought yogurt containing live cultures and milk, backslopping to make new batches in the future. Eventually their yogurt starter will die off, however, because the few bacteria strains selected in a lab can’t work together to stave off all the competing bacteria and viruses that see the milk as a promising food source. A wild ferment has staying power that scientists struggle to copy using state-of-the-art technology.

Re-embracing the funk of wild fermentation

Wild microbes produce a huge number of chemicals that affect the flavors of what they ferment. To make sure they know what they’re getting, producers commonly use sulfites, a preservative and natural byproduct of fermentation, to kill off any unwanted yeast and bacteria to prevent these flavors from developing. Wild fermented foods are still ubiquitous around the world and have always been essential to communities in the U.S. However, commercial producers, winemakers, beer brewers, and even home bread bakers have re-embraced the funky, more unpredictable flavors of wild microbes to make foods with more character, bringing them to a wider audience.

A close up of a dog

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Figure 3: Wild fermentations are like wild animals, while the domesticated yeast and bacteria used in many commercially fermented foods are more like domesticated dogs.

To use an analogy, you can think of making bread or beer from a store-bought yeast-packet as akin to getting a pure-bred dog: you know exactly what you’re getting every time. Wild fermentations, on the other hand, are like a feral and undomesticated relative of the dog – they interact with other organisms in their ecosystem, have many more flavors, and are harder to control. However, that is what makes them interesting and delicious.


Mary May is a PhD candidate in the Chemical Biology Program at Harvard.

Aparna Nathan is a fourth-year Ph.D. student in the Bioinformatics and Integrative Genomics Ph.D. program at Harvard University. You can find her on Twitter as @aparnanathan.

Cover Image: “দই (Yogurt)” by Nasir Khan Saikat is licensed under CC BY-SA 2.0

For More Information:

  • Learn how to make and characterize your sourdough starter from this lab
  • World-famous restaurants, like Noma in Copenhagen and Momofuku in New York, have labs set up to experiment with fermentations based on traditional techniques

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