Restoring Digestive Health with Fermented Foods

By eating a variety of live fermented foods, you promote diversity among microbial cultures in your body. Biodiversity, increasingly recognized as critical to the survival of larger-scale ecosystems, is just as important at the micro level. Call it microbiodiversity.

The ancient Greeks understood that important chemical changes took place during fermentation, calling it “alchemy.” With vegetables and fruits, as with dairy products, preservation by the process of lacto-fermentation has many advantages beyond simply maintaining the edibility of fresh food.  In the process of fermentation, starches and sugars in vegetables and fruits are converted into lactic acid, which is a natural preservative because it inhibits the bacteria that cause foods to rot and putrefy.  Lactic acid producing bacteria, or lactobacilli, produce enzymes that enhance digestion, increase vitamin levels, and promote the growth of healthy flora throughout the intestines.

Microflora, Probiotics and Healthy Gut Ecology

There are three phases in the process of fermentation.  In the first phase, anaerobic bacteria begin producing an acidic environment, and in the second phase the acid levels become too high for some bacteria, but allowing “friendly” bacteria to become dominant.  In the third phase, various types of Lactobacillus bacteria are greatly increased and continue to ferment any remaining sugars, lowering the overall pH. These lactobacilli are present on the surface of all living things, and are especially numerous on leaves, roots, and plants growing in or near the ground, and their numbers are greatly increased in this process.

The increased vitamin and micronutrient levels of fermented foods are significant in the promotion of health.  Fermented dairy products have increased levels of folic acid, pyroxidine, B vitamins, riboflavin, and biotin, depending on the strains of bacteria present.  Fermenting vegetables and fruits increases the bioavailability of amino acids, particularly lysine and methionine, and the anaerobic environment of the fermentation process preserves the vitamin C content of the foods.  When grains are fermented, the activity of phytic acid is decreased.  Phytic acid is an “anti-nutrient” that binds minerals, particularly zinc, calcium, iron and magnesium, preventing their full absorption in the intestines.  Since fermenting grains reduces the phytic acid content, it enables the body to absorb more minerals.

Research clearly shows that fermented foods aid digestion, support immune function, and increase overall nutritional status by adding B vitamins and omega-3 fatty acids.  Consuming foods that contain live lacto-bacteria also has protective benefits against harmful pathogenic microorganisms.  Lactobascillus microbes, an effective probiotic, proliferate in the intestines and crowd out or overwhelm pathogenic bacteria.  Lactic acid, hydrogen peroxide, and other byproducts of the fermentation process also make the intestinal environment hostile for undesirable organisms.  As a byproduct of their metabolism, probiotics create a short chain fatty acid that is used as a source of “fuel” by intestinal cells to promote healthy intestinal tissue.

Empirical research has identified a long list of health conditions that may be helped by consuming foods containing lactic acid bacteria, including colitis, constipation, diarrhea, gas, gastric reflux, heartburn, Crohn’s disease, gum disease and high cholesterol. Recent studies have even shown a positive effect of probiotics on autism and obesity.

In short, “good” bacteria or “probiotics” such as Lactobacilli and bifidobacteria:

  • Help to maintain healthy intestinal flora by greatly increasing the numbers of beneficial microorganisms
  • Prevent colonization of pathogenic organisms
  • Preserve nutrients and break them down into easily digestible form, increasing the nutritive value of foods due to improved bioavailability
  • Create new cultures that increase B vitamins such as folic acid, riboflavin, niacin, thiamin, biotin, and B12
  • Enhance the absorption of minerals, particularly calcium, iron, zinc, magnesium, phosphorus and copper
  • Neutralize toxins, such as phytic acid, that block mineral absorption

Sandor Ellix Katz, in his excellent book “Wild Fermentation: the Flavor, Nutrition, and Craft of Live-Culture Foods” (Chelsea Green, 2003), has this to say:  “By eating a variety of live fermented foods, you promote diversity among microbial cultures in your body. Biodiversity, increasingly recognized as critical to the survival of larger-scale ecosystems, is just as important at the micro level. Call it microbiodiversity. Your body is an ecosystem that can function most effectively when populated by diverse species of microorganisms. By fermenting foods and drinks with wild microorganisms present in your home environment, you become more interconnected with the life forces of the world around you. Your environment becomes you, as you invite the microbial populations you share the earth with to enter your diet and your intestinal ecology.”

Cultured Foods: A Worldwide Tradition

Around the world, traditional foods have been fermented for ages, for both preservation and for their health benefits.  There is evidence of cultured milk products being produced as a food as long ago as 10,000 BC.  With the increased incidence of gastrointestinal problems in the modern Western culture, often due to poor diet and a reliance on processed foods, interest in traditional foods and eating habits are regaining popularity. But it wasn’t long ago that families on the farm regularly had a crock of sauerkraut fermenting in the basement, and in many Asian cultures, the use of fermented foods has never fallen out of favor.


In East and Southeast Asia, miso, tempeh, natto (fermented soy), kimchi (fermented cabbage), tamari, fermented fish sauce, fermented shrimp paste, are all used on a regular basis at home and in restaurants.   Douchi is a fermented black bean used in Chinese for making black bean sauce, but it is also considered to have medicinal properties. In Central Asia they make kefir, kurmis (fermented mare milk), and shubat (fermented camel milk).  Fermented pickles, various yogurts, and torshi (mixed vegetables) are common in the Indian and Middle Eastern diet.  The Pacific region is known for their tradition dishes of poi (taro root that is fermented and mashed) and “kanga pirau”, made from rotten corn.

In Europe and the U.S., there is sauerkraut, traditional cucumber pickles, and kombucha.  Ann Wigmore is famous for her detoxification diet using rejuvelac, a beverage made from fermented sprouted grains.  But back as far as the time of Captain Cook, sailors always took a store of sauerkraut on their long voyages, as experience taught them that it was an effective prevention for scurvy.  This dietary practice was widespread until the British Royal Navy switched to using limes to provide necessary vitamin C.

Simple Steps to Fermenting Veggies

Beneficial bacteria are readily available on vegetables and in the air, so no starter culture is necessary to stimulate fermentation.  The process is simple and it is hard to go wrong, as long as you keep in mind the key to success – always keep your veggies submerged in liquid.  The liquid is usually salty water, referred to as brine, but fermentation can be done without salt or with other liquids such as wine or whey.

1) Choose the vegetables that you want to ferment.  You can use almost anything, but if this is your first ferment, you may want to start by making a simple cabbage sauerkraut. You can use both green and purple cabbage if you like, which will create a bright pink kraut.  Chop or grate the cabbage, and any other veggies you choose, into fine or coarse pieces.  The smaller the pieces are, the more readily they will release their liquids and the faster they will culture.

2) In a bowl, add salt to the cabbage as you go. The salt pulls water out of the vegetables, creating the brine. The salt will soften and ferment the cabbage, while keeping it crunchy, by inhibiting enzymes that break down the vegetable cell walls. It also helps prevent the growth of unwanted organisms. There is no need to measure the salt, but the average amount used is about 3 tablespoons for 5 pounds of cabbage (or about one quart of kraut).

3) If you want to add other vegetables, cut or grate them and add to the cabbage mixture. Carrots, turnips, bok choy, or kale are nice additions, and onions or garlic are commonly used. Experimenting is good – so try burdock root, horseradish, beets, chilis, or even seaweed. You may also add herbs and spices. Consider caraway or celery seed, dill, or juniper berries. Fruits may also be added, but they will ferment quickly, giving you a sweeter, less sour kraut. Apples are a classic fruit addition.

4) Choose a container for your vegetable mixture. It is best to use a cylindrical ceramic crock or glass jar with wide mouth opening. Pack the vegetables into your container with some force (unless they are whole), in order to break down the cell walls and release the juices. Traditionally, a blunt wooden tamping tool is used. You can improvise with a piece of wood or your fist, or you can manually massage and squeeze the vegetables.


5) Cover the kraut with a plate or lid that fits as tightly as possible to the inside of the container. Then place a weight on top (a smaller glass jar filled with water and capped works well). This weight helps force the water out of the veggies and keeps them submerged in the liquid. It is important that the vegetables stay submerged in order to inhibit mold growth, so if the brine does not rise above the plate by the next day, add more salt water (about one teaspoon of salt dissolved per cup of water). Cover all this with a cloth to keep out any flies or other insects, or cap the jar if you are using a glass container with top. If you are using a capped jar, you need to open it daily to release the pressure.

6) The vegetable should be kept at room temperature for at least 4 to 7 days, and often for 2-3 weeks. The ideal temperature is about 60-64 degrees F. Cool temperatures will lead to slower fermentation and a taste that keeps improving for months, while warmer the temps hasten the culturing process and will eventually lead to softening of the vegetables and a less pleasant taste. Taste the mixture every day or two until it is to your liking. If you are using a capped jar, it will pop or fizz when you open it. Over time, the volume reduces and the taste will become increasingly sour, so when it tastes the way you want, place the jar in the refrigerator to stop the fermentation process. It can be kept there indefinitely.

Sometimes mold appears on the surface as a result of contact with the air. As long as the vegetables remain submerged they are protected in an anaerobic environment. This is not a problem, but you should skim off as much of the mold as you can and rinse off the plate and weight.

7) When the kraut is young, you can eat it over time and enjoy its evolving flavor. The juice is a wonderful digestive tonic and can be eaten in its own right. Each time you remove some of the kraut and juice, make sure you repack the rest carefully and that the mixture stays submerged below the brine. Enjoy the great taste and health benefits!

Other Vegetable Combinations

Turnips, Radishes, Carrots: Slice them into planks or chunks and cover with brine. Try these will dill seed and garlic or with mustard seed and red pepper flakes. Turnips tend to be a bit spicy when fermented, but are great on salads.
Beets: Beet and carrots together create a thick, sweet and deep red liquid and the vegetables are deliciously tender, sour, and sweet.

Green Beans or Asparagus: Trim the veggies to fit in the jar and add a garlic clove and maybe a small, dried red chili. Try doing the same with okra.

Mushrooms: White or baby ‘bella mushrooms can be pickled in brine into a very tasty appetizer. Try adding black peppercorns and mustard seed as well as a small garlic clove.

Summer Relish: Use corn, chopped green tomato, red bell pepper, and onion with mustard seeds. It takes a month or so for the flavor to develop but is fantastic.
Pickled Garlic: Peel the cloves, fill the jar and cover with brine. It will take 4-5 months for the cloves to ferment fully but it will be worth it. They ferment into a mellow, garlicky, almost sweet tangy condiment. Perfect for salad dressings and topping soup.

Commonly Asked Questions, and Answers

What kind of container should I use to hold the fermentation mixture?

It is best not to use metal as the salt added to the mixture, and acid created by fermentation, will tend to cause corrosion. Traditionally, a heavy ceramic crock is used, but glass containers work just as well. When possible, chose a container with a cylindrical shape or a wide mouth so that it is easy to pack the vegetables inside, and also easy to insert a suitable plate and weight inside to keep the vegetable from floating to the top of the container. All plastic containers should be avoided.

There are specially designed fermenting crocks that create an oxygen-free airspace around the ferment, in order to decrease the tendency for mold to grow. See “Resources” at the end of this article.


What kind of vegetables should I use?

Pretty much any vegetable can be fermented. Use what is abundantly available in your region and season. Seaweeds are a good addition to ferments, as are fruits, though most will go through their fermentation process very quickly. The spicing of vegetable ferments varied according to various traditions. Kimchi typically includes red chili peppers, garlic, ginger, and scallions. Sauerkraut might include caraway seeds, juniper berries, apples, or cranberries. New York–style sour pickles are spiced with dill, garlic, and sometimes hot peppers. To keep cucumbers crunchy, add grape leaves or leaves of horseradish, oak, currant, or cherry to the brine.

How small should I cut my vegetables?

The smaller the pieces, the quicker the vegetables will ferment. The size of the pieces is really a personal preference. Some ferments are traditionally done with larger chunks such at turnip kimchi, or smaller grated pieces such as in a traditional cabbage kraut. Larger pieces will generally take a longer time to ferment and create a less sour end product.

What kind of salt and how much should I add?

Traditionally vegetables have been fermented with lots of salt. In addition to pulling water from the vegetables, salt hardens pectins in the vegetables, making them crunchier. It also discourages the growth of bacteria other than lactobacilli. By inhibiting competing bacteria, salt enables the vegetables to ferment and to be stored for longer periods of time. Since preservation has historically been one of the important motivations for fermentation, ferments have tended to be quite salty, but for health-conscious people interested primarily in flavor and nutrition, less salt can be better.

Salt lightly, to taste. It is easier to add salt than to take it away, but if you oversalt, you can dilute by adding water and/or more vegetables. As a general guideline, about three tablespoons of salt per five pounds of vegetables is a good place to start. Coarse or fine sea salt is the recommended form to use in fermenting. Avoid iodized or other processed salt.

Keep in mind that more salt will slow the fermentation process; less will speed it up. Ferments with less salt may be more prone to surface molds. You can leave out the salt or use various mineral-rich substitutes such as celery juice or seaweed, but be sure the vegetables are submerged in liquid.

How long should I ferment the vegetables?

Many recipes advise “ferment until ripe”, but it really depends on personal preference. The sour flavor, which develops from lactic acid, gets stronger over time, so longer fermentation leads to tangier flavor. This happens more quickly in warm temperatures than in cool ones, so if you start your ferment in cool weather, you may be able to let it go for six months or longer. This is how people survived before refrigeration and globalized food. However, many prefer the flavor of a mild ferment to that of a strongly acidic one. When you are first experimenting,. familiarize yourself with the spectrum of flavors that fermentation can create by tasting your ferments often.

Is it really safe to eat fermented vegetables that have been left un-refrigerated for weeks

Leaving foods urefrigerated for two weeks or more can be disturbing to those who weren’t raised with this traditional food. But U.S. Department of Agriculture research service says properly fermented vegetables are actually safer than raw vegetables, which might have been exposed to pathogens like E. coli on the farm. The lactic acid bacteria that carry out the fermentation are effective killers of “bad” bacteria.

There are no documented cases of food-borne illness in fermented food and they are considered safer for novices to make than canned vegetables. Sterilizing jars or crocks for sauerkraut or pickles is optional. It is fine to simply wash the jars in hot, soapy water. Just make sure that the fruits and vegetables stay completely submerged in the brine.

If the vegetables float to the top and remain exposed to air, they are likely to develop mold. Sometimes, especially in hot weather, the ferment may then develop a film of white mold on its surface. This is very common and will not hurt you or the kraut. Scrape off the mold as best you can, don’t worry about particles that mix into the vegetables.

More Recipes

Multi-Veggie Fermented Kraut

  • 1 head cabbage
  • 1 onion (or leeks, green onion, shallots)
  • 3-8 cloves garlic
  • 1 bunch carrots
  • 1 bunch daikon radishes
  • 1 Tablespoon red pepper flakes
  • 1-2 inch piece ginger
  • 2 Tablespoons dried dill, or 4 tablespoons fresh dill
  • 1 ½ Tablespoons caraway seed
  • 2 Tablespoons sea salt – or more as needed

Process all vegetables in batches in a food processor to whatever thickness you desire. You may also chop/grate the vegetables by hand. Mix the vegetables with the sea salt, dill, caraway and red pepper flakes in a large bowl.

Pack the mixture into ½ gallon glass jars leaving at least an inch of room at the top so the juices do not leak out of the jar when the sauerkraut expands during the fermentation process. It is important to pack the veggies down with a wooden spoon until the liquid released from the vegetables rises above the vegetables. This is key because fermentation is an anaerobic process that occurs in the absence of oxygen. If there is not enough juice to cover the veggies you may have to pound them with a wooden spoon (the smaller you have chopped your veggies the more juice will be released).

Put a lid on the jar and leave it to ferment. As the veggies ferment you will see bubbles form and the mixture will expand. If it expands above the level of the liquid the veggies may become gray where they come in contact with the air. This is not a problem but you should push the sauerkraut back down below the liquid.

Alternatively, you may also pack your sauerkraut into a crock and weight it down with a plate and another jar filled with water and capped, to keep the sauerkraut below the level of the liquid. In this case, mold may grow on the top of the liquid but it is easily scraped off and the sauerkraut below the liquid is not affected, as it is preserved and protected by the good bacteria fermenting it.

Try your fermented veggies on different days to see how you like them, as the flavor will change over time. The usual time for fermenting is 4-10 days. You may then refrigerate them for months or longer.

Lacto-fermented Peach Chutney

Makes 1 quart: Total time: 1 1/2-2 1/2 days

This recipe for spicy, fresh chutney is adapted from “Full Moon Feast,” by Jessica Prentice (Chelsea Green, 2006). You can also add unpeeled chopped tomatoes and 2 teaspoons fenugreek seeds for more of a savory flavor.

  • 1/4 cup boiling filtered water
  • 8 to 10 peaches, peeled and cut into small dice
  • Juice of 1 lemon
  • 1 tablespoon whole cumin seeds
  • 2 teaspoons black or brown mustard seeds
  • 1 teaspoon fennel seeds
  • 1 4-inch piece of ginger, peeled and grated
  • 1 teaspoon powdered turmeric or one 1-inch piece fresh turmeric, peeled and grated
  • 1 tablespoon Sucanat or rapadura
  • 1/4 cup yogurt whey (see note below)
  • 4 teaspoons sea salt
  • 1/4 teaspoon cayenne (optional)

Put the fenugreek seeds in a small bowl and pour the boiling water over them. Let them soak overnight or for at least 6 hours. Put the peach pieces in a large bowl. Drain the water from the fenugreek seeds and add the seeds to the peaches. Squeeze the lemon juice over the peaches.

In a small cast-iron skillet, toast the cumin, mustard and fennel seeds over medium heat until they begin to smell fragrant. Add the seeds to the peaches with the ginger, turmeric, Sucanat, yogurt whey, salt and cayenne. Stir thoroughly and taste. The mixture should be salty.

Transfer to a 2-quart jar and gently weigh down the top of the chutney so the liquid rises above the solids by filling a small, narrow jar with water and setting it inside the other jar so that it gently pushes the chutney down but allows the liquid to come to the top.

Ferment at room temperature, at least overnight. If it is hot, 24 hours may be enough. If it is cool or just warm, ferment for 48 hours. Chutney can be eaten immediately or can be refrigerated for up to 1 month.

Note: To make yogurt whey, take 2 cups of live-culture whole milk yogurt and pour it into a colander or strainer lined with cheesecloth set above a bowl or pot. Let drip for up to 8 hours in the refrigerator. The whey will be in the bowl and the yogurt in the cheesecloth can be used like cream cheese.

Brined Snap Beans or Asparagus

Makes 1 gallon : Total time: 2 weeks

This recipe is adapted from “Joy of Pickling,” by Linda Ziedrich (Harvard Common Press, 1998). You can substitute trimmed asparagus for the snap beans.

  • 2 pounds tender young snap beans, trimmed
  • 6 small dried chile peppers
  • 6 garlic cloves, chopped
  • 12 black peppercorns, crushed
  • 6 dill sprigs
  • 1/2 cup sea salt
  • 3 quarts water

Layer beans, chili peppers, garlic, peppercorns and dill in a 1-gallon jar. Dissolve salt in the water and pour enough brine over the beans to cover them. Cover the mixture with a plate, and place a weight on top (a capped jar filled with water will do fine). Store at room temperature with the top of the container loosely covered.

Within 3 days you should see tiny bubbles rising. If scum forms on top of the brine, skim it off daily and rinse off the plate and weight. The bean pickles should be ready in about 2 weeks, when the bubbling has stopped and the beans taste sour. Remove the plate and weight, skim off any scum, and cap the jar. Refrigerate.

Dongchimi (Young Radish Kimchi)

Makes 3 quarts: Total time: 2-3 days

Fermented FoodThis recipe is adapted from “A Korean Mother’s Cooking Notes,” by Chang Sun-Young (Ewha Womans University Press, 1997). Roasted salt and Korean radish is available at Korean grocery stores. Look for the young radishes measuring about 4 inches with the leaves still attached.

  • 3 bundles Korean white radishes (9 radishes)
  • 3 tablespoons roasted salt (or substitute regular sea salt)
  • 3 tablespoons sugar
  • 1 bunch green onions
  • 1 large clove garlic, thinly sliced
  • 1 knob of ginger similar in size to the garlic clove, peeled and thinly sliced

Clean radishes under cold running water, making sure to remove any dirt between the radish and the leaves. Use a small knife to cut off any hairy roots and yellow leaves. Do not peel the entire radish or the liquid will become too milky.

In a small bowl, mix 1 1/2 tablespoons roasted salt with 1 1/2 tablespoons sugar. In a large container, place a layer of the washed radishes and sprinkle with some of the salt and sugar mixture. Repeat this step until all of the radishes are in the container. Top with slices of the garlic and ginger. Cover and let stand at room temperature for 24 hours.

The next day, bring 6 cups of water with remaining roasted salt and sugar to a boil. After the sugar and salt is dissolved, remove from heat and while the water is still warm (about 100°F), pour it over the radishes. Once the water is cool, cover the container and leave at room temperature for 1 to 2 days to ferment.

After 1 to 2 days, store dongchimi in the refrigerator. When ready to serve, peel the radish and cut into 1/4 inch thick, bite-size portions. Also, cut the leaves to bite size and serve with the radish and plenty of liquid.

References, Resources, and Recommended Reading

Katz, Sandor Ellix. Wild Fermentation. Chelsea Green Publishing. 2003.

Gates, Donna. The Body Ecology Diet. Body Ecology. 2002.

DeBusk, Ruth, Genetics: The Nutrition Connection, American Dietetic Association; January 2003.

Duggan, Tara, San Francisco Chronicle, June 2009

Cultures for Health: Online probiotic fermented food cultures such as sourdough, kefir, water kefir, kombucha, and yogurt starters. Also carries high quality earthenware crocks that create an oxygen-free space around the ferment.

Vitamin Profiles of Kefirs Made from Milk of Different Species. International Journal of Food Science & Technology. 1991. Kneifel et al

Evaluation of lysine and methionine production in some Lactobacilli and yeasts. International Journal of Food Microbiology. Odunfa et al



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