In this post I try to explain the microbiome and the microbiota. I try to show what it is and why the gut microbiome is important for us. Does it make sense to test and build up your intestinal flora? At the end I describe how you can positively influence the intestinal microbiome, the so-called intestinal flora, in order to avoid dysbiosis. Without dietary supplements, completely natural. Even with intolerances.

Our body: a zoo for microorganisms

Various microorganisms colonize our body. Especially our surfaces that are exposed to the environment are colonized by bacteria, viruses, protozoa, mites* or fungi. These include our skin, the respiratory tract and the gastrointestinal tract. The so-called co-evolution, i.e. the joint evolution of us and the microorganisms that belong to it, has led to this microbial zoo having a wide range of effects on all possible aspects of our biological functions.

Functions of microorganisms

The entirety of all microorganisms that live on and in us, i.e. all bacteria, fungi, viruses and the like, is called the microbiota. The entirety of their genes is called the microbiome. In the past, for example, all bacteria living in the gut were simply called “gut flora”. Today, this is correctly called the “gut microbiome” because we now know that there is more than “just” bacteria there.

The microbiota is therefore the totality of living organisms in an environment (e.g. in the gut), the microbiome is the totality of their genes (e.g. the gut microbiome).

The functions of the microbiota for our well-being are far-reaching. For example, they serve to protect us from local infections. On the one hand, this happens through competition for colonization sites, the direct production of inhibitors or the shortage of nutrients that would be needed by pathogenic microorganisms. But the microbes also ensure that the immune system is prepared for an attack by “bad” microorganisms. So if we come into contact with a “bad” bacterium, it has no chance of colonizing us and making us ill. Incidentally, this happens every day. We constantly come into contact with small amounts of pathogenic germs. On the subway, at your desk, putting on your shoes. Everywhere. But we are well protected.

The microbes affect not only their local environment, but also distant tissues in the body. These superficial microorganisms therefore have an effect throughout the human body. These “good” microorganisms therefore play an essential role in protecting us from infections, in shaping and regulating immune responses and in maintaining our immune homeostasis.

A healthy intestinal microbiome provides nutrients for the intestinal cells, prevents the invasion of pathogenic germs, strengthens the intestinal barrier function, modulates the immune system and is involved in the synthesis of various vitamins and hormonally active messenger substances. It helps us to survive.

Dysbiosis: When the balance gets confused

However, if there is an imbalance or disruption of this protective microbial shield, we call this dysbiosis. Pathogenic germs therefore have a greater chance of surviving and multiplying. This can happen, even with an intact protective shield, due to an overpowering of pathogenic germs. This is how classic bacterial gastroenteritis spreads. The weaker the protective shield, the fewer pathogenic germs we need to get sick. Therefore, you should not disinfect household surfaces such as kitchen worktops or desks, as this only creates space for pathogenic germs. It would be better to use cleaning agents that contain “good” germs and spread them on the surfaces. This is called “effective microorganisms”.

Dysbiosis in the gut

Many people have the same image in their minds when they think about building up their intestinal flora. But it’s not that simple and the gut is not a desk.

Dysbiosis in the gut has various effects. The intestinal bacteria ensure a balance in the intestine and ensure that pathogenic germs are suppressed. They ensure that the mucous membrane remains intact, heals well and can perform its function. They produce fatty acids that our intestinal cells use as energy and they support the immune system. A well-functioning and diverse gut microbiota is therefore very important. Diverse means that there are many different species in sufficient numbers. You can compare this with monocultures in agriculture. They are also more susceptible to diseases and other problems. We don’t want a monoculture in the gut, but a diverse microbial zoo.

Knowledge about the microbiome is increasing rapidly. Therapies to change the microbiota are currently being researched and some are already being used in clinical practice. The best working remedy to make and keep the microbial zoo diverse is very simple. It’s called a balanced diet.

Combating dysbiosis: my tips

High doses of saturated fatty acids and sugar, but consumed over a longer period of time, can lead to dysbiosis, for example. The same applies to an unbalanced diet, which is also often seen in people with intolerances. Dietary fiber, on the other hand, helps to maintain diversity. In fact, it is not necessary to take probiotics if you eat a balanced diet. And this is also possible with intolerances. You should not be afraid of dietary fibers such as inulin and oligofructose, especially if you are fructose intolerant. Some time ago I started to consciously introduce small amounts back into my diet. Initially I had a lot of flatulence, but after a few weeks this improved and today I no longer have any problems with it, my digestion is better than ever before and my mood has also improved considerably. I have summarized here what has helped me.

• I try to give preference to plant-based food. This is not always possible due to fructose intolerance, but it works well. For example, I drink oat milk in my coffee instead of lactose-free cow’s milk. My rule: If there are plant-based alternatives that are compatible, then I prefer them. For example, in the university canteen: there’s beef stew or soy strips. Then I take the soy. However, if the vegan dish is incompatible, e.g. vegetable casserole with eggplants, then I use the meat dish. If cappuccino is also available with oat milk, I take it instead of the cow’s milk version. This works quite well.
• I eat natural yogurt every day because it contains bacterial cultures. I eat soy skyr or yogurt because it has no carbohydrates and is lactose-free and fructose-free.
• I eat fewer carbohydrates and if I do, then hardly any white flours, almost only wholemeal flours. This is because the short-chain carbohydrates are a breeding ground for the “bad” bacteria.
• I hardly eat any added sugar or sweets any more. This allows me to increase the amount of vegetables I can tolerate. After all, my fructose barrel is not filled by sweets, but by vegetables.
• I eat beans! I eat about three tablespoons of beans or chickpeas in my salad two or three times a week. These plants contain fiber (prebiotics), which is food for the good bacteria. I have slowly increased this and now have no more flatulence because of it.
• I’m eating fish again… at least temporarily… I have my ethical problems with that.
• I eat very little meat, only about 400 g per week. I prefer white meat. I only eat this because I have not yet found a way to avoid eating it due to my fructose intolerance.
• Meat substitutes are usually well tolerated by people with fructose intolerance. However, as they are highly processed foods, try not to eat them too often.
• I eat different types of cheese. This is important because the mold and the bacteria in the cheese have a positive influence on the intestinal microbiome. You can diversify the bacterial zoo in your gut very easily and, above all, very tastily with various high-quality cheeses.
• I snack on a handful of peanuts (the ones with the shell, not roasted and salted), walnuts and almonds every day. They have a positive influence on the intestinal microbiome and are well tolerated. I like to sprinkle pumpkin seeds or sunflower seeds on my salad.
• Fruit: I eat 2-3 bananas a week, sometimes a mandarin orange in winter. I tried apples once but quickly regretted it… I’ll give them a miss again.

Of course, this is not a nutritional or dietary recommendation, it shows what has helped me. Perhaps it will inspire some of you to rethink your diet despite your intolerance, make it more diverse and thus positively influence your gut microbiome.

Intestinal flora analysis. A repetition

I’ ve written this many times before, so I’ll just repeat it here: intestinal flora analyses and attempts to colonize certain types of bacteria with probiotics based on their results do not make sense. There are no recognized limits for the frequency of certain microorganisms. There are also no values for diversity above which adverse health effects would be expected. The test methods are always superficial and not sufficient for a good evaluation and our microbiome tends to return to the initial situation when we stop taking probiotics.

I hope this blog article has helped you a little to understand the complex system of the gut microbiome and microbiota in the human body.

Further literature / sources

Frost, F. Introduction to the microbiome. Internal Medicine 2022, 63 (10), 1015-1021. https://doi.org/10.1007/s00108-022-01395-9.

De Waal, G. M.; De Villiers, W. J. S.; Pretorius, E. The Link Between Bacterial Inflammagens, Leaky Gut Syndrome andColorectal Cancer. CMC 2021, 28 (41), 8534-8548. https://doi.org/10.2174/0929867328666210219142737.

Massier, L.; Kovacs, P. The human “tissue” microbiome in the metabolic syndrome: on the trail of the “leaky gut” hypothesis. Obesity – causes, sequelae, therapy 2019, 13 (04), 190-196. https://doi.org/10.1055/a-0966-9694.

Hof, H.; Dörries, R. Medical Microbiology; Georg Thieme Verlag, 2014.

Mack, I. Microbiome and Inflammation in Obesity. In Handbuch Essstörungen und Adipositas; Springer Berlin Heidelberg: Berlin, Heidelberg, 2022; pp 473-479. https://doi.org/10.1007/978-3-662-63544-5_60.

Campos, S. B.; Oliveira Filho, J. G. D.; Salgaço, M. K.; Jesus, M. H. D.; Egea, M. B. Effects of Peanuts and Pistachios on Gut Microbiota and Metabolic Syndrome: A Review. Foods 2023, 12 (24), 4440. https://doi.org/10.3390/foods12244440.