III. 4 Fermented foods

Fermented foods have been bringing live cultures to our plates for thousands of years. In the next three days you'll learn why they can be allies of your flora, and how to introduce them sensibly, in small steps – paying attention to what suits your healing gut.

What are fermented foods, and why are they useful?

Fermentation is an ancient method of preservation: beneficial microbes – bacteria, yeasts – "work" the food and transform it in the process. This is what gives yoghurt its tangy taste, sauerkraut its crisp freshness, kefir its fizz. These fermented foods^[G] can help your gut in two ways: on the one hand, many of them contain live microbes; on the other, fermentation produces substances that nourish and soothe the gut environment.

It is important, however, to draw a distinction. A shop-bought probiotic capsule contains one or two selected bacterial strains in large, concentrated amounts – which is precisely why we ask you to avoid them during the DiffBiome course, so they don't disturb the freshly forming balance. A traditional fermented food, by contrast, introduces many kinds of microbe in small amounts, in natural form, as part of a food. This is closer to how humans ate for thousands of years, and is generally gentler.

Not every "sour" food is fermented, and not every fermented food contains live cultures. Pickled gherkins, for example, are often simply soaked in vinegar and do not contain live bacteria. In heat-treated or pasteurised products (many shop-bought sauerkrauts, some yoghurts) the heat may destroy the microbes. Products stored in the chiller and labelled "live cultures" are generally better – but the details come later; for now, the point is to get acquainted cautiously.

How to introduce them?

Here too, gradualness and observation are the key, perhaps even more so than with fibre. Your healing gut is more sensitive now, so introduce a single new fermented food at a time, in a very small portion: a few spoonfuls of plain yoghurt, a small sip of kefir, a forkful of sauerkraut. Watch for a day or two how you respond, and only then increase the portion or try something new.

The gentlest entry points are usually the dairy-based, live-culture products: plain (unsweetened) yoghurt and kefir, provided you tolerate dairy well. Plant ferments – sauerkraut, kimchi – can be stronger, so start with a very small amount, and rather as a side dish, not a main. Leave the very hot, spicy versions (strong kimchi) for later.

Most importantly: discuss the introduction of any new fermented food with your treating physician, especially while the course is ongoing. There are situations – for example a weakened immune system – when live cultures call for greater caution. Your physician knows your condition and can tell you when and what is worth trying. Your diary helps here too: note what you ate and how you tolerated it, so you can see what does you good.

🍽️ Eating during these days

The theme of these three days is the cautious introduction of fermented foods, and the three days' concrete eating task is exactly about this: a single gentle fermented food – a few spoonfuls of plain, unsweetened yoghurt – in a very small portion, observing tolerance (day 34); based on yesterday's experience, a cautious increase or a sip of kefir, or slowing down if it caused bloating (day 35); and finally a plant fermented food – a forkful of live-culture sauerkraut – as a side dish (day 36). The guiding principle is only one novelty at a time, in a small portion, tracked in the diary.

The Plant Calendar (Appendix F) recommends gentle, steamed vegetables and leafy greens for these days: cooked celeriac (day 34), steamed spinach (day 35) and steamed chard (day 36) – these days fall into the calendar's "gradual expansion" (days 31–50) phase, where the goal is to gradually increase steamed vegetables and plant diversity. These sources provide gentle, fermentable fibre and folate; fibre is substrate for fibre-degrading bacteria (towards short-chain fatty acids, butyrate), so the live cultures of fermented foods and the steamed vegetable fibres complement one another in supporting the diversity and resilience of the engrafting flora.

Why does this matter?

Fermented foods can be valuable allies of your engrafting flora: they bring live cultures and beneficial substances into your gut, in natural, food form. In these days you learned the most important difference between a fermented food and a concentrated probiotic capsule, and that the secret of sensible introduction is one novelty at a time, in a small portion, with observation – all in consultation with your treating physician. Your diary shows what does you good right now. In the next three days we'll talk about protein and the gentle diet.

References

[12] Zmora N, Zilberman-Schapira G, Suez J et al. Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell. 2018. Link

Sequential invasive multi-omics profiling of the mucosal-associated gastrointestinal microbiome in mice and humans during consumption of an 11-strain probiotic versus placebo showed that probiotics remained viable through gastrointestinal passage but encountered marked mucosal colonization resistance in colonized hosts. Humans displayed person-, region- and strain-specific mucosal colonization patterns predictable from baseline host and microbiome features, while stool probiotic presence was uninformative. Stool microbiome correlated only partially with mucosal microbiome. The findings challenge the empiric use of probiotics in healthy individuals.

[106] Wastyk HC, Fragiadakis GK, Perelman D et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021. Link

17-week randomized prospective trial (n=18/arm) in healthy adults comparing high-fibre versus high-fermented-food diets with multi-omics microbiome and host immune profiling. The high-fibre diet increased microbiome-encoded glycan-degrading CAZymes despite stable diversity. The high-fermented-food diet increased microbiome diversity and decreased multiple inflammatory markers. Findings demonstrate diet-specific microbiome–immune effects and support fermented foods as a strong, diversity-promoting modulator of the gut–immune axis.

[107] Marco ML, Heeney D, Binda S et al. Health benefits of fermented foods: microbiota and beyond. Curr Opin Biotechnol. 2017. Link

Review of fermented foods, among the first processed food products consumed by humans (yogurt, cultured milk, wine, beer, sauerkraut, kimchi, fermented sausage). Originally valued for shelf life and palatability, fermented foods are now recognized as having enhanced nutritional and functional properties through substrate transformation and bioactive end-product formation. Many fermented foods contain living microorganisms with potential health effects. The review consolidates fermented foods as a microbiome-relevant dietary category.

[339] Suez J, Zmora N, Zilberman-Schapira G et al. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018. Link

In a controlled study of post-antibiotic microbiome reconstitution, multi-strain probiotic supplementation, autologous fecal microbiota transplantation (aFMT) or spontaneous recovery were compared in mice and humans, sampled via invasive mucosal biopsies. Antibiotics enhanced probiotic mucosal colonization in humans but only mildly in mice. Compared with spontaneous recovery, probiotics induced a markedly delayed and persistently incomplete reconstitution of indigenous stool and mucosal microbiota and host transcriptome, while aFMT produced rapid, near-complete recovery within days. In vitro, Lactobacillus-secreted soluble factors contributed to probiotic-mediated suppression of indigenous taxa. The findings caution against routine post-antibiotic probiotic use and support aFMT as a recovery strategy.