The gut microbiome has become the subject of intensive research across biology, medicine and chemistry¹. As a chemist, I see it not only as a collection of microorganisms, but also as a chemical factory where hundreds of metabolic reactions take place that affect our health.
You may not have known that the bacteria in our gut can produce molecules with surprising potential for our health². Their metabolites are not just a by-product of digestion – they can affect immunity, mood, and even communication between the gut and the brain. Every piece of food that passes through our digestive tract encounters a rich population of microorganisms that convert it into thousands of different bioactive molecules. Some are neutral, while others can boost immunity, regulate inflammation, or modulate neurotransmitters. In this blog, we will look at what lies behind these processes and how they can be useful.
Bacteria in the gut take in food residues that we ourselves cannot digest and convert them into metabolites³. These are substances that can act locally on the intestinal mucosa or enter the bloodstream and affect other organs. These include indoles, phenols, and short-chain fatty acids (SCFAs), which affect the immune system, metabolism, and even brain function.
Interestingly, some of these metabolites even have neuroactive properties and can modulate the serotonin system, which is key to mood, appetite and even sleep. One such example is indole, which is produced by the breakdown of tryptophan (an amino acid commonly found in proteins) and is involved in the regulation of neurotransmitters and the gut-brain axis. Phenols produced from plant fibre can also influence oxidative stress and inflammatory pathways.
A study published in Nature Reviews Gastroenterology & Hepatology (2017) showed that the production of these metabolites is directly dependent on the composition of the microbiota and diet, and that their effect on the host can be surprisingly strong⁴.
Intestinal metabolites act as silent messengers between the gut and the brain, influencing the nervous system, hormonal signals and even blood circulation. Short-chain fatty acids (SCFAs), indoles, and phenols act on the nervous system and modulate neurotransmitters that shape our mood, attention, and cognitive functions.
Interestingly, a simple change in diet can immediately alter the chemical “dialogue” between the gut and the brain. Foods rich in fibre, such as whole grains, beans, lentils, fruits and vegetables, promote SCFA production. Polyphenols from berries, chocolate or green tea increase phenol production. Tryptophan found in nuts, seeds and eggs promotes the formation of indoles. Clinical studies (Journal of Clinical Investigation, 2016) show that such a diet can improve mood and is associated with lower levels of anxiety and depression⁵.
Did you know that some bacteria can directly influence mood and behaviour? These microorganisms are referred to as psychobiotics. Their action is linked to the production of neurotransmitters and metabolites that enter the bloodstream or communicate via the vagus nerve, the main link between the gut and the brain.
For example, Lactobacillus rhamnosus increased levels of GABA, a neurotransmitter associated with calmness and reduced anxiety, in experiments on mice. In humans, clinical studies show that regular consumption of fermented foods such as yoghurt, kefir, kimchi and sauerkraut can promote similar effects⁴.
The effect of these bacteria may not be immediate. Changes in the microbiome occur gradually, and therefore improvements in mood and cognitive function tend to be gradual as well. This concept shows how sophisticated and interconnected our organism is – the gut and brain communicate constantly, even if we are not aware of it. Taking care of the gut microbiome is not just a trend, but actually has an impact on mental and cognitive health.
When we look at the microbiome through the lens of metabolite chemistry, a whole new world opens up before us. It is not just about which bacteria live in our gut, but rather about their product, the molecules that are produced as a result of their activity. The metabolites of the gut microflora are not just chemical by-products. They are active molecules that affect our health, immunity and even our brain. Understanding their formation and mechanisms of action allows us to make informed decisions about diet and supplements. The right microbiota and a suitable diet can be extremely effective tools for promoting health.
Ing. Mária Zajičková, PhD.
organic chemist, science populariser
1. Agus, A., Planchais, J., & Sokol, H. (2018). Gut microbiota regulation of tryptophan metabolism in health and disease. Nature Microbiology, 3, 1–10.
