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Gut microbiome & fermentation

Barbara Philipps - 25/06/2024 - 0 comments


How fermented foods can boost your gut microbiome

The gut microbiome plays a large role in our overall physical and mental health, which is why it is so important to keep it balanced. Our science department has been doing extensive research on how to get and keep a healthy microbiome, and we want to share one of the best ways to do it: eating fermented foods. Let us take a closer look at how and why they are so great for the gut. We are also going to share some of our favorite recipes so you can try out fermentation for yourself.

How important the gut microbiome is for your health

The gut microbiome is made up of thousands of different species of bacteria living in the gut. These microorganisms can help digest food, prevent pathogens from spreading in the intestine, and contribute to the functioning of our immune system. They can even influence our brain and our behaviour. In summary: they are immensely important to our health.

Each human’s gut microbiome is slightly different, depending on their diet and immunological processes. Science has proven that the composition of the microbiome has a big impact on our physical and psychological wellbeing. Things like stress, unhealthy food, or taking antibiotics can negatively influence the bacteria living in your gut and lead to health issues, which is why it is so important to look after your gut health.

Testing the microbiome can indicate which bacteria are present in the gut. If you’re fasting at one of our clinics, you can take the test there. Our test will provide you with a snapshot of your entire gut microbiota composition. This includes the levels of health-associated or pathogenic bacteria in the intestines as well as markers of a leaky gut and chronic inflammation. There are “good” bacteria that support our bodily functions and “bad” bacteria that can make us sick. A balanced microbiome, in which a lot of the “good” bacteria are present, is essential.

Your diet has a significant impact on your gut microbiome, which in turn influences your health. This is particularly the case during the food reintroduction after fasting, which is a moment when you can boost your gut microbiota composition with a healthy and balanced diet. And one of the best ways to boost the healthy bacteria in your gut, is to eat fermented foods.


One of the best ways
to promote the healthy bacteria in your gut
is to eat fermented foods.

The benefits of fermented food for your gut microbiome

Fermented foods are living ecosystems that are providing all the biotics that support gut health. When you eat fermented foods, you’re consuming a full spectrum of beneficial compounds: probiotics, prebiotics, and postbiotics.

Let us take a closer look at what they are. By consuming fermented foods, you get live beneficial bacteria (probiotics), the food these bacteria thrive on (prebiotics), and the health-boosting substances they produce (postbiotics). This comprehensive package of gut-friendly compounds makes fermented foods one of the best ways to achieve optimal gut health, often surpassing the benefits of supplements.

At Buchinger Wilhelmi, our team of chefs always stay up to date with the latest scientific findings on health nutrition. The recipes we follow at our clinics are led by the ideas of Steve Flügge, and we are currently focusing on a special program regarding longevity and how to build up a strong microbiome. We have already integrated fermented products like whey, kimchi, and kombucha into our recipes and plan to introduce more soon.

They are especially beneficial for our patients who have finished their fast, as these foods help them build up a strong and healthy microbiome after fasting. We are even considering offering a fermentation kitchen in the future to teach others how to make fermented foods at home.

Steve Flügge (left) & Hubert Hohler (right)
manage the kitchen at the clinic in Überlingen

Can microbes survive digestion?

The microbes in fermented foods face a tough trip through our digestive system, dealing with stomach acid, bile salts, and enzymes. Although not all microbes survive this journey, many do eventually reach the gut. For example: 73% of people who regularly eat yogurt are shown to have lactobacillus bulgaricus in their gut. Compared to 28 % of people who don’t eat yogurt regularly, that is a big difference. Similarly, microbes in fermented vegetables can survive stomach acid but may not stay in the gut permanently. Therefore, we have to consume these healthy foods regularly.

Did you know that even dead microbes can be beneficial? They are known as postbiotics. For instance, wholemeal sourdough bread is made through fermentation, but the baking process kills the microbes. Yet, sourdough still contains beneficial compounds produced during fermentation, that can support gut health and overall wellness.

Why kombucha can be great for your gut health

Kombucha is a fermented drink which supports gut health through its rich probiotic content, including lactic acid bacteria like lactobacillus and bifidobacterium, which help balance gut bacteria. The fermentation process produces antioxidants like polyphenols, which protect the gut lining. These are especially found in green tea-based kombucha.

Organic acids such as acetic, gluconic, and lactic acid can inhibit harmful bacteria. Kombucha also increases gut microbiome diversity, reduces inflammation, and aides digestion by breaking down foods and enhances nutrient absorption.

However, be aware that commercial kombucha is often high in sugar and additives, which diminishes its health benefits. Instead, always choose organic and additive-free options if you want to build up your gut health.

Health effects of fermented beetroot

Fermented beetroot is another food that offers multiple health benefits, especially for the gut microbiome. Studies show that fermenting beetroot for 72 hours significantly boosts its antioxidant activity, making it a powerful antidiabetic functional food.

Research also indicates that fermented beetroot juice positively impacts the gut microbiome. Additionally, organic fermented beetroot juice has stronger anticancer activity compared to conventional ones, likely due to higher antioxidant levels. These benefits are largely attributed to polyphenols like betacyanin, which give beetroot its vibrant color.

Altogether, fermented beetroots are a potent addition to your diet for enhancing gut health and overall wellness. We use it for dishes in our clinics and have shared the recipe for making fermented beetroot at home down below.

How to use fermented foods to build up your gut health

If you want to boost your microbiome by eating fermented foods, you need to consider a few things. These are our tips on how best to do it.

🥗 Include a variety of fermented foods in your diet

Try to incorporate a diverse range of fermented foods like yogurt, kefir, sauerkraut, kimchi, and kombucha into your diet. These different foods provide a rich source of probiotics that help replenish and diversify your gut microbiome.

🌿 Choose natural and organic options

As with most foods, organic is best. For example, studies have shown that organic fermented beetroot has stronger anticancer and antioxidant properties, enhancing its overall health benefits.

🍏 Balance with whole foods

Combine fermented foods with a diet rich in whole foods like vegetables, fruits, and whole grains. This ensures your gut bacteria receives both probiotics and prebiotics, which are essential for their optimal growth and activity.

🍽️ Moderation is key

While fermented foods are very beneficial, make sure you consume them in moderation. Start with small amounts to allow your gut to adjust, then gradually increase your intake to avoid digestive discomfort.

🧃 Avoid high-sugar commercial products

Be cautious of commercial fermented products that are high in sugar and additives. These can negate the health benefits you’re looking for. For instance, counting on sugary kombucha for gut health is like expecting the benefits of fresh orange juice from a sugary soft drink.

👨‍🍳 DIY fermentation

Consider making your own fermented foods at home, since homemade versions often have higher probiotic content and fewer additives than store-bought ones. Following recipes for sauerkraut, kimchi, and yogurt can be a fun and rewarding way to ensure you’re getting high-quality fermented foods and you’re in full control of everything that is put into them.

Recipes: Fermented Beetroot, Porridge, and kimchi

Since fermenting foods yourself is a great way to build up your gut microbiome, we asked our kitchen chef Hubert Hohler for some easy-to-make fermentation recipes. Many of these can be made in advance and kept in the fridge. They provide a great addition to a gut-friendly diet.

We hope you enjoy our fermented recipes – your gut certainly will!

Fermented beetroot


You will need:

  • a preserving jar with 600ml capacity
  • 500g beetroot
  • 500ml water
  • 20g salt
  • cumin


How it works:

Start by making the brine by adding 20g of salt to 500ml of water and bringing it to a boil. Let it cool down, while you peel the beetroot (we recommend wearing gloves) and slice it into thin strips. You can add apple, onion or cumin to taste. Next, layer the beetroot in the preserving jar and cover with brine. Make sure the beetroot is fully covered by the brine.

Store the jar at room temperature for at least 2–3 days, since the fermentation process takes several days. The longer the beetroot is stored this way, the more intense the taste will become. Depending on the room temperature (ideally at 12-15°C), the jar can be left standing for longer. Afterwards, it can be kept in the fridge for several weeks to months.

It is important that the preserving jar is boiled in hot water beforehand and that all cooking utensils are clean to avoid mold. Do not fill the jar to the very top, as the liquid may overflow during the fermentation process. The jar should not be opened too often to avoid contamination.

Homemade Kimchi


You will need:

  • 1kg Chinese cabbage
  • 25-30g salt
  • 125ml water
  • 2 tbsp. rice flour
  • 2 tbsp. cane sugar
  • 20ml soy sauce
  • 20g chili flakes
  • 1 grated pear/nashi pear/apple
  • 130g grated horseradish
  • 70g grated carrots
  • 1 finely chopped spring onion
  • 1 small shallot
  • 4 cloves of garlic
  • 2cm grated ginger

How it works:

Quarter the Chinese cabbage and cut it into mouth-sized pieces. Then wash and drain in a sieve. Put cabbage into a bowl with salt and mix well. Leave it for half an hour and do not throw away the liquid that forms.

Next, add the water, rice flour and cane sugar to a small pan and boil until it thickens. Blend the shallot, garlic, ginger, soy sauce, chili flakes, nashi pear and rice paste in a mixer. Depending on how hot you like it, we recommend using fewer chilli flakes. Now marinate the Chinese cabbage with the blended ingredients.

For fermenting, we recommend using a preserving jar with a rubber ring. Put the kimchi in the jar and keep it at room temperature for two days. Make sure you do not fill the jar to the very top so that the cabbage is covered by the marinade. If needed, you can add some brine (3%). During fermentation, gases will form and escape. You should therefore place a cloth underneath the jar and check it from time to time.

Finally, put the jar in the fridge and store for another 3–5 days (or longer). For a sourer taste, leave the kimchi in the fridge for longer.

Our signature fermented porridge


You will need (for two people):

  • 80g roughly ground spelt
  • 160g kombucha
  • 150g water
  • 80g grated apples*


How it works:

We serve this porridge to guests on the first day after breaking their fast. To make it yourself, mill the spelt coarsely, then soak it in kombucha (we use kombucha refined with ginger/lime in a 50:50 ratio) and leave it in the fridge overnight (approx. 16-24 hours).

The next morning, add the spelt to a saucepan, add water and heat it up. As soon as it thickens, put in the grated apple and simmer over a low heat. When the spelt has softened, the porridge can be served. Add fruit, sugar-free fruit puree or cinnamon to taste.

*Apples contain pectins, a type of soluble fiber that acts as a prebiotic by serving as food for beneficial gut bacteria. These bacteria, in turn, produce short-chain fatty acids that nourish the cells lining the colon, enhance immune function, and improve overall digestive health. Apples contain their own microbiota, a community of beneficial microorganisms. A scientific study even showed that organic apples harbor a healthier and more diverse microbiota compared to apples treated with pesticides, contributing to better gut health and overall well-being.

From farm to fork: a holistic view of the earth microbiota

At our core, we deeply care about the environment. Our kitchen proudly sources ingredients from local farms that embrace regenerative agriculture and organic practices. We believe that soil is the earth’s intestine and that nurturing the earth’s microbiota is as vital as caring for our own. Just as we rely on a healthy gut microbiome for our well-being, the earth depends on a thriving soil microbiome to sustain its health and fertility. This holistic approach not only ensures the highest quality ingredients for our dishes but also supports the broader ecosystem, fostering a sustainable future for all.

Intensive farming has caused significant damage to soil health around the world, reducing the amount of usable farmland. The use of heavy machinery, single-crop farming, and frequent plowing compacts the soil, leads to erosion, and depletes nutrients, ultimately making the soil less fertile. Additionally, pesticides and fertilizers harm essential soil microorganisms, which play a crucial role in maintaining the ecosystem and human health. These microorganisms, including bacteria, fungi, and viruses, are found in all soils and on common fruits and vegetables, making human exposure unavoidable.

Soil microorganisms offer several direct health benefits. They help regulate the immune system and reduce allergy risks by interacting with the gut microbiome, potentially lowering the chances of chronic diseases like heart disease, diabetes, and certain cancers. Some soil microbes produce antimicrobial compounds effective against antibiotic-resistant bacteria, highlighting their role in developing antibiotics like streptomycin. Interestingly, exposure to soil microorganisms has been linked to mental health benefits, such as reduced stress and anxiety, as shown in studies where soil bacteria influenced serotonin production in mice.

Moreover, soil microbes contribute to gut health by promoting beneficial bacteria like Bifidobacteria and Lactobacillus. They also provide crucial ecosystem services that affect the nutritional quality of agricultural products and participate in water purification, pollutant degradation, and carbon storage.

Human alterations to soil ecosystems threaten not only agricultural productivity and biogeochemical cycles but also human health. Few studies have connected the richness of soil microbiomes in agricultural products to health benefits, and even fewer have linked these factors to farming methods. A pioneering study comparing organic and conventional apple cultivation highlighted significant differences in microbial presence and function, underlining the urgent need for more comprehensive research in this area.

By choosing to support farms that prioritize the health of our soil, we are taking a stand for a healthier planet and a brighter future from farms to forks.