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The Best Fermented Foods for Gut Health and The Microbiome

If you’re looking to improve your gut health and heal your microbiome, incorporating fermented foods into your diet is a fantastic starting point. Fermented foods can provide a beneficial boost to your digestive system, thanks to the probiotics they contain. But what exactly are fermented foods?,  how do they improve gut health and how do they influence the microbiome? If this sounds like a topic of interested in stay tuned! I will also include some instructions on how you can get started making your own fermented foods (yoghurt,  at the end of the article.

What Are Fermented Foods?

Fermented foods have been celebrated for centuries across various cultures for their unique flavors, textures, and health benefits. What makes these foods so special isn’t just the taste, but the remarkable array of beneficial compounds they contain.

Fermented foods are foods and beverages that have undergone the process of lacto-fermentation, where natural bacteria feed on the sugar and starch in the food, creating lactic acid. This process not only preserves the food but also creates beneficial enzymes, B vitamins, polyphenols, acids, and various strains of probiotics. Probiotics are essential for gut health, as they help balance the gut microbiome and improve digestion and gut health.

9 Way Fermented Foods Improve Gut Health

Fermented foods are pivotal in supporting gut health due to their rich content of beneficial bacteria, commonly known as probiotics. Here’s why I reccoemend fermented foods and how they work to strengthen the gut microbiome.

1. Contain High Levels of Probiotics

Fermented foods are teeming with live microorganisms, primarily beneficial bacteria from the genera Lactobacillus, Bifidobacterium, and others. When you consume these foods, you introduce these live cultures into your digestive system directly. Common Probiotics in Fermented Foods include Lactobacillus, Bifidobacterium, and Saccharomyces: A beneficial yeast found in some fermented foods and beverages such as kefir and kombucha.

2. Contain High Levels of Prebiotics

Fermented foods not only contain probiotics but also naturally occurring prebiotics—types of dietary fibers that feed the friendly bacteria in your gut. These prebiotics help support the growth and activity of beneficial microbes, enhancing the effects of the probiotics. In the early stages of SIBO, avoiding probiotics may be necessary. Here’s an article on the best probiotics to take in the early stages of treating SIBO. 

3. Competitive Exclusion

Outcompeting Harmful Bacteria. The beneficial bacteria from fermented foods help to outcompete pathogenic bacteria for resources and space in the gut. This concept, known as competitive exclusion, leads to a reduction in harmful microorganisms, allowing beneficial bacteria to thrive.

4. Enhancement of Gut Flora Diversity

Fermented foods are known to increase Microbial Diversity. A diverse gut microbiota is a hallmark of good health. Fermented foods introduce various strains of probiotic bacteria and good yeast, thereby increasing the diversity of your gut flora. This enhanced variety supports numerous digestive and immune functions.

5. Production of Short-Chain Fatty Acids (SCFAs)- Feed Existing Beneficial Bacteria:

Fermented foods themselves often serve as prebiotics (food for beneficial bacteria) and promote the production of short-chain fatty acids (SCFAs) within the gut. SCFAs, including butyrate, propionate, and acetate, are produced when beneficial bacteria ferment dietary fibers. These SCFAs not only nourish gut bacteria but also help maintain gut barrier integrity,  modulate inflammation, and support gut microbiome health. You can learn more about Short Chain Fatty Acids (SCFA’s) here

6. Improvement of Gut Environment

Regulation of pH Levels: Beneficial bacteria produce lactic acid during fermentation, which lowers the pH in the gut environment. A more acidic gut environment limits the growth of harmful bacteria, such as Clostridium difficile, controls gastric emptying, helps with Mucin secretion, and promotes the growth of acid-tolerant beneficial strains. Low stomach acidity (more alkaline gut) increases susceptibility to gastrointestinal infections and conditions like Small Intestinal Bacterial Overgrowth (SIBO). While most doctors in traditional medicine are trying to stop acid production with proton pump inhibitors, antacids, and histamine blockers, in functional medicine we look at stomach acid a bit differently.

The two main types of acid produced by fermented foods and beverages are Lactic acid and acetic acid. Lactic Acid is common in sauerkraut, kimchi, and yogurt, lactic acid aids gut health by lowering the pH in the intestines and promoting the growth of beneficial bacteria. Another acid found in Fermented food is Acetic Acid. Acetic acid is found in vinegar and pickled products, acetic acid has antimicrobial properties that can help to inhibit pathogenic bacteria.

7. Strengthening of Gut Barrier Function

Promotion of Gut Lining Health: Probiotics from fermented foods help maintain and strengthen the gut lining. A healthy gut barrier prevents harmful substances and pathogens from passing into the bloodstream, reducing the risk of systemic infections and chronic inflammation. Some fermented foods, especially those involving plant ingredients such as grapes, pomegranates, or kombucha, contain polyphenols—natural compounds known for their antioxidant and anti-inflammatory properties.

8. Immune System Support Interaction with Immune Cells:

Probiotics interact with the gut-associated lymphoid tissue (GALT) and other immune cells, stimulating immune responses that enhance the body’s ability to fight infections and reduce inflammatory responses. This collaboration helps maintain a balanced immune system which supports overall gut health.

9. Fermented foods Improve Digestion

The fermentation process generates enzymes that help break down the food substances into simpler forms that your body can easily absorb. Enzymes like lactase, protease, and lipase are a few examples found in fermented foods that aid digestion and nutrient assimilation.

The Best Fermented Foods to Eat for Gut Health

1. Sauerkraut:

Sauerkraut is made from fermented cabbage and is rich in probiotics, fiber, and vitamins C and K. The fermentation process not only enhances its nutrient content but also makes it easier for your gut to absorb these nutrients. Plus, making sauerkraut at home is simple: all you need is cabbage, salt, and time!

See the instructions below on how to make this 

2. Kefir:

Kefir is a fermented milk drink that is packed with probiotics and beneficial yeast. It’s often more potent than yogurt in terms of probiotic diversity. Making kefir involves adding kefir grains to milk (or water for a dairy-free option) and allowing it to ferment for 24-48 hours.

3. Kimchi:

Kimchi, a staple in Korean cuisine, is made from fermented vegetables like cabbage and radishes, combined with a variety of seasonings like chili pepper, garlic, and ginger. It’s rich in probiotics and fiber, which support digestive health. To make kimchi at home, you’ll need the vegetables, salt, spices, and a few days for fermentation.

See the instructions below on how to make this 

4. Yogurt:

Yogurt is one of the most well-known fermented foods. It’s created by fermenting milk with beneficial bacteria, usually Lactobacillus and Bifidobacterium strains. Opt for plain, unsweetened yogurt with live and active cultures for maximum gut health benefits. You can even make yogurt at home using a starter culture and milk.

See the instructions below on how to make this 

5. Tempeh:

Originating from Indonesia, tempeh is made from fermented soybeans. It’s not only rich in probiotics but also an excellent plant-based source of protein and vitamins. You can ferment soybeans with a starter culture to make tempeh, which can then be cooked and incorporated into various dishes.

6. Kombucha:

Kombucha is a fermented beverage made from sweetened tea that is transformed by a symbiotic culture of bacteria and yeast (often abbreviated as SCOBY). It’s known for its tangy, effervescent quality and is consumed for its purported health benefits, primarily related to gut health.

See the instructions below on how to make this 

How to Make Fermented Foods For Better Gut Health

Fermented foods can be made using a variety of ingredients and processes, but the basic principle involves creating an environment where beneficial bacteria and yeasts can thrive and transform the food. Here are some common methods for making different types of fermented foods:

Basic Fermentation Principles

1. Sterilization: Clean all equipment (jars, utensils, etc.) to prevent contamination by unwanted bacteria or mold.

2. Salt: Often used to create an environment that suppresses harmful bacteria while promoting beneficial ones.

3. Temperature: Maintain appropriate temperatures to ensure the correct microbial activity.

4. Time: Allow sufficient time for the fermentation process to develop the desired flavors and benefits.

Recipes for Common Fermented Foods

 1. Sauerkraut (Fermented Cabbage)


– 1 medium head of cabbage

– 1-3 tablespoons of salt


1. Shred the cabbage finely.

2. Sprinkle the salt over the cabbage and massage it with your hands until it starts to release liquid.

3. Pack the cabbage tightly into a clean glass jar or fermentation crock.

4. Place a weight on top to keep the cabbage submerged in its own juice.

5. Cover the jar with a cloth and secure it with a rubber band.

6. Let it ferment at room temperature for 1-4 weeks, checking daily to ensure the cabbage remains submerged.

2. Kimchi (Korean Fermented Vegetable Dish)


– 1 medium napa cabbage

– 1/4 cup sea salt

– 1 tablespoon sugar

– 4 cloves garlic, minced

– 1-inch piece of ginger, minced

– 2 tablespoons fish sauce (optional)

– 2 tablespoons gochugaru (Korean red pepper flakes) or to taste

– 4 green onions, sliced

– 1 carrot, julienned

– 1 daikon radish, julienned


1. Cut the cabbage into quarters and soak it in salted water for a few hours, then rinse and drain.

2. Mix the garlic, ginger, fish sauce, sugar, and gochugaru into a paste.

3. Coat the cabbage with the paste, mixing in the green onions, carrots, and radish.

4. Pack the mixture into a jar, pressing firmly to remove air pockets and ensure it’s submerged in its own juice.

5. Leave a little headspace and seal the jar loosely.

6. Allow it to ferment at room temperature for 3-7 days, then refrigerate.

3. Pickles (Fermented Cucumbers)


– 5-6 small to medium cucumbers

– 2 tablespoons sea salt

– 2 cups water (non-chlorinated)

– 2-3 garlic cloves

– Fresh dill or dill seeds

– Optional: cherry leaves or grape leaves (for crispness), mustard seeds, peppercorns


1. Dissolve the salt in water to create a brine.

2. Place the cucumbers in a glass jar with garlic, dill, and any other spices or leaves.

3. Pour the brine over the cucumbers, ensuring they are completely submerged.

4. Weigh them down with a fermentation weight or a clean jar filled with water.

5. Cover with a cloth and let ferment at room temperature for 3-10 days, checking daily to ensure they’re submerged.

4. Yogurt (Fermented Milk)


– 1 quart of milk (whole, low-fat, or skim)

– 2 tablespoons of plain yogurt (with live cultures)


1. Heat the milk to 180°F (82°C) to kill any unwanted bacteria.

2. Let the milk cool to 110°F (43°C).

3. Stir in the plain yogurt until combined.

4. Pour the mixture into a clean container and keep it at about 110°F (43°C) for 4-8 hours, or until it reaches the desired thickness.

5. Refrigerate before eating.

5. Kombucha

At the time of writing this article, I have a batch of Kombucha almost ready for its 2nd fermentation. Heres how you can make your own Kombucha.

The key ingredients are tea, sugar, water, a SCOBY (Symbiotic Culture Of Bacteria and Yeast), and starter tea (which is usually some kombucha from a previous batch). Here’s a detailed Explanation to help you make kombucha:


6–8 tea bags or 1/2 cup of loose tea (Black Tea/English Tea).

1 cup of sugar

14 cups of water

1 SCOBY (Symbiotic Culture Of Bacteria and Yeast) (Market Place or a Friend who Brews Kombucha are great places to get your SCOBY)

2 cups of starter tea** (from a previous kombucha batch or store-bought unflavored kombucha)


– Large pot for boiling water

– 1-gallon glass jar for fermenting

– Clean cloth or coffee filter

– Rubber band

– Bottles for storing the finished kombucha (glass bottles with tight-fitting lids are ideal)

Steps to Make Kombucha

1. Prepare the Sweet Tea

2. Boil Water: Bring about 3-4 cups of water to a boil in a large pot.

3. Add Sugar: Stir in the 1 cup of sugar until it dissolves completely, creating a sugary solution.

4. Add Tea: Add the tea bags or loose tea, then remove from heat. Let the tea steep for 10-15 minutes, depending on the desired strength.

4. Cool the Tea**: Remove the tea bags or strain out the loose tea leaves. Add the remaining water to the pot to dilute the tea. Ensure the temperature comes down to room temperature (about 70°F – 90°F or 21°C – 32°C). I usually add ice cubes to bring temp down.

2. Combine Ingredients in the Fermenting Jar

1. Sterilize Your Jar: Clean the 1-gallon glass jar thoroughly with hot water and soap. Rinse well to remove any soap residue.

2. Add the Sweet Tea: Pour the cooled, sweetened tea into the jar.

3. Add Starter Tea: Add 2 cups of starter tea to the jar. This lowers the pH and helps prevent the growth of unwanted bacteria and mold.

4. Add the SCOBY: Carefully place the SCOBY into the jar. It might sink, float, or stand on end — all are normal.

3. Ferment

1. Cover the Jar: Cover the jar with a clean cloth or coffee filter and secure it with a rubber band. This keeps contaminants out while allowing the mixture to breathe.

2. Fermentation Environment*: Place the jar in a warm, dark, and well-ventilated area. The optimal temperature for kombucha fermentation is around 68°F – 85°F (20°C – 29°C).

3. Wait: Let it ferment for 7-14 days. The timing depends on your taste preference; a longer fermentation will yield a more acidic kombucha.

Bottling and Flavoring (Second Fermentation)

1. Remove and Store SCOBY: With clean hands, remove the SCOBY and put it into a clean bowl. Reserve some kombucha (about 2 cups) to use as starter tea for the next batch.

2. Flavor (Optional): If you want to add flavors, pour the fermented kombucha into bottles leaving about an inch of headspace. Add fruit, juice, herbs, or spices as desired. I almost always add Ginger as Ginger provides great carbonation.

3. Cap and Store: Seal the bottles tightly. Leave them at room temperature for an additional 2-7 days to allow carbonation to develop (this is the second fermentation phase). Taste periodically to avoid over-carbonation.

Refrigerate and Enjoy

After the desired carbonation level is reached, store the kombucha in the refrigerator to halt fermentation and enjoy!

Tips and Reminders

Hygiene: Hygiene is crucial at every stage to prevent contamination. Always use clean hands and equipment.

Tea and Sugar: Do not reduce the sugar; it is necessary for fermentation. Avoid teas with added oils or flavors, which can harm the SCOBY.

Adjusting Fermentation Time: The cooler the environment, the slower the fermentation. In warmer environments, check the taste more frequently.

Safety: Check for mold, which will look distinctly fuzzy and usually white/black or green. If mold develops, discard the batch and start fresh with a new SCOBY and starter tea.

Making kombucha is an engaging fermentation project that opens a world of flavor possibilities and probiotic health benefits. Enjoy experimenting with different tea bases and 

Here’s What You Need To Remember About Fermented Foods and Your Gut Microbiome

Fermented foods are treasure troves of beneficial compounds that contribute to various aspects of health, particularly the gut microbiome. From live probiotics and prebiotics to essential vitamins, minerals, and unique bioactive substances, incorporating fermented foods into your diet can greatly enhance your overall well-being and promote a healthy gut microbiome. So next time you savor a spoonful of yogurt, a bite of kimchi, or a sip of kombucha, remember that you’re nourishing your body with a wealth of health-boosting elements.

Incorporating fermented foods like sauerkraut, kefir, kimchi, yogurt, and tempeh into your diet can significantly enhance gut health and support a balanced microbiome. These foods are rich in probiotics and beneficial nutrients, helping to improve digestion, reduce inflammation, and strengthen your gut barrier. Whether you choose to make these foods at home or purchase them from the store, your gut (along with your overall health) will thank you. Explore these delicious and nutritious fermented foods today to embark on a path toward better gut health and overall well-being.

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