You’ve probably heard that gut microflora plays an important role in maintaining comfortable digestion, strong immune defenses, and healthy and beautiful skin. However, few people know that beneficial bacteria can regulate nervous system function and support mental health, and that an imbalance in the microbiota can lead to the development of anxiety-depressive disorders and neurodegenerative pathologies.
The connection between the brain and the gut
Scientists have long known that our gut and brain “talk” to each other. And relatively recently it has become known that a third party – the gut microbiota – is involved in this “conversation”. This trio makes up the microbiota-gut-brain axis.
The gut contains a diverse group of microorganisms. These are predominantly bacteria, but also fungi and viruses. The community of microbes is called the microbiota. The set of genes of these microbes constitutes the microbiome.
We start collecting our own “collection” of microbes during childbirth or even in the womb. After birth, we “save” microbes from food and the environment. The microflora makes up a significant part of our body. There is approximately one microbe for every human cell. The vast majority of bacteria are found in the colon. But they also inhabit the skin, eyes, and other parts of the body.
We and our gut microbiota can live in a mutually beneficial relationship. While in the colon, bacteria eat fiber and other digestive debris. In turn, they can keep our mind and body healthy. After all, the gut microbiota interacts with the brain and the intestinal (enteric) nervous system.
How exactly does the brain “talk” to the gut?
Scientists have identified several different ways in which this communication works.
When microbes release neurotransmitters, they send messages to the intestinal nervous system and those messages reach the brain through the bloodstream.

Another important communication pathway is through the vagus nerve. It starts at the base of the neck and extends to the abdomen, connecting to the intestines and other organs.
Technically, we have two vagus nerves – one on each side of the body. They carry messages from the gut to the brain and vice versa.
So, brain to gut messages sent via the vagus nerve control the release of stomach acid and digestive enzymes. They also help regulate inflammation levels, appetite and the body’s response to stress.
The messages carried by the vagus nerve are largely dependent on the microbiota. When microbes release neurotransmitters and short-chain fatty acids, they can activate the vagus nerve.
If the microbiota is diverse and includes more “good” microbes, there will be better messaging between the gut and the brain. But when gut bacteria are out of balance, that communication changes out of whack. And it’s very likely that mental health problems, brain and gut dysfunction can develop.
Consequences of microbiota imbalance
Microbiota imbalance, or dysbiosis, occurs when harmful bacteria outnumber beneficial bacteria, which can lead to inflammation and oxidative stress, exacerbating chronic diseases.
- Mental Health:
It was previously thought that mental health problems, such as depression and anxiety, were only related to imbalances in the brain. However, new research suggests that gut dysbiosis may be a major cause. For example, butyric acid (butyrate) deficiency increases inflammation, which can lead to depression and other mental disorders. Also, increased intestinal permeability (leaky gut syndrome) has been linked to poor mental health.
- Neurodegenerative diseases:
Gut dysbiosis can impair memory and increase the risk of Alzheimer’s and Parkinson’s diseases. Research shows that some gut microbes may improve brain function, while an excess of others promotes inflammation and protein buildup, leading to the development of neurodegenerative diseases.
- Insomnia:
Disruption of the microbiota-gut-brain axis is linked to insomnia, which increases the risk of emotional disorders such as anxiety and depression. Research suggests that restoring a healthy microbiota may help combat these issues, although more research is needed.

What disrupts the connection between the microbiota and the brain
Many factors can affect the connection between the microbiota and the brain, including:
- Heavy metals – Toxic substances, such as those in pollutants and amalgam fillings, can damage cells and mitochondria, disrupting the microflora.
- Glyphosate and pesticides – These substances, such as glyphosate, can kill beneficial gut bacteria, contributing to dysbiosis.
- Parasites – Protozoan parasites and helminths can alter the microbiota and cause inflammation or increased intestinal permeability.
- Viruses – Viruses can cause inflammatory bowel disease and contribute to brain diseases such as Alzheimer’s.
- Diet – Lack of fiber and high sugar foods disrupt the microbiota, increasing the risk of dysbiosis and “leaky gut.”
- Antibiotics and medications – Antibiotic use destroys beneficial bacteria, allowing harmful microbes to multiply rapidly, worsening the microflora.
- Chemicals – Toxic substances from food and the environment can damage the gut, increasing inflammation.
- Stress – Emotional and physical stress disrupts the balance of the microbiota, which can affect digestion and nutrient absorption.
Disrupted communication between the gut and the brain makes it difficult for the body’s organs and systems to function, affecting physical and mental health.
Food and mood: how to eat to feel well
Diet is one of the key factors that determine the composition of the gut microbiota. Diet affects the bacterial community in the gut for both better and worse.
Western Diet – A diet rich in fatty and sugary foods is associated with an increased risk of depression, obesity and cardiovascular problems
Certain eating styles are consistently associated with improved mood and cognitive performance.

For example, the Mediterranean diet, which is rich in complex carbohydrates, that is, plant fiber – fruits, vegetables, legumes, nuts and seeds (chia, flax). This style of eating shows potential in treating depression and protecting against neurodegenerative diseases.
The above foods are prebiotic, meaning they promote the growth of beneficial bacteria and help increase the diversity of microflora and promote overall gut health.
In addition, prebiotic fiber rich foods include:
- chicory root
- topinambour
- ginger
- asparagus
- bananas
- onion
When we eat complex carbohydrates, the enzymes in our body do little to break them down, so they enter the large intestine undigested.
Conclusion
The gut microbiota has a significant impact on our mental and physical health, interacting with the brain through complex mechanisms. The balance of the microflora plays an important role in maintaining a normal psycho-emotional state, and its imbalance can lead to depression, anxiety and neurodegenerative diseases. The most important factors affecting the microbiota are diet, stress, medications and environment.
A proper diet rich in fiber and prebiotics can improve microbiota composition and support gut and brain health. The Mediterranean diet, with its wealth of plant foods, is one of the most effective approaches for maintaining mental health and preventing neurodegenerative diseases.