Instructions on how to manage your germs.

What can we do to make the beneficial bacteria feel comfortable and work hard for your health? How can we make our stomachs resemble a thriving metropolis with no room for harmful gangbusters? Can we breed good bacteria? Here’s a guide to managing your own microbes.

– Experts recommend that we take care of our intestinal microbiome. Is there something to feed it first?

– The bacteria living in our intestines undoubtedly feed on the same things we do. Interestingly, studies show that the composition of our intestinal microbiota is influenced by the food we have eaten in the last 24 hours. Consequently, this bacterial composition can be partially manipulated.

– But, unfortunately, it cannot be quickly and significantly changed once and for all.

– Yes, but it’s worth a try. Any change for the better has its effects. You just have to be committed.

– Do “good” bacteria like what we eat?

– The microbes that populate our intestines certainly don’t like what modern humans eat, which is processed, high-energy foods high in sugars and animal fats.

The microbiome also dislikes trendy diets, such as gluten-free. There is evidence that such diets can reduce the number of bifidobacteria, i.e. healthy intestinal bacteria. This is proof that it is not wise to completely eliminate gluten from the diet without a medical reason.

It is now fashionable not to eat gluten, although less than 1% of people suffer from cereal protein intolerance. For the rest, avoiding it can be harmful: There is evidence that a gluten-free diet can impair the composition of the intestinal microflora.

On the other hand, foods which are high in gluten, such as white bread and pasta, contain more simple sugars, to which our microbiome also reacts negatively. So, in everything we need to observe moderation. For fighting germs, these medications at are very helpful.

– But are sweets good?

– For our taste buds, maybe so. But gut microbes don’t like sweets or fatty foods. They also do not like it when there is too little fibre in the diet. This is the main ‘food’ for the inhabitants of our intestines.
Soluble dietary fibre plays a key role, as it feeds the beneficial bacteria, but so does insoluble fibre. Previously, the latter were considered superfluous waste or ballast.

It is now known that they create a kind of scaffolding in the intestine to which the good bacteria can attach. That is, they build a home for them.

– Do all kinds of sugars have an adverse effect?

– The simple ones, yes. These include white, brown and cane sugar, fructose, dextrose, lactose, maltose, molasses, honey, glucose-fruit syrup, malt, syrups…

– And fats?

– Certainly essential fatty acids, monounsaturated and polyunsaturated, especially omega acids, are recommended. Studies show that the key factor is the type of these fatty acids. Omega-3 acids are said to have a positive effect on the microbiome, while omega-6 is exactly the opposite, for the reason that they are pro-inflammatory acids. Their overabundance should be avoided.

The ratio of omega-3 to omega-6 fatty acids in the diet cannot be equal! When there are too many omega-6 acids, they block the effects of omega-3 and produce pro-inflammatory molecules. Interestingly, the enzymes responsible for the metabolism of these acids are the same. Excessive consumption of omega-6 fats with omega-3 deficiency has been shown to lead to many inflammatory and degenerative diseases. Omega-3, in turn, protects us against them.

Therefore, the proportions are paramount. It is believed that there should be 4-5 times more omega-3 acids in the diet than omega-6, i.e. the ratio of one to the other should be 4-5:1.

– What foods contain omega-3 acids?

– Primarily oily marine fish such as mackerel, salmon, herring, sardines, jalibut, and some freshwater fish such as trout, but also walnuts, flaxseed oil, flax seeds, seed hemp and chia. Omega-6 acids are found mainly in plant foods. They include pumpkin seeds, sunflower seeds, sesame seeds, almonds, peanuts and some vegetable oils: corn, sunflower, soya, rapeseed, peanut, sesame, coconut, olive and grape seed oils.

Rapeseed and flaxseed oils have a good ratio of omega-6 to omega-3 acids.

It is not that omega-6 acids are not in our diet at all! We need them, just in much smaller amounts than omega-3.

Interestingly, the so-called FODMAP diet is excellent for feeding beneficial bacteria. Professionally speaking, it is a diet low in fermentable oligo-, di- and monosaccharides, as well as polyols. It is recommended for people suffering from, for example, IBS or other functional bowel disorders. A poor microbiome also plays a role in these disorders.

In practice, it is very difficult to find a good list including recommended foods without the ‘involvement’ of FODMAP. There are still controversial points here. For example, there is controversy about legumes, which are not included in the FODMAP diet, because they actively promote mal-fermentation in the intestine. However, in the light of the latest research, it turns out that this is not the case. Obviously, the best way out is not to completely eliminate these foods from your diet, but to limit them.

Synopsis: What is FOODMAP

Australian nutritionists P.R. Gibson and S.J. Shepherd found that there is a specific list of foods that provoke irritable bowel syndrome. These foods contain poorly absorbed carbohydrates (oligosaccharides, disaccharides, monosaccharides and polyols) that cause fermentation in the intestines and eventually lead to pain, gas, diarrhoea or constipation.

FODMAP is the abbreviation for fermentable oligo-, di-, and monosaccharides and polyols. There is also a special diet for irritable bowel syndrome, which includes a maximum restriction of FODMAP substances.

– Why is it important? You can just not eat legumes, that’s all.

– Exactly, paradoxically – you can’t, if we want to have a healthy microbiome. Some bean products contain compounds that are tasty for healthy bacteria. Like tofu, for example. Although it is a soy product, it works wonderfully in the FODMAP diet – without any adverse effects.

– But tofu doesn’t taste good!

– Oh, you can always make something out of it! Meat is also tasteless unless it’s seasoned, baked or stewed.

In feeding the microbiome, the subject of alcohol comes up. Of course, alcohol has pro-inflammatory effects, but research shows that one glass of red wine a day is beneficial to the gut microbiota due to its high polyphenol content.

Hannah is speaking at WFK 2018.

– Bacteria probably only like plant-based foods.

– Undoubtedly! However, not only, although plants are what they need most to live. Chia seeds, for example. They are a very valuable source of omega-3 acids.

– Should you grind them or can you add whole chia seeds, for example, to desserts by pre-moistening?

– Today, fruit mousses, millet puddings and vegetable smoothies with the addition of whole chia seeds are in vogue. It certainly looks pretty, but it has little to do with the health-promoting effects. In order to extract their health benefits, the seeds need to be crushed. Whole ones are not digested.

– What else to add to the menu?

– The intestinal microbiome loves cinnamon. Turmeric and ginger can also be added to this list, i.e. spices that have a strong anti-inflammatory effect, as well as cayenne pepper because of the active ingredient capsaicin.

Next are berries, especially high-grade blueberries. They have a low glycemic index, and the gut microbiota love anything with this low index. Green tea and avocados come next, as they contain healthy fats, valuable phytonutrients, lots of fibre and a fair amount of protein.

Quinoa should also be on the menu – it’s true that it’s gluten-free, but it’s high in fibre and protein and also has a low glycaemic index.

– Was there anything that surprised you about this healthy bacteria list?

– Yes, I was surprised by whey protein. Studies show that if whey protein – without the milk protein casein and sugar (lactose) – is added to the diet, it is extremely beneficial for the nutrition of the microbiome. Such protein is particularly recommended for people suffering from Crohn’s disease or other intestinal permeability disorders.

Whole grains are also important, as they have the highest fibre content, as well as nuts, especially walnuts. Only you can’t go overboard with them – they’re an energy product.

Short-chain fatty acids (SFAs) also appear in studies. The related butyric acid, or butyrate, has repeatedly proven beneficial effects on the gastrointestinal tract. Due to their anti-inflammatory and regenerative effects, butyric acid may be effective in the prevention of inflammatory processes in the colon. For this reason, butyrate is being considered for use in the treatment of non-specific inflammation of the colon.

Butyrate in the process of fermentation of dietary fibre synthesises the good bacteria living in our colon. Some BCA is also present in coconut oil. It is very popular now, and I think we are overdoing it. Coconut oil can be eaten, but only in small amounts, because its composition paradoxically resembles animal fat rather than vegetable fat. In spite of its vegetable origin it contains a lot of saturated fats.

– And animal fats?

– Not recommended, although tolerated in small quantities. They are not particularly bad for our bacteria, but they don’t help much either. On the other hand, saturated animal fats are known to play a significant role in the formation of atherosclerotic plaques, so they should not be overused in any case.

The Food Pyramid ‘advises’ eating a maximum of 500 g of meat per week, preferably in three portions of 150-170 g. Well, more often than not, we eat a lot more meat. Not to mention animal fats like butter and lard.

Conjugated linoleic acid also seems interesting. It is commonly found in milk fat, i.e. in dairy products as well as beef, and has a proven beneficial effect on the intestinal microbiota. Some species of beneficial microbes are known to produce conjugated linoleic acid themselves. Studies have linked the production of these acids with overall weight loss.

Fermented, i.e. fermented vegetables are also important because they provide us with natural probiotic bacteria.

– I’ve always wondered if they break down completely in the stomach.

– Not completely. Some of the leavened vegetables pass into the intestines, so eating them definitely makes sense.

A variety of vegetables is important. Not only sauerkraut is recommended, but also cucumbers, radishes, beetroot, kimchi, and fermented soy products: tempeh, miso, and natto.

Of course, dairy products are also recommended, but be careful with yoghurt. Yoghurt has a probiotic effect if it contains 1 million bacteria in one cubic metre, but most products available on the market do not contain that amount.


Those whose weekly diet contains more than 30 plant species have a more diverse microbiome than those who limit their intake to 10 or fewer plants per week, said researchers from the University of California, San Diego, who are studying the microbiota of volunteers who give scrapings as part of the American Gut Project. The researchers also collect information on the lifestyles and diets of those ‘providing’ the samples, so they are aware of the number of plant species eaten.

– Are there any plants that have an exceptionally strong prebiotic effect? Plants that our bacteria absolutely adore?

– Every “microbiotic restaurant” client wants cherries, berries, bananas, asparagus, topinambur, salad chicory, cruciferous vegetables and legumes. Also oats (including oat flakes), kale, bok choy, green leafy vegetables, miso, wine vinegar, sprouts (mostly broccoli), artichokes. Also apples, because of pectin, and bitter chocolate, which contains polyphenols. Coffee remains controversial, although an increasing number of studies show that it has beneficial effects.

But more and more research is being done. If we abstract and look at the list I just presented, I see just healthy foods that have been recommended by nutritionists for years, and not at all because of feeding a good gut microbiota. This way of eating is good for our health, and perhaps the mechanism behind it is precisely the activity of the gut microbiome.

Your bacteria definitely need to be taken care of. You should not take laxatives or cleanse your body with questionable methods, such as hydrocolonoscopy, which simply destroys your intestines. A strict diet has a similar effect. Just because your bowels will be clean doesn’t mean they will be healthy. The intestines cannot be clean!

And to conclude one more thing – we often say that diet must be combined with movement. For some reason, this state of affairs is the most beneficial for us. And studies have already emerged proving that the microbiome has something to say here too. Those who exercise have a richer gut flora than those who don’t move. It’s worth keeping that in mind too.


To summarise, the nutritionist’s recommendations in the text:

  • berries, bananas, cherries, apples;
  • oatmeal;
  • asparagus, chicory, kale, broccoli, cabbage, topinambur;
  • legumes;
  • rapeseed and olive oils, avocados, walnuts;
  • kefir;
  • fermented foods;
  • green tea;
  • turmeric, ginger, cayenne pepper, cinnamon;
  • chia and flax seeds.

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