Fermented Foods and Gut Health – What Properties Do Natural Fermented Products Have?

Fermented foods are natural fermented products that, thanks to lacto-fermentation, become a source of live lactic acid bacteria, lactic acid itself, vitamin K2, and bioactive compounds that positively influence the gut microbiome and immune system. The condition for achieving a probiotic effect (live cultures) is to choose unpasteurized products – pasteurization destroys bacteria, although the fermented matrix retains some bioactive properties. In a clinical study from 2021 (Stanford University), a diet rich in fermented foods increased microbiome diversity and lowered 19 inflammatory markers more effectively than a high-fiber diet.

The article explains how lactic acid fermentation works and what distinguishes true fermented food from vinegar-preserved products, discusses the nutritional and bioactive composition of fermented foods, cites current clinical studies on the microbiome and gut barrier, compares the most popular fermented products, and advises on how and how much fermented food to include in a daily diet. A separate chapter is dedicated to groups who should exercise particular caution – people with SIBO, histamine intolerance, IBS, or hypertension.

1. What is lactic acid fermentation and how are fermented foods made?

Fermented foods represent one of the oldest methods of food preservation, known long before the invention of refrigeration or pasteurization. However, what for thousands of years was primarily a way to store vegetables for winter is now gaining entirely new significance – as one of the most effective ways to supply the gut with live bacterial cultures through everyday food. To fully understand why fermented foods work, it's worth looking under the lid of a jar to see what's actually happening there.

1.1. Lacto-fermentation step by step

Lactic acid fermentation – also known as lacto-fermentation – is a biochemical process in which lactic acid bacteria (LAB) convert sugars in vegetables into lactic acid. They do not require any starters, yeasts, or vinegar. All necessary microorganisms are present on fresh vegetables from the moment of harvest – you just need to provide them with the right conditions to multiply.

The process proceeds in two sequential phases:

Phase 1 – heterofermentative (first few days): Leuconostoc mesenteroides bacteria are activated first. They initiate fermentation, rapidly consuming available oxygen and producing carbon dioxide, lactic acid, and acetic acid. The released CO₂ displaces residual oxygen from the space between vegetables, creating an anaerobic environment essential for further processing. By-products of this phase also build the initial flavor profile of the fermented food.

Phase 2 – homofermentative (from a few days to several weeks): When the pH drops sufficiently low, the environment becomes too acidic for Leuconostoc, and Lactiplantibacillus plantarum (formerly: Lactobacillus plantarum) takes over – a more acid-resistant species that dominates in mature fermented food. It mainly produces lactic acid, deepening the acidification and stabilizing the product. In the background, other LAB are also active – Pediococcus, Weissella, and other Lactobacillus species.

1.2. The role of lactic acid bacteria – who actually makes fermented food?

Lactic acid bacteria are a numerous and diverse group of gram-positive microorganisms that naturally colonize the surface of vegetables, fruits, and grains. They are not pathogens – on the contrary, they are some of the best-studied microorganisms in the history of food science. In fermented foods, key roles are played by:

• Leuconostoc mesenteroides – fermentation initiator, heterofermentative, produces CO₂ and lactic acid; responsible for starting the process and creating an anaerobic environment
• Lactiplantibacillus plantarum (syn. Lactobacillus plantarum) – dominant species in mature fermented foods, homofermentative, exceptionally acid-resistant, best studied for probiotic properties
• Levilactobacillus brevis – heterofermentative, present in vegetable ferments and sourdoughs
• Pediococcus pentosaceus and Pediococcus acidilactici – active in the middle phase of fermentation, resistant to high salt concentrations
• Weissella spp. – less frequently mentioned, but regularly detected in traditional fermented foods

It is worth distinguishing two types of LAB fermentation:

• Homofermentative – almost exclusively lactic acid is produced from sugars; maximally acidifies the environment
• Heterofermentative – in addition to lactic acid, acetic acid, ethanol, and CO₂ are also produced; gives the fermented food a complex, multi-dimensional flavor

1.3. Fermented vs. vinegar-preserved products – a key difference worth knowing

In a grocery store, pickled cucumbers and preserved cucumbers often stand side-by-side on the shelf. They look similar, taste sour – but they are completely different products with completely different health impacts.

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A vinegar-preserved product may taste sour, but acetic acid kills bacteria instead of cultivating them – there is no fermentation here. When buying, always read the label: if vinegar is listed, it's not a fermented product.

1.4. Why do salt, temperature, and anaerobiosis matter?

Lactic acid fermentation is not a process that occurs spontaneously under any conditions. Three factors determine whether healthy fermented foods or inedible putrefactive fermentation products will form in the jar.

Salt – natural selection in the jar

Salt plays a selective rather than a traditional preservative role in fermented foods. Its appropriate concentration (usually 1.5–2% relative to the weight of vegetables) inhibits the multiplication of spoilage bacteria and molds, which are less resistant to saline environments than LAB. Too little salt – risk of spoilage; too much – fermentation proceeds too slowly, and the bacterial profile is poorer. The optimal concentration for spontaneous cabbage fermentation is 1–2% salt.

Temperature – pace and quality regulator

Fermentation occurs over a wide range of temperatures (5–30°C), but the optimal conditions for obtaining a rich bacterial profile and good flavor are 15–20°C. At lower temperatures, fermentation is slower but yields a fermented product with a more complex flavor and usually a higher bacterial content. At temperatures above 22–25°C, the process accelerates, but the risk of dominance by undesirable strains and the formation of products with poorer sensory quality increases.

Anaerobiosis – a necessary condition

Lactic acid bacteria are anaerobic microorganisms (or microaerophilic – tolerating trace amounts of oxygen). The presence of air in the fermenting mass, however, favors yeasts and molds. Therefore, vegetables must be completely submerged in the brine – a classic mistake with homemade fermented foods is when vegetables emerge above the liquid level. In traditional barrels, a weighting stone served as a seal; today, ceramic or glass weights replace it.

2. What do fermented foods contain? Nutritional and bioactive composition

Fermented foods are much more than just acidified vegetables. Lactic acid fermentation is essentially a biological "factory" operating inside the jar: bacteria not only preserve the vegetable but actively process its ingredients, synthesize new compounds, and remove anti-nutritional substances. This means that a finished fermented product has a completely different bioactive profile than the raw material.

2.1. Live bacterial cultures – how many are there and what does it mean in practice?

The most important component of unpasteurized fermented food are live lactic acid bacteria. In mature sauerkraut and pickled cucumbers, their concentration in the brine ranges from 10 to 100 million colony-forming units per milliliter (10⁷–10⁸ CFU/mL). For comparison: many probiotic supplements contain 1–10 billion CFU per capsule, but these are lyophilized bacteria that must survive storage and pass through the acidic environment of the stomach. Bacteria from fermented foods enter the digestive tract in an active, live state, within a natural, protective fermentative environment.

The dominant strains are primarily Lactiplantibacillus plantarum and Leuconostoc mesenteroides, which together constitute over two-thirds of the total bacterial population of a mature fermented product. Alongside them are Pediococcus pentosaceus, Levilactobacillus brevis, and Weissella spp. The diversity of strains is one of the advantages of fermented foods over single-strain probiotic supplements.

2.2. Vitamins – what does fermentation contribute?

Vitamin C

Raw white cabbage contains 36 to 50 mg of vitamin C per 100 g – a quite respectable result for a vegetable. After fermentation, its content is partially reduced due to the metabolic activity of bacteria, however, the acidic environment of the brine (low pH) effectively inhibits further oxidation of ascorbic acid and stabilizes what remains.

Sauerkraut is historically one of the first "medicines" used by Polish and Scandinavian sailors for scurvy – and for good reason: even after fermentation, it provides real amounts of vitamin C, especially when consumed raw, without cooking.

Vitamin K2 (menaquinone)

This is one of the most interesting aspects of fermentation. Cabbage naturally contains vitamin K1 (phylloquinone), typical of green leafy vegetables. During fermentation, lactic acid bacteria synthesize vitamin K2 in MK-4 and MK-7 forms (menaquinones). K2 in the form of MK-7 has a much longer half-life in the body than K1 and plays a key role in calcium metabolism (directing it to bones and teeth, and not to soft tissues and vessels).

Fermented foods – especially sauerkraut – are one of the few fermented plant products that are a source of K2, which makes them particularly interesting for people on a vegan diet.

B vitamins

Fermenting bacteria are capable of synthesizing a range of B vitamins, including folates (B9). Depending on the bacterial strain and substrate, fermentation can increase the folate content in the final product. Data regarding vitamin B12 in vegetable ferments are inconclusive – although some soil and fermenting bacteria can synthesize it, the quantities in traditional vegetable ferments are too small and too variable to be treated as a reliable source of B12.

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2.3. Lactic acid – more than a preservative

Lactic acid is the main metabolic product of LAB bacteria and is responsible for the characteristic sour taste of fermented foods. However, it plays several roles in fermented foods simultaneously:

• Preservation – lowering the pH to 3.5–4.0 inhibits the growth of pathogens and spoilage bacteria
• Mineral bioavailability – the acidic environment improves the absorption of iron, zinc, and calcium by increasing their solubility
• Digestion – stimulates the production of gastric juices and the activity of digestive enzymes
• Prebiotic effect – lactic acid can directly influence the composition of the colon microbiota, although the mechanisms of this action are still being studied

Lactic acid in fermented foods is completely safe – it's the same molecule produced by muscles during intense exercise. Not to be confused with lactic acid in the context of muscle soreness – that's a separate physiology.

2.4. Digestive Enzymes – Fermentation as Pre-Digestion

During fermentation, lactic acid bacteria produce a series of enzymes that break down vegetable components: hydrolases, esterases, decarboxylases, and phenolic acid reductases. The practical effect is twofold.

Firstly, fermentation breaks down anti-nutrients – primarily phytic acid (phytates), which in raw vegetables and grains binds minerals such as zinc, iron, and calcium, limiting their absorption. After fermentation, the bioavailability of these minerals increases.

Secondly, bacterial enzymes process phenolic compounds – flavonoids and other polyphenols present in vegetables – into biologically active metabolites with higher antioxidant potential than their initial forms. Fermentation transforms a raw vegetable into a product with greater antioxidant activity.

2.5. Short-Chain Fatty Acids (SCFAs) – How Fermented Foods Support Their Production?

Short-chain fatty acids (SCFAs) – primarily acetate, propionate, and butyrate – are key metabolites influencing gut health, the immune system, and the metabolism of the entire organism. However, it's important to explain precisely where they come from in the context of fermented foods, as this issue is sometimes presented imprecisely.

Direct SCFAs in Fermented Foods

Fermented foods contain acetate and lactate produced during fermentation by LAB bacteria. These are SCFAs present directly in the product – we consume them along with the fermented food. Sauerkraut and other fermented vegetables are cited in literature as one source of a diet rich in SCFAs.

SCFAs Produced by the Gut Microbiome

The second, more important mechanism is indirect: fermented foods deliver live bacteria and fiber to the gut, which become a substrate for intestinal microorganisms. The colon microbiome ferments this fiber, producing SCFAs – including butyrate, which is the main energy source for colonocytes (intestinal epithelial cells). Butyrate supports the integrity of the intestinal barrier and has anti-inflammatory properties, which we discuss in detail in Chapter 4.

2.6. Comparison of Raw and Fermented Vegetable Composition

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3. Fermented Foods and the Gut Microbiome – What Do Studies Say?

Intuition suggests that eating products full of live bacteria should have some impact on what happens in the gut. For a long time, however, hard scientific evidence was scarce – most knowledge about fermented foods and the microbiome was based on observational and mechanistic data, not controlled clinical trials. This is starting to change. Below, we discuss three of the most significant studies that have provided concrete data.

3.1. Stanford Study (Wastyk et al., 2021) – Fermented Products vs. Fiber

One of the most widely cited studies on fermented foods and the microbiome comes from Justin and Erica Sonnenburg's team at Stanford University and was published in August 2021 in the prestigious journal Cell.

Study Design

36 healthy adults were enrolled in the study and randomly assigned to one of two intervention groups for 10 weeks:

• Group 1 – a diet rich in fermented products (yogurt, kefir, buttermilk, kimchi, fermented vegetables, kombucha)
• Group 2 – a diet rich in plant fiber (legumes, whole grains, nuts, vegetables, fruits)

The study lasted a total of 17 weeks (including preliminary and observational phases). Participants were monitored using advanced tools: microbiome sequencing, broad immunological profiles (CyTOF), and metagenomics.

Results

Both diets produced distinctly different, specific effects:

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Particularly striking was the finding regarding fiber: in participants with low baseline microbiome diversity, switching to a high-fiber diet was associated with an increase in inflammatory markers, not a decrease. The authors interpret this as a signal that a microbiome lacking appropriate bacteria is unable to efficiently ferment fiber – and instead of beneficial SCFAs, more pro-inflammatory metabolites may be produced.

Source: Wastyk HC, Fragiadakis GK, Perelman D et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021;184(16):4137-4153.e14. PMID: 34256014.

3.2. Sauerkraut and the Gut in IBS Patients

The study by Nielsen and colleagues from 2018 is currently the only published RCT investigating the effect of sauerkraut (not fermented foods in general) directly on patients with irritable bowel syndrome (IBS).

34 Norwegian IBS patients consumed sauerkraut daily for 6 weeks – half of the group received unpasteurized product (with live bacteria), and half received pasteurized product (without live bacteria). Both groups reported a statistically significant improvement in IBS symptom severity (measured by the IBS-SSS scale, p < 0.04), and the improvement was similar in both groups. Simultaneously, significant changes in microbiome composition were observed in both groups.

The fact that pasteurized sauerkraut worked as well as unpasteurized suggests that the effect is not solely due to live bacteria, but also to prebiotic components and fermentation metabolites present in the product regardless of pasteurization.

Source: Nielsen ES et al. Lacto-fermented sauerkraut improves symptoms in IBS patients independent of product pasteurisation – a pilot study. Food Funct. 2018;9(10):5173-5179. PMID: 30256365.

3.3. Freiburg Study (Schropp et al., 2025) – How Much Does 4 Weeks of Sauerkraut Change?

The latest and largest study to date on sauerkraut and the microbiome was published in 2025 by researchers from the University of Freiburg and the Helmholtz Centre for Infection Research in Braunschweig.

87 healthy participants consumed fresh or pasteurized sauerkraut daily for 4 weeks (crossover – each participant received both versions for a period). The results were nuanced: changes in the abundance of individual bacterial species were noted in both groups, with changes being more pronounced in the group consuming pasteurized cabbage. However, neither variant changed the overall alpha diversity of the microbiome. Only pasteurized cabbage increased serum short-chain fatty acid concentrations.

The authors' conclusion is important and worth quoting: "The microbiome of healthy individuals is quite resilient to short-term dietary interventions, although sauerkraut consumption can affect individual species."

Source: Schropp N, Bauer A, Stanislas V et al. The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial. Microbiome. 2025. PMID: 39940045. DOI: 10.1186/s40168-024-02016-3.

3.4. Mechanism: Colonization or Transient Support?

One of the key questions is: do bacteria from fermented foods permanently "settle" in the intestines, or do they merely pass through, acting temporarily?

Current scientific data consistently point to the latter answer. The adult human gut microbiome is a very stable structure and resistant to colonization by foreign strains – there is no readily available "ecological niche" that external bacteria could occupy. Most LAB strains from fermented products can be detected in stool 24–48 hours after consumption; a few days after discontinuing the product, their number usually returns to pre-intervention levels.

However, this does not mean that fermented foods have no effect. Transient bacteria act in several ways even without permanent colonization:

• Metabolite production – bacteria from fermented foods produce lactic acid, acetate, and other bioactive compounds directly in the intestines during transit
• Interaction with resident microbiome – transient bacteria can stimulate or inhibit the activity of strains permanently residing in the intestines, indirectly affecting their metabolism
• Immune system stimulation – contact with a large number of live bacteria trains the immune cells lining the intestines, regardless of the residence time of these bacteria
• Prebiotic matrix effect – as shown by the IBS study, the fermented food matrix itself (fiber, metabolites) can influence the microbiome without the involvement of live bacteria

3.5. Limitations of Current Research – What Else Don't We Know?

Research on fermented foods and the microbiome is promising, but the evidence base has significant limitations that are worth noting:

• Small sample sizes – the Stanford (n=36) and IBS (n=34) studies involved groups that are too small for the results to be generalized to the entire population. The Freiburg study (n=87) is larger, but still relatively small.
• Short observation periods – most interventions last 4–10 weeks. We don't know what happens after a year of systematic consumption of fermented foods.
• Product heterogeneity – "fermented foods" is a broad category: sauerkraut, pickled cucumbers, kimchi, fermented beets, and dozens of other products differ in bacterial profile, salt content, and prebiotic composition. Results from one product cannot be directly transferred to another.
• Lack of standardized dosage – studies use different amounts of product, making it difficult to compare results and establish an optimal "dose."
• Individual variability – as the Stanford study showed, the baseline state of the microbiome strongly influences the response to intervention. The same applies to fermented foods – the effect may differ in a person with a well-balanced microbiome compared to someone after antibiotic therapy.
• Methodological difficulties – designing nutritional studies is technically challenging: a double-blind trial cannot be applied to fermented foods due to their characteristic taste and smell.

4. How Fermented Foods Affect the Gut Barrier and Immune System?

The gut is not just a digestive organ – it's the largest immunological organ in the human body. It is estimated that about 70% of the body's immune cells reside in the intestinal tissue and its immediate surroundings. Fermented foods, by providing live bacteria and their metabolites, directly enter this environment – and that is why their impact on immunity is the subject of intense research.

4.1. What is the intestinal barrier and why is it important?

The intestinal barrier is a single layer of epithelial cells lining the large and small intestines – literally one cell layer separating the gut lumen from the circulatory system and the rest of the body. Its efficient functioning relies on tight junction proteins, such as claudin, occludin, and ZO-1, which act like zippers to connect adjacent epithelial cells and control the permeability of this layer.

A healthy intestinal barrier allows nutrients and water to pass through, while blocking pathogens, bacterial toxins, and undigested food particles. When tight junctions weaken, intestinal permeability increases – and substances that should not enter the bloodstream can do so, triggering inflammatory responses. This topic is actively researched; the role of impaired intestinal permeability in various chronic diseases remains a subject of scientific debate, but its significance in conditions like celiac disease and inflammatory bowel diseases is well-documented.

4.2. Butyrate – how do fermented foods support epithelial protection?

Butyrate is a short-chain fatty acid that is the primary energy source for colonocytes – epithelial cells of the large intestine. It is estimated to cover up to 60–70% of their daily energy needs. Without sufficient butyrate, epithelial cells literally have less fuel to maintain barrier integrity.

In vitro and animal model studies have shown several mechanisms by which butyrate can strengthen tight junctions:

• Increases claudin-1 protein expression at the gene transcription level
• Stabilizes the localization of occludin and ZO-1 in the cell membrane
• Activates AMPK kinase, which accelerates the repair of tight junctions after damage
• Indirectly protects epithelial cells from damage caused by pathogenic bacterial lipopolysaccharides

The connection between fermented foods and butyrate is indirect: as described in Chapter 2, fermented foods primarily contain acetate and lactate, not butyrate. Their role is to provide fiber and bacteria, which in the colon become a substrate for butyrate production by the resident microbiome. This is an important distinction, as it means the effect depends on the initial state of an individual's microbiome.

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4.3. Modulation of the immune system by fermentation bacteria

Lactic acid bacteria from fermented foods come into contact with immune cells lining the intestines already during their transit through the digestive tract. Dendritic cells and macrophages of the intestinal mucosa constantly "sample" the intestinal content through special protrusions – and it is at this stage that recognition and immune response to LAB bacteria occur.

Th1/Th2 balance and regulatory cells

Studies indicate that LAB bacteria can modulate the balance between different arms of the immune system. One of the described mechanisms is the induction of regulatory T lymphocytes (Treg) – cells whose role is to suppress excessive inflammatory reactions and autoimmune responses. However, LAB strains differ significantly in this regard – the immunomodulatory effect is highly strain-dependent, which makes it difficult to generalize results from one product to another.

Pro-inflammatory cytokines – clinical data

The strongest clinical data in humans was provided by the previously discussed Stanford study (Wastyk et al., 2021). In the group consuming a diet rich in fermented products for 10 weeks, a decrease in the level of 19 pro-inflammatory proteins in blood serum was observed, including cytokines such as IL-6, IL-12, and CXCL10. Significantly, none of these 19 cytokines decreased significantly in the high-fiber diet group. This result is promising, although the sample size was small (n=36) and involved healthy adults, not people with inflammatory diseases.

4.4. Fermented foods and inflammatory bowel conditions – where does science end and marketing begin?

In the wellness community, fermented foods are sometimes presented as a remedy for "leaky gut," ulcerative colitis, or Crohn's disease. It's important to clearly delineate between what is supported by research and what is a marketing overinterpretation.

What the research actually shows

• Systematic reviews of clinical trials have shown that probiotic LAB and bifidobacteria have a positive effect on the treatment and maintenance of remission of ulcerative colitis, while for Crohn's disease, the evidence is weaker and mainly concerns synbiotics.
• The mechanisms of LAB action on the intestinal barrier are well described at the cellular and molecular level.
• The Stanford study showed a reduction in inflammatory markers in healthy adults after a 10-week diet rich in fermented products.

Where the evidence ends

• Lack of large RCTs directly investigating the effect of fermented vegetables (not probiotic supplements) on human intestinal permeability parameters.
• "Leaky gut" as a clinical diagnosis does not exist in ICD classifications – it describes a mechanism, not a disease entity; its causal role in various diseases is still being intensively researched.
• Fermented foods are not a therapy for inflammatory bowel diseases and should not replace pharmacological treatment or gastroenterological consultation.

5. Which fermented foods are the healthiest? Comparison of popular fermented products

The answer to "which fermented food is best?" is similar to asking about the best vegetable: the best one is the one you eat regularly. Each fermented product has a different microbiological profile, different bioactive compounds, and a different role in the diet. Below you will find a reliable comparison – noting when we are talking about live bacteria and when about nutritional value without them.

5.1. Comparative table of fermented products

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5.2. Unpasteurized vs. Pasteurized – a key difference when buying

This distinction is fundamental if you are looking for live bacteria – and not just taste or nutritional value of vegetables.

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5.3. Kimchi vs sauerkraut – which is richer in LAB?

Kimchi is often considered a "more probiotic" product than sauerkraut. Is this justified? Partially, yes – kimchi is characterized by a richer and more diverse profile of LAB strains, thanks to the presence of Lactobacillus sakei and Leuconostoc kimchii, among others, which are not found in sauerkraut. Additionally, the bioactive matrix of kimchi is much more complex: capsaicin from chili peppers, allicin from garlic, and gingerol from ginger are compounds with their own documented properties.

On the other hand, good Polish unpasteurized sauerkraut provides comparable amounts of live bacteria and has its own unique strain profile. Both products deserve a place in the diet: they are not substitutes, but rather complements.

6. Fermented vegetables vs other fermented products – how do they differ?

Fermented vegetables are just one of many ways humans ferment food. Kefir, yogurt, kombucha, miso, and tempeh operate on completely different microbiological principles and provide the body with different populations of microorganisms. This is not a competition – it's a complementarity. However, to properly combine fermented products, it is worth understanding how they differ from each other.

6.1. Kefir – dairy fermentation with yeasts

Kefir is one of the most microbiologically complex fermented products available in the daily diet. Kefir fermentation relies on so-called kefir grains – structures made of an exopolysaccharide called kefiran, in which live microorganisms forming a stable consortium are embedded. Sequencing studies have shown the presence of even several dozen distinct species of microorganisms in a single kefir sample, which in terms of diversity surpasses most probiotic supplements.

Microbiological profile

Dominant bacteria include Lactobacillus kefiranofaciens, Lentilactobacillus kefiri, Lactococcus lactis, and Leuconostoc mesenteroides. Unlike fermented vegetables, kefir also contains yeasts (Saccharomyces cerevisiae, Kluyveromyces marxianus, Kazachstania unisporus), which produce carbon dioxide and trace ethanol responsible for the slightly effervescent texture of the drink. Acetic acid bacteria (Acetobacter aceti) and bifidobacteria complete the picture – none of these groups are typical components of fermented vegetables.

How does kefir differ from fermented vegetables?

• Matrix – kefir is a dairy product; it provides complete protein, calcium, and vitamin B12, which are absent or present in trace amounts in fermented vegetables.
• Yeasts – the presence of wild yeasts is a unique element of kefir; vegetable ferments ferment without the involvement of yeasts.
• Lacto-fermentation vs other LAB – the dominant strains in kefir (L. kefiranofaciens, L. kefiri) are not found in sauerkraut or pickles; this is a separate pool of microorganisms.
• Kefiran – an exopolysaccharide produced by L. kefiranofaciens exhibits its own properties – it is studied as a potential prebiotic.

6.2. Yogurt – simplicity versus diversity

Yogurt is the most widely consumed fermented product in the world, but from a microbiological standpoint, it is also one of the simpler ones. Traditional yogurt is fermented exclusively by two species: Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus. Both are homofermentative – they produce almost exclusively lactic acid, do not create CO₂, and do not exhibit yeast activity.

For both strains, there is an EFSA-approved health claim (Regulation 432/2012): live yogurt bacterial cultures contribute to better lactose digestion in individuals with lactose intolerance. This is one of the few cases of an approved claim for a specific fermented product.

"Probiotic-enriched" yogurts (usually containing Lactobacillus acidophilus or Bifidobacterium) have a broader profile, but the survival rate of these strains in the product can vary and depends on the manufacturer. In terms of microbiological diversity, yogurt is inferior to both kefir and good fermented vegetables.

6.3. Kombucha – a completely different type of fermentation

Kombucha is a fermented tea drink based on SCOBY (Symbiotic Culture of Bacteria and Yeast) – a gelatinous structure composed of microorganisms embedded in cellulose. Its microbiology differs fundamentally from fermented vegetables and dairy products.

SCOBY composition

Contrary to popular belief, the dominant organisms in kombucha are not lactic acid bacteria, but acetic acid bacteria – primarily the genus Komagataeibacter (formerly Gluconacetobacter), accounting for an average of about 45% of all bacterial sequences in kombucha samples. LAB bacteria (Lactobacillus) take second place with an average of 20%. Yeasts – Brettanomyces, Zygosaccharomyces, Saccharomyces cerevisiae – dominate the liquid phase.

The products of kombucha fermentation are primarily acetic and gluconic acids, not lactic acid as in fermented vegetables. The finished drink also contains tea polyphenols, organic acids, and trace amounts of alcohol (usually below 0.5%).

Scientific evidence versus marketing

Kombucha enjoys immense popularity in the wellness segment, but the evidence base from human clinical trials is still much weaker than for fermented vegetables, kefir, or yogurt. Most studies come from animal models or cell cultures. Large, controlled clinical trials in humans are still scarce. This should be taken into account when interpreting marketing messages about kombucha.

6.4. Miso, tempeh, natto – Asian fermentations

In Chapter 5, we discussed miso and tempeh in the context of comparing fermented products. It is worth adding a third, microbiologically most interesting product from this group, which appears less frequently on Polish tables – natto.

Natto is fermented Japanese soy, where fermentation occurs not through fungi (as in tempeh and miso), but through the bacteria Bacillus subtilis var. natto. This is a completely different microbiological domain than LAB or filamentous fungi. Natto is probably the best source of vitamin K2 in the form of MK-7 among all known fermented products – its content ranges from 1000 to 1100 μg/100 g, which is many times what sauerkraut provides. For those interested in K2 supplementation, natto is therefore a product of exceptional importance, although its specific smell and slimy consistency pose an entry barrier for Western European consumers.

The key principle regarding miso, tempeh, and natto: the fermentation value of these products lies mainly in the altered nutritional profile of the raw material (better protein bioavailability, reduction of anti-nutritional phytates, vitamin synthesis), not in delivering live bacteria to the intestines. Miso added to hot soup, tempeh fried in a pan, and natto subjected to heat treatment lose live microorganisms – the nutritional benefit remains, the probiotic one disappears.

6.5. What to combine – diversity as a strategy

Each fermented product provides the intestines with a different pool of microorganisms, different metabolites, and a different food matrix. A study published in Frontiers in Nutrition (2025) showed that microbes from fermented foods can constitute up to 3% of the adult gut microbiome – a small but measurable and functionally active fraction.

The logic of combining different fermented products is simple: the broader the range of fermentation types in the diet, the more different strains and metabolites reach the intestines. The Stanford study (Wastyk 2021) also showed that the effects increased with the number of servings of fermented products consumed – diversity and regularity were more important than concentrating on a single "superferment."

7. How many fermented vegetables to eat and how to incorporate them into your diet?

There are no official dietary guidelines specifying the daily portion of fermented vegetables – neither in Poland nor at the European level. This is often the case in functional nutrition: we know that a product is beneficial, but the precision of recommendations is limited by available research. However, we do have a few reference points that are worth using.

7.1. Recommended portions and frequency – what do studies say?

Let's start with the numbers from the studies we've already discussed. In the Stanford study (Wastyk 2021), participants consumed a target of 6 servings of fermented products daily for 10 weeks, with one cup of yogurt, one cup of kimchi, or ~450 ml of kombucha counting as a serving. The effects – increased microbiome diversity and decreased inflammatory markers – were stronger with higher intake. However, the study clearly showed that the products were mixed and diverse, not limited to fermented vegetables alone. Translating these 6 servings solely to sauerkraut would be both impractical and methodologically unjustified.

A more targeted reference point is provided by a study on fermented vegetables and IBS (Nielsen 2018): participants consumed 75 g of sauerkraut daily (approximately half a cup) for 6 weeks and reported improved symptoms and changes in microbiome composition. This is a realistic, achievable, and research-verified portion.

Sodium in fermented foods – what to remember

Fermented foods contain salt used for fermentation – its content at a standard concentration of 2% is about 240-260 mg of sodium per 30 g of product. For a 75 g portion, this is about 600-650 mg of sodium, almost 1/4 of the recommended daily maximum (2400 mg). For healthy individuals, this is not a reason to forgo fermented foods – however, individuals diagnosed with hypertension and on a low-sodium diet should account for fermented foods in their sodium balance and consult a doctor or dietitian about quantities.

7.2. How to introduce fermented foods gradually – especially with sensitive intestines?

Suddenly introducing a large amount of fermented foods into a diet that previously lacked fermented products often results in bloating, excessive gas, and intestinal discomfort. This is not a sign that fermented foods are harmful to you – it's a typical reaction of the microbiome, which needs to adapt to new bacteria and a higher amount of organic acids.

Gradual introduction step by step

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7.3. Fermented foods in culinary practice – when to add them and what to combine them with?

This is one of the most important and often overlooked aspects: fermented foods should be eaten cold or at room temperature. Heating above 50–60°C destroys live LAB bacteria – and while cooked fermented food still tastes good and retains fiber and minerals, it loses its probiotic character.

Rule number one – do not cook

• Bigos, kapuśniak, stuffed cabbage with sauerkraut – tradition and taste are absolutely fine, but the probiotic effect disappears in the pot
• If you care about live cultures – eat some fermented foods raw as an addition to a finished dish, added after removing the dish from the heat
• Miso for soup: add after turning off the heat and allowing it to cool slightly – at around 60°C, bacteria begin to die off

What to combine fermented foods with?

Fermented foods naturally pair well with heavy, fatty, or protein-rich dishes – not only due to culinary tradition, but also due to the physiology of digestion. Lactic acid stimulates the production of stomach acids and aids protein digestion, while fermented vegetables provide fiber, which slows down fat absorption.

• With meat and fish – sauerkraut and pickled cucumbers as a classic accompaniment; kimchi as a spicy contrast to grilled meat or tofu
• For sandwiches and wraps – pickled cucumbers, cabbage, kimchi as a substitute for classic sauces and marinades
• For salads – chopped fermented cabbage instead of part of the dressing; brine as a natural, probiotic base for vinaigrette sauce
• As a quick snack – a pickled gherkin with hard-boiled eggs, a piece of fermented beetroot with cheeses
• In the morning on an empty stomach – a shot of beetroot or fermented vegetable brine to stimulate digestive juices before breakfast

8. Who should be careful with fermented foods?

Fermented foods are safe and beneficial for the vast majority of people. However, there are groups for whom standard recommendations do not apply – and who should consider several important factors before incorporating fermented foods into their diet. The following section is not meant to scare, but rather to provide an honest review of situations requiring an individual approach.

8.1. SIBO – when bacteria are in the wrong place

SIBO (Small Intestinal Bacterial Overgrowth) is an overgrowth of bacteria in the small intestine – a condition where bacteria typically inhabiting the large intestine migrate and multiply in the small intestine, where they should not be present in such large numbers. It manifests as chronic bloating, gas, abdominal pain, diarrhea or constipation, and malabsorption of nutrients.

Fermented foods in the active phase of SIBO can exacerbate symptoms for two reasons:

• Live LAB bacteria supplied with fermented foods enter the small intestine and can increase the already excessive bacterial population there – producing hydrogen or methane, which exacerbates bloating and discomfort.
• Mannitol – a sugar alcohol formed during the fermentation of white cabbage (see subsection on IBS) – serves as a substrate for small intestinal bacteria, which can intensify fermentation in the wrong place.

It's worth adding that SIBO and probiotics are an actively researched and ambiguous topic: some data suggest that certain probiotic strains can support healing after SIBO treatment, while other studies indicate a possible worsening of symptoms. One should not apply other people's experiences to their own case – consultation with a specialist is more necessary here than for any other condition mentioned in this chapter.

8.2. Histamine intolerance – an enzymatic problem, not an allergy

Histamine is a biogenic amine produced by some fermenting bacteria from the amino acid histidine. For the vast majority of people, this is irrelevant: histamine from food is efficiently broken down by the DAO enzyme (diamine oxidase) in the intestines before it enters the bloodstream. However, in an estimated 1–3% of the population, DAO activity is reduced – and it is in these individuals that excessive consumption of histamine from food can cause symptoms resembling an allergic reaction: facial flushing, headaches, nasal congestion, hives, and also intestinal complaints.

How much histamine is in fermented foods?

The answer is not obvious and depends on the product. In a study analyzing 120 commercial sauerkrauts, histamine content ranged from 0 to 229 mg/kg – an enormous spread. The explanation lies in the composition: white cabbage contains very little histidine, so fermenting bacteria have a limited substrate for histamine production. Fermented cabbage, pickled gherkins, or beetroot kvass are therefore products with relatively low histamine content. Significantly higher levels may be found in fermented products involving protein components, such as traditional kimchi with added fish or anchovies, soy sauce, tempeh, or miso.

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Histamine intolerance requires medical diagnosis – it is not a condition that can be reliably assessed on one's own. If headaches, facial flushing, or stomach symptoms regularly appear after consuming fermented foods, red wine, or cheese, it is advisable to consult an allergist or internal medicine specialist who can order a DAO activity test.

8.3. IBS with predominant bloating – FODMAP hidden in fermented foods

Irritable Bowel Syndrome (IBS) is a heterogeneous functional disorder, and the reaction to fermented foods varies widely among patients. A study by Nielsen (2018) showed an improvement in IBS symptoms with regular consumption of sauerkraut – but there is an important context here that is often overlooked.

During the fermentation of white cabbage, LAB bacteria convert fructose into mannitol – a sugar alcohol belonging to the FODMAP group (fermentable oligo-, di-, monosaccharides, and polyols). Mannitol can exacerbate bloating and intestinal discomfort in sensitive individuals with IBS. Data from Monash University tests show:

• 20g of sauerkraut from white cabbage (1 tablespoon) → low FODMAP content
• 30g → moderate mannitol content
• 75g (½ cup) → high mannitol content; may exacerbate symptoms in sensitive individuals

If you are following a Low FODMAP diet protocol (e.g., under the guidance of a dietitian), standard Polish white cabbage sauerkraut requires particular caution and should be limited to a maximum of 1 tablespoon per serving. Kimchi containing garlic and onion (typical ingredients) is high in FODMAPs due to the fructo-oligosaccharides from these ingredients – look for versions without garlic and onion or start with a ½ tablespoon portion and observe your reaction.

8.4. Hypertension and low-sodium diet

Salt is essential for the proper fermentation of pickled foods, but its presence in the final product is not insignificant for individuals on a sodium-restricted diet. At a standard salt concentration of 2%, a 75g portion of pickled food provides approximately 600–650 mg of sodium – this is about 25–27% of the maximum recommended daily sodium intake according to WHO guidelines (2g Na, or about 5g salt). For a 100g portion, this is already 800–870 mg.

For healthy individuals, this is not a reason to eliminate pickled foods from the diet. However, individuals with diagnosed hypertension and on a low-sodium diet should:

• Account for pickled foods in their daily sodium balance (rather than treating them as a "free" addition)
• Prefer smaller portions, e.g., 30–40g instead of 75g
• Avoid pickled brine, which has the highest salt concentration
• Consult a doctor or clinical dietitian for individual limits

8.5. Other situations requiring caution

Anticoagulants (warfarin, acenocoumarol)

Fermented foods contain vitamin K – both K1 (from the base vegetable) and K2 synthesized by bacteria. Patients taking vitamin K antagonists (warfarin, acenocoumarol) must maintain a consistent, stable level of vitamin K intake in their diet – fluctuations can destabilize INR values. Fermented foods are not forbidden, but should be consumed regularly, in similar amounts, without sudden changes. If you plan to introduce fermented foods into your diet for the first time, inform your treating physician and check your INR after 1–2 weeks.

Reduced immunity and immunosuppression

Individuals who have undergone organ transplants, are undergoing chemotherapy, or are taking long-term immunosuppressants should exercise caution when consuming unpasteurized fermented foods. Live bacteria from fermented foods are safe for a healthy immune system, but in individuals with profound immunosuppression, they may – in theory – pose a risk. The decision to consume them should be discussed with the treating physician.

Reflux and hyperacidity

The high acidity of fermented foods can exacerbate symptoms of gastroesophageal reflux disease (GERD) in particularly sensitive individuals. This is not an absolute contraindication – many people with reflux tolerate fermented foods well, especially when consumed during a meal rather than on an empty stomach. It is worth observing individual reactions and adjusting the time of consumption.

9. FAQ – frequently asked questions about fermented foods

9.1. Can fermented foods be eaten during pregnancy?

Traditional fermented vegetables – sauerkraut and pickled gherkins – are generally considered safe during pregnancy. The acidic environment of fermented foods inhibits the growth of pathogens, and the product provides vitamins C, K, folates, and live LAB bacteria. However, kombucha should be avoided due to its trace alcohol content and the risk of uncontrolled yeast fermentation.

If you have concerns about specific products or quantities, it is advisable to discuss the matter with your gynecologist or midwife.

9.2. From what age can children eat fermented foods?

Fermented foods can be introduced into a child's diet gradually from around 1 year of age, starting with small amounts – a teaspoon of finely chopped sauerkraut or a slice of pickled gherkin. The main limitation is the salt content: large portions for small children can provide excessive amounts of sodium. Before serving, it is advisable to rinse the fermented food with water, which reduces the salt concentration by as much as 30–40%, while retaining most of the bacteria and lactic acid. Vinegar-pickled products (marinades) are not a suitable substitute – the child will not gain live bacteria, and salt and vinegar can strain the digestive system.

9.3. Does fermented brine have the same properties as whole fermented food?

Brine is the liquid fraction of fermented food containing live LAB bacteria, lactic acid, acetic acid, and water-soluble vitamins. In terms of probiotic and bioactive properties, it is similar to the fermented food itself – the difference lies in the absence of fiber from vegetable particles. For individuals with a very sensitive digestive system who react to fiber, 1–2 tablespoons of brine before a meal is a good and milder option. Brine should not be cooked or heated – it will lose its probiotic properties, just like whole fermented food subjected to heat treatment.

9.4. Do fermented foods help during and after antibiotic therapy?

Antibiotics eliminate both pathogenic bacteria and a significant portion of beneficial intestinal microflora. Regular consumption of fermented foods and other fermented products during antibiotic treatment is widely recommended as a dietary supplement, but with one important caveat: fermented foods (or probiotic supplements) should be consumed at least 2–3 hours after taking the antibiotic, so that the drug does not deactivate the delivered bacteria before they reach the intestines. After completing antibiotic therapy, regular consumption of fermented products can support the gradual rebuilding of microbiome diversity. Fermented foods do not replace completing the full course of antibiotics – this is a matter of health safety, not negotiable.

9.5. Are fermented foods suitable for a ketogenic diet?

Yes – fermented vegetables have a very low net carbohydrate content: sauerkraut approx. 2–3 g/100g, pickled gherkins approx. 1–2 g/100g. They easily fit within the daily carbohydrate limit on a ketogenic diet. Additionally, fermented brine is a natural source of sodium and electrolytes, which is especially important on keto, when the kidneys excrete more sodium along with ketones. Mannitol from white cabbage sauerkraut (sugar alcohol, see chapter 8) counts towards the total carbohydrate pool, but has a minimal effect on blood glucose levels and insulin.

9.6. How long can fermented foods be stored after opening?

Unpasteurized fermented foods, once opened, should be stored in the refrigerator, submerged in brine – vegetables exposed above the liquid level are susceptible to mold. At 2–6°C, sauerkraut retains its properties for 2–4 weeks after opening, and pickled gherkins for 1–2 weeks. Fermentation does not stop in the refrigerator – the product will gradually become more acidic, which changes the taste but does not make it unfit for consumption. A white sediment at the bottom and cloudy brine are normal effects of bacterial activity. A sign of spoilage, however, is an unpleasant odor (putrid, not sour), slimy vegetable consistency, or visible mold on the surface.

10. Summary

Fermented foods are one of the few food products that combine nutritional, probiotic, and bioactive value in one natural and inexpensive package. Lactic fermentation not only preserves vegetables but actively changes their composition – it synthesizes vitamin K2, improves mineral bioavailability, produces lactic acid and short-chain fatty acids, and above all, populates the product with billions of live bacteria that no standard dietary supplement can replace.

Clinical studies – primarily the Stanford study from 2021 – show that regular consumption of fermented products can increase gut microbiome diversity and lower inflammatory markers more effectively than a high-fiber diet alone. However, this is not a license for oversimplification: the evidence base for fermented vegetables is still being built, short-term interventions only temporarily change the microbiome, and the effects are strongly dependent on the individual's initial gut health.

Key practical takeaways from the article:

• Choose unpasteurized – only these contain live bacteria; check the label for ingredients: vegetable + salt, no vinegar or sugar
• Regularity over quantity – daily small portions work better than a single large consumption once a week
• Do not cook – add fermented foods to cold or lukewarm dishes; heating above 60°C destroys live cultures
• Start slowly – especially with sensitive intestines; fermented brine is a milder starting point than a whole vegetable
• Variety matters – sauerkraut, pickles, kimchi, kefir, and miso provide different populations of microorganisms and metabolites
• Fermented foods are food, not medicine – individuals with SIBO, IBD, histamine intolerance, on anticoagulants, or with immunosuppression should consult a specialist about their consumption

Fermented foods are not a panacea – but in the context of a daily diet, they are one of the most well-justified and easily accessible tools to support gut health. In Poland, we have exceptional access to them: sauerkraut and pickled cucumbers are products rooted in culinary tradition, inexpensive, easy to make at home, and available in every greengrocer. It's hard to find a healthier habit that costs less.

11. Sources

1. Wastyk HC, Fragiadakis GK, Perelman D et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021;184(16):4137-4153.e14. DOI: 10.1016/j.cell.2021.06.019. PMID: 34256014.
2. Nielsen ES, Garnås E, Jensen KJ et al. Lacto-fermented sauerkraut improves symptoms in IBS patients independent of product pasteurisation – a pilot study. Food Funct. 2018;9(10):5173-5179. DOI: 10.1039/c8fo00968f. PMID: 30256365.
3. Schropp N, Bauer A, Stanislas V et al. The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial. Microbiome. 2025. DOI: 10.1186/s40168-024-02016-3.
4. Saez-Lara MJ, Gomez-Llorente C, Plaza-Diaz J, Gil A. The Role of Probiotic Lactic Acid Bacteria and Bifidobacteria in the Prevention and Treatment of Inflammatory Bowel Disease and Other Related Diseases: A Systematic Review of Randomized Human Clinical Trials. Biomed Res Int. 2015;2015:505878. DOI: 10.1155/2015/505878. PMID: 25793197.
5. Ross FC, Patangia D, Grimaud G et al. Impact of fresh and fermented vegetable consumption on gut microbiota and body composition. Front Nutr. 2025. DOI: 10.3389/fnut.2025.1623710.
6. Monash University FODMAP Diet App – laboratory data on FODMAP content in sauerkraut and kimchi. Available at: monashfodmap.com.
7. Commission Regulation (EU) No 432/2012 of 16 May 2012 establishing a list of permitted health claims made on foods, other than those referring to the reduction of disease risk and to children’s development and health. Official Journal of the EU L 136/1. Available at: eur-lex.europa.eu.