Microbiome fact check

What influence does the gut microbiome have on us? And how can we influence it ourselves? Maria Luisa Balmer and Melanie Scalise from the Department of Biomedical Research at the University of Bern and the University Hospital Bern provide information.

The microbiome comprises all bacteria and other microorganisms in the gastrointestinal tract and is also called intestinal flora. It is often attributed great importance in public discourse, in the media or in product advertising. But what does science know about the microbiome? How does it influence us: our health, our mood and our decisions?

uniAKTUELL: What did you have for lunch today?

Maria Luisa Balmer: I had a Singaporean dish in the canteen with noodles, prawns and vegetables.

Melanie Scalise: I chose something simpler, I had a sandwich with "Poulet Lyoner".

Did you make this choice or did your microbiome?

Scalise: I definitely did – it was cheaper. (laughs)

Balmer: In the canteen, I like to have something that I don't cook myself at home. The other menu was spaghetti bolognese and I often cook that at home.

Can the microbiome influence our decisions at all? If so: how?

Scalise: On the one hand, it is known that some intestinal bacteria can produce certain metabolic products that have direct effects on the brain. These include, for example, the neurotransmitter serotonin – the so-called happiness hormone, which can have a positive effect on our mood. We know from everyday life how a good mood can influence our decisions: we tend to make optimistic decisions and are more willing to take risks than when our mood is bad. On the other hand, certain bacterial metabolites and bacterial components can have an indirect influence.

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Scalise: Bacterial components that – especially in the case of a disturbed microbiome – repeatedly enter the bloodstream from the intestine can chronically activate our immune system at a low level. This condition favours depression, anxiety disorders, Parkinson's and Alzheimer's, among others. These diseases can in turn affect our decisions or our ability to make decisions.

Are there any other notable influences of the microbiome on our decisions?

Balmer: The microbiome can also trigger the release of appetite-regulating messenger substances – such as the GLP-1 hormone, which is currently often the subject of discussion because it is used in drugs for weight reduction.

About the person

Maria Luisa Balmer

is an assistant professor at the University of Bern and the University Clinic of Diabetology, Endocrinology, Nutritional Medicine and Metabolism (UDEM) at Inselspital, University Hospital Bern. She and her team are researching new methods to study the complex interaction between intestinal flora, metabolism and immune function to understand how these factors contribute to the development of obesity and diabetes. She received this year's Marie Heim-Vögtlin Prize for her achievements.

So the microbiome can influence whether I choose to eat something or not. In other words: it can help you lose weight?

Balmer: Yes, you could say that. Besides the direct influence via messenger substances such as GLP-1, it also has an indirect effect: If we eat a lot of fibre-rich foods such as fruits and vegetables, intestinal bacteria can use these fibres as "food" and in the process produce beneficial metabolic products that regulate our digestion and help us lose weight.

How can we influence the microbiome?

Balmer: There are many factors that influence the microbiome, such as diet or hygiene standards. Genetics also plays a role. The strongest effect is probably antibiotics. For example, it has been shown that treatments with broad-spectrum antibiotics can cause a permanent collapse in the diversity of organisms in the microbiome. This in turn can have a negative effect on our digestion, hormone balance or immune system.

Scalise: Some studies have also shown that the microbiome recovers but does not function the same as before. In children whose microbiome is still developing, the effects of antibiotics are even more serious.

“In children whose microbiome is still developing, the effects of antibiotics are even more serious”

Melanie Scalise

But sometimes antibiotics are indispensable. How can the microbiome be rebuilt?

Balmer: On the one hand, we are passively colonised again and again by our environment. But you can also replenish the microbiome through a balanced diet. This means eating lots of fruits and vegetables that are rich in fibre and roughage. Even if the diversity does not reach the previous state, the existing microbiome can be "trained" to perform functions that were previously taken over by other microbes. In serious cases – such as severe intestinal inflammation – targeted therapies are also available, for example "fecal microbiota transplantation", in which microbial cultures are inserted directly into the intestine via a tube.

About the person

Melanie Scalise

is a PhD student of Maria Luisa Balmer at the University Department of Diabetology, Endocrinology, Nutritional Medicine and Metabolism (UDEM) at Inselspital, University Hospital Bern.

The dietary route takes time, the transplantation is unpleasant. Is there not an easier way, for example with a "microbiome pill"?

Balmer: Unfortunately, we are still far away from such a pill, because we still do not know in detail how a healthy microbiome should be composed. Which bacteria and, above all, which bacterial functions are important, and is this the same for every individual? Even with our most modern methods, we often only measure stool samples, as these are the easiest to collect. But what happens in the whole gastrointestinal tract is still a big black box.

“To this day, we basically do not know exactly how a healthy microbiome should be composed.”

Maria Luisa Balmer

What about the much-publicised probiotics?

Balmer: I think the concept of probiotics – taking viable microorganisms – is basically strong. However, there is currently no good scientific evidence to support the widespread use of probiotics developed to date. However, there is scientifically supported evidence that a daily intake of about seven grams of dietary fibre – which is a prebiotic – has a beneficial effect on high blood pressure and cardiovascular disease.

How do I get seven grams of dietary fibre a day?

Balmer: That is quite doable. A slice of whole-grain bread contains about three grams, a portion of whole-grain pasta about seven grams. An apple with peel contains three grams.

“There is currently no good scientific evidence to support the widespread use of probiotics.”

Maria Luisa Balmer

What else can we look out for?

Scalise: Stress also has an effect on the microbiome through the stress hormones cortisol and adrenaline. It's well known: when you're stressed, your gut goes crazy. If you can reduce the stress, the gut also calms down again.

Balmer: Stress also has indirect effects: When you are stressed, you hastily eat a sandwich or other fast food between meals and have less time for physical activity. This in turn has a negative effect on the composition of the microbiome. Overall, however, it is often difficult to draw firm conclusions from studies.


Balmer: Usually, studies are based on correlations and observations. For example, we observe that patients with a certain disease have a different microbiome than healthy people. However, this observation does not allow any causal conclusions: we do not know what is cause and what is effect.

How do you solve this problem?

Balmer: One approach we are pursuing is animal experiments with mice that live completely sterile lives and have no microbiome. We can then specifically colonise these animals with the bacteria whose effects on certain diseases we want to investigate. This works very well for many diseases such as obesity or diabetes. In behavioural research or with mental illnesses, however, it becomes difficult, because in order for the animal to remain sterile, it has to be kept under special conditions that can also affect its development and behaviour.

Despite these uncertainties: how do you deal with microbiomes in your private life?

Balmer: Basically, I'm pretty relaxed about it. People are very robust. But if I had to break it down: eat as much variety as possible and as few highly processed foods as possible, such as crisps, frozen pizza or soft drinks. The longer and more complex the list of ingredients in a food, the more likely I am to leave it out.

“The longer and more complex the ingredient list of a food, the more likely I am to leave it out.”

Maria Luisa Balmer


Balmer: Anything that is already pre-produced gives the microbiome little to do compared to fibre that still needs to be processed. This simply did not exist in the course of our evolution, we are not used to it – at least not yet.

About the Department of Biomedical Research (DBMR)

The Department for BioMedical Research (DBMR) of the Medical Faculty of the University of Bern was founded in 1994 by the University of Bern and the Inselspital, University Hospital Bern. The DBMR is divided into 13 research programmes with around 100 participating individual laboratories and several independent research laboratories whose research spans all biomedical areas. To bridge the gap between the laboratory and the bedside, DBMR promotes clinical research with a strong emphasis on the development of translational approaches, the use of "omics" and other cutting-edge technologies, and extensive collaboration between laboratory-based and patient-oriented clinical research. The DBMR is also committed to promoting young scientists.