Gut Health and Fermented Foods
Why Traditional Wisdom Still Matters
There are whole shelves of books, documentaries, TV shows, and articles on gut health these days—your microbiome, the gut-brain connection, gut health for immune-boosting, anxiety, depression, bad guts, clever guts. Books on what not to eat, how to eat, when to eat, what's bad about fermented foods or great about them, and gut-health specific diets.
It's overwhelming, and honestly, a bit absurd.
When I started talking to health-conscious friends about our wild, slow-fermented kraut back in 2013, they'd go straight to their naturopath for confirmation. At that time, most practitioners had never heard of ferments, or they'd simply prescribe a probiotic supplement. Then shows like Dr Mosley: Gut and Catalyst's Gut Revolution started appearing on TV, and suddenly we were validated.
I appreciate the timing, but it also shows how far we've drifted from trusting common sense and traditional, ancestral foods. Science is valuable, but our ancestors survived remarkably well without clinical trials telling them what to eat. They used their senses, listened to their bodies, thought about where food came from and how it was made, and trusted whether it was truly good for them.
When Fermented Foods Became Medicine
I stopped actively recommending our ferments for gut health when people started asking how much they should "take."
Take. As if sauerkraut were a prescription.
I understand that stomachs can be out of balance and may need time to adjust to a specific food. But it makes me sad when living foods like kimchi and sauerkraut—foods that entire populations have eaten daily for centuries—are prescribed by practitioners in tiny doses. "Start with a teaspoon of kraut juice and build up slowly before eating it."
These aren't supplements. They're food.
In Korea, where I trained extensively, kimchi appears at every meal. In Japan, tsukemono (pickled vegetables) are part of breakfast, lunch, and dinner. Nobody's measuring out teaspoons or "building tolerance." They're eating food that's been part of their culture for generations, and their guts handle it just fine because that's what guts evolved to do.
The medicalisation of fermented foods reflects our modern disconnection from traditional eating patterns. We've stripped our diets of living foods for so long that reintroducing them feels radical, even risky. That's not a fermentation problem—that's a modern diet problem.
Gut Healing Is Not a Destination
It's an uncomfortable truth but healing your gut isn't a one-off project you complete and move on from. It's an ongoing process, much like exercise or sleep. You don't "fix" your gut and then return to your old habits. People are all so willing to take pills every day but don't seem to understand the practice of consistently consuming living foods. As though having some one day of the week is enough.
Your digestive system is essentially a complex tube—what goes in goes out. This includes your probiotics, prebiotics, sauerkraut, kimchi, kefir, vinegar, bread, and tempeh. Nothing stays permanently. Your gut is a dynamic ecosystem that requires consistent tending.
Gut healing means recognising that we've been missing these foods from our diets, and that our current food environment doesn't support wild, living foods. We're also no longer exposed to soil, dirt, and the diverse microbial environment our ancestors lived in daily. Modern cities, industrial food systems, and food science have made it harder to access good, real food—but it's still out there.
The solution isn't complicated supplements or restrictive protocols. It's relearning how to eat the way humans ate for thousands of years before packaged food became the norm.
How to Eat for Your Gut
If you don't have a specific medical condition requiring detailed intervention, here's what I recommend:
Eat less. Not restrictively, but mindfully. Stop before you're uncomfortably full. Let you digestive system rest - try not to keep it working all day long. Have long breaks between eating. (ie less snacking)
Eat fewer simple carbohydrates. Prioritise whole grains, vegetables, and complex carbohydrates over refined sugars and white flour. Don't buy processed foods.
Eat slowly, chewing well. Digestion starts in your mouth. Give your body time to register what you're eating.
Aim for mostly whole, unprocessed foods. If it comes in a package with ingredients you can't pronounce, reconsider. All ingredients should be available for you to make in your own kitchen.
Eat living foods, often. This is where fermented foods come in—not as medicine, but as regular parts of meals.
Eat lots of plants. Vegetables, fruits, legumes, whole grains. Fiber feeds your gut bacteria.
Consider yourself: Good food requires some intentionality in our current food system. It can be difficult - your regular large supermarket shopping trip will feel quite upsetting when you start looking at labels and food miles etc. Going back to basics is easier than you think - give that sliced white loaf a rest for most of the time. Keep those foods for now and then. Real food is simple and really doesn't take much prep once it becomes the norm. We are definitely an 'ingredients' house - but we can also make beautiful meals from the pantry pretty easily.
Don't eat for weight loss. Eat for energy, vitality, and long-term health.
Eat and prepare food with people. Cooking and eating together is as nourishing as the food itself. Feeling happy and relaxed when you eat and making it a lovely part of your day is a worthy goal.
Prebiotics, Probiotics and Postbiotics: What are they and what do you actually need
The supplement industry loves to sell prebiotics and probiotics separately, and add the word postbiotics - but here's the reality: if you're eating living foods that bacteria naturally grows on, you don't need to worry about "taking" those.
A prebiotic is simply food for your gut bacteria—fiber and resistant starches that your body can't digest but your microbiome can. If you eat a fibrous, varied diet with plenty of vegetables, whole grains, and legumes, your gut already has prebiotics.
Probiotics are the living bacteria themselves. When you eat fermented foods, you're consuming bacteria that's already thriving on that food. The kraut isn't just a delivery vehicle—the bacteria on the cabbage is part of the food itself, doing the work of fermentation.
Postbiotics are the newest buzzword, but they're not new at all. They're the beneficial compounds that bacteria produce during fermentation: short-chain fatty acids, enzymes, vitamins (particularly B vitamins and vitamin K2), peptides, and organic acids like lactic acid.
These compounds do real work in your body. Short-chain fatty acids, for example, feed the cells lining your gut and have anti-inflammatory effects. Some postbiotics interact with your immune system, helping it respond appropriately to threats while staying calm around harmless substances. The organic acids created during fermentation help maintain the right pH in your gut, creating an environment where beneficial bacteria thrive and harmful ones struggle.
Here's what's interesting: you get postbiotics whether the bacteria is still alive or not. When you eat sauerkraut, you're getting the living bacteria (probiotics), the fiber from the cabbage (prebiotics), and all the beneficial compounds the bacteria produced during fermentation (postbiotics). When you eat cooked tempeh or miso, the bacteria is dead, but the postbiotics remain—the vitamins, the broken-down proteins, the transformed nutrients that support your gut and immune function.
You don't need to separate these concepts or buy them in pill form. When you eat fermented vegetables, and you get both the bacteria and the food that feeds them.
The Diversity of Bacteria: What's Actually in Your Ferments
Not all fermented foods contain the same bacteria. Each type of ferment has its own ecosystem, and understanding this helps you appreciate why variety matters.
Wild Fermented Sauerkraut and Vegetables
When you ferment cabbage with just salt and time, you're relying on the bacteria that naturally live on the cabbage leaves. The fermentation happens in stages, with different bacteria dominating at different times.
Early colonizers like Leuconostoc mesenteroides get things started, producing the first acids and carbon dioxide. As the pH drops, more acid-tolerant species take over - primarily Lactobacillus plantarum, which becomes the dominant bacteria in mature sauerkraut. You'll also find Lactobacillus brevis, Pediococcus pentosaceus, and various other Lactobacillus species.
This succession creates complexity. Each bacterial species contributes different flavors, different acids, different enzymes. That's why homemade sauerkraut tastes so much more interesting than the pasteurized stuff - you're getting the full spectrum of wild fermentation.
Kimchi
Kimchi follows a similar pattern to sauerkraut but tends to be more diverse because of the additional ingredients - garlic, ginger, fish sauce, radish. You'll find many of the same Lactobacillus species (L. plantarum, L. brevis), plus Lactobacillus sakei, which is more common in kimchi than other vegetable ferments. Weissella species also appear frequently, and sometimes you'll find Leuconostoc kimchii, a bacteria specific to Korean kimchi.
The spices, aromatics, and seafood in kimchi create a different environment than plain cabbage, so you get different bacterial communities and different flavor profiles.
Milk Kefir
Milk kefir grains contain a complex symbiotic culture of dozens of bacterial and yeast species living together in a polysaccharide matrix (the "grains" themselves).
The bacteria include Lactobacillus kefiranofaciens (specific to kefir grains), Lactobacillus kefiri, Lactococcus lactis, Streptococcus thermophilus, various Leuconostoc species, and Acetobacter (which produces acetic acid, giving kefir its slight tanginess beyond just lactic acid).
The yeasts include multiple species of Saccharomyces, Kluyveromyces, and Candida. These yeasts contribute to kefir's slightly effervescent quality and complex flavor. They also produce small amounts of alcohol (usually less than 1%), B vitamins, and other beneficial compounds.
This is why milk kefir is so different from yogurt, even though both are fermented dairy. Yogurt typically contains just two or three bacterial species in a controlled culture. Milk kefir contains 30-50 different species of bacteria and yeasts working together. The diversity is extraordinary.
Water Kefir
Despite the name, water kefir grains are different from milk kefir grains and contain different microorganisms. You can't convert one to the other - they're distinct cultures.
Water kefir contains Lactobacillus hilgardii, Lactobacillus casei/paracasei, Leuconostoc mesenteroides, and Zymomonas mobilis (a unique bacteria that produces alcohol and carbon dioxide efficiently). The yeasts vary but often include Saccharomyces species and others that thrive in sugary environments.
Water kefir tends to be lighter, more effervescent, and fruitier than milk kefir because of its different bacterial and yeast balance.
Why This Matters
You don't need to memorize these bacterial names to ferment successfully - I certainly don't walk around reciting them. But understanding that different ferments contain genuinely different ecosystems explains why variety is so valuable.
Each ferment brings different bacteria to your gut. Each one produces different acids, enzymes, vitamins, and beneficial compounds. Rotating between sauerkraut, kimchi, milk kefir, and water kefir means you're feeding your gut a much wider range of beneficial organisms than if you ate just one ferment repeatedly.
Think of it like planting a garden - you wouldn't plant just one species and expect a thriving ecosystem. Your gut is the same. Diversity creates resilience.
Living Foods vs. Pasteurised Products
This is crucial: not all fermented foods contain live bacteria.
Living ferments are found in the refrigerated section. They're actively fermenting, bubbling slightly, developing flavor over time. The bacteria is alive and will remain alive if kept cool. These are the ferments that deliver beneficial bacteria to your gut: raw sauerkraut, unpasteurized kimchi, fresh milk kefir, living water kefir, traditional miso kept refrigerated.
Pasteurised products sit on the shelf at room temperature. They've been heat-treated to kill all bacteria—including the beneficial ones—so they're shelf-stable. These products were fermented at some point, which developed their flavor, but they no longer contain living organisms. Examples include most commercial pickles, shelf-stable sauerkraut, and bottled kombucha that doesn't require refrigeration.
Respectfully, that's the fundamental difference between a ferment and a pickle. Both are preserved in acid, but only one is still alive.
This doesn't mean pasteurised ferments are worthless—they can still taste wonderful and have culinary value—but they won't deliver the probiotic benefits of living ferments. If gut health is your goal, look for refrigerated products and check labels for "unpasteurised" , "raw" "living" or "contains live cultures."
The Value of Cooked Ferments
Some fermented foods aren't full of living bacteria by the time you eat them, but they're still incredibly valuable.
Sourdough bread, Ethiopian injera, Indian dosa, tempeh, and miso are all fermented, but they're cooked before eating. The heat kills the bacteria that did the fermentation work. Does that make them pointless?
Not at all. These foods are transformed by fermentation—more digestible, more complex in flavor, often more nutritious, with gentler textures. The fermentation process breaks down proteins and starches that would otherwise be harder to digest. Even though the bacteria don't survive cooking, the beneficial changes they made to the food remain.
Think of it this way: the bacteria did the hard work of pre-digesting the food for you. Your gut doesn't have to work as hard to break down fermented bread or tempeh as it would to digest their unfermented equivalents.
These foods are almost always highly nutritious and gentle on your digestive system, even without live bacteria. They're part of a well-rounded diet that includes both living and cooked ferments.
Starting Your Fermentation Practice
Begin with what you can—buy some different kinds of living ferments and try them. A spoonful of sauerkraut with lunch. A small bowl of kimchi with dinner. A glass of water kefir in the afternoon. Milk kefir before bed.
Don't overthink portions or timing. Just eat them regularly, as you would any other vegetable or condiment. Having said that - I have found so many people really benefit from a night time - right before bed milk kefir. It lines your gut and helps you get a good. night sleep. Have it again upon waking - and you'll notice a change. Regular poop for one - less sugar and simple carbohydrate cravings.
Variety matters. Different ferments contain different strains of bacteria and offer different flavors and nutrients. Rotate between sauerkraut, kimchi, pickled vegetables, kefirs, and other living ferments. Each one contributes something unique to your gut ecosystem. It's not about the count of bacteria in each product necessarily but the variety of bacteria you consume.
Regularity matters more than quantity. A small amount of living ferment daily is more beneficial than a large amount once a week. Your gut bacteria need consistent feeding. It's a goal of ours to have everyone have at least a tablespoon a day. Even better - a tablespoon with every meal. But even we don't adhere to that - we need it to be a delicous addition and condiment to your life - not something you have to do.
Start small if you're genuinely sensitive. Some people do need to build tolerance gradually, especially if they've been on antibiotics recently or have significant gut issues. Some people have histamine intolerances. So do start small if you think you need to. That's fine. Start with small amounts and increase as your body adjusts. But don't mistake "start small" for "treat it like medicine." It's still just food.
Make your own when you're ready. Buying ferments is a great way to explore variety and find what you like, but making your own connects you to the process in a different way. It's simpler than you think, and homemade ferments often taste better and cost significantly less than commercial versions. Our own products are made the same way as we make them from home. No different. So yes - you can trust ours - and do buy ours if you're able to. Fermenting your own food does connect you to the invisible magic that is sometimes missing from our day to day life. It's a lovely thing to experience that.
What I've Learned from Teaching Thousands of People
Over the past 14 years running The Fermentary, teaching workshops here as well as internationally, and helping thousands of people discover fermentation, I've noticed something: people often approach fermented foods with fear—fear of doing it wrong, fear of making themselves sick, fear of bad bacteria. A kind of 'mines not working' vibe.
This fear is recent. Traditional cultures don't fear fermentation. They trust it because they understand it, because their grandmothers taught them, because it's woven into their food culture. They've seen it. Just as we all know that a cake can sometimes come out dry - or even that it requires cooking. Or toast can burn, bread can stale. Not many of us grew up with that kind of intimate knowledge around simple home fermentation.
Whereever I've spent time or trained, I watched women ferment foods with confidence and ease. They didn't need thermometers or pH strips or sterile equipment. They used their senses—smell, taste, touch, sight—to know when something was ready. They trusted the process because they'd seen it work hundreds of times. It was natural, intuitive, passed down through generations - mostly through women's hands.
But there's a pattern with traditional domestic skills: they get taken up, made technical and complicated, turned into something requiring expensive equipment and specialized expertise. Think about what happened to bread baking, to brewing, even to cooking in restaurants ... and now fermentation itself.
There are a few high-end restaurants that have built fermentation labs with precise temperature controls to achieve what Indonesian women have been doing with banana leaves and ambient temperature for generations. The techniques get credited to chefs, not to the cultures they came from. Suddenly you need thermometers, pH meters, sterile conditions - as though the grandmothers who perfected these methods over centuries were doing it wrong.
They weren't. You don't need a laboratory. You need salt, clean equipment, and your senses. Trust the simplicity. That's where the real knowledge lives.
That's what I try to teach: trust. A return to your senses and through that - your own history. And - fermentation is remarkably forgiving. The beneficial bacteria are hardy and competitive. They want to grow. If you create the right conditions—salt, oxygen exclusion, clean equipment—they'll outcompete harmful organisms (if there are any) every time. Your senses will tell you when something's gone right or wrong.
The bacteria want to ferment. Your job is simply to give them favorable conditions and get out of the way.
A Final Word
There will be more wild things living inside you if you eat raw, living foods—small amounts, as varied as possible, as regularly as you can. Enjoy their flavours. Be gentle on yourself.
Keep moving. Just a short walk after eating will make a difference. Breathe deeply. Meditate if that calls to you. Eat with people, and try to make a situation whereby you can enjoy your meals slowly.
Don't worry about being too clean or waging war on bacteria. Most bacteria are beneficial, and your body has evolved to work with them, not against them.
Be curious—there's a whole world of ferments out there beyond sauerkraut and kombucha. Explore Korean kimchi variations, Japanese tsukemono, Indonesian tempeh, Indian dosa, Ethiopian injera, Eastern European kvass, Mexican tepache. Every culture has fermented foods, and each offers something different.
Find the ones you love, not just the ones you think you should eat. Food is meant to be enjoyed, not endured.
Your gut will thank you, but more importantly, you'll rediscover what humans have known for millennia: fermented foods taste good - and feel good inside. Ferments also enhance the nutritional value of the food you eat with it - and make them easier to digest.
Written by Sharon Flynn
Founder of The Fermentary, author of "Ferment for Good" and "Wild Drinks"
Related: The Science of Fermentation | Making Milk Kefir | Making Sauerkraut | Understanding Water Kefir
