Over the past decades, research on the human microbiome — the collection of microorganisms inhabiting the human body — has become one of the most rapidly developing fields in medicine. Not only gastroenterology and immunology, but also psychiatry, neurology, and endocrinology now consider the influence of the microbiota on health. Particularly significant is the connection between the gut and the brain — the so-called gut-brain axis. This area opens new horizons in understanding depression, anxiety, autism, stress, and cognitive disorders, providing additional tools for diagnosis and therapy.
Today it is clear that mental health is not only a matter of neurotransmitters and psychotherapy. It is closely linked to the state of the gut microbiota, levels of inflammation, metabolism, and immune response. The influence of the microbiome goes far beyond digestion—it affects mood, behavior, memory, and resilience to stress.
What the Microbiome Is and How It Works
The microbiome is the collection of bacteria, fungi, viruses, and other microorganisms living in the human body. The highest concentration of microbiota is found in the gut, although microbes also inhabit the skin, mucous membranes, respiratory tract, and reproductive organs.
The gut microbiome is particularly important because it:
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Participates in metabolism and produces metabolites (e.g., short-chain fatty acids, SCFAs) that nourish intestinal cells and influence systemic metabolism;
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Shapes the immune system, maintaining a balance between pro-inflammatory and anti-inflammatory processes;
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Synthesizes neurotransmitters and bioactive molecules that affect the nervous system;
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Interacts with the endocrine system, regulating stress responses and hormonal balance.
Today, the microbiome is considered a regulatory organ involved in maintaining homeostasis and the functioning of multiple body systems.
The Gut-Brain Axis: Mechanisms of Connection
The connection between the gut and the brain is not a metaphor but an objective physiological process, involving several interconnected pathways:
Neurochemical Mechanisms
Certain gut bacteria are involved in the synthesis of neurotransmitters:
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Serotonin — about 90% is produced in the digestive tract. Serotonin regulates mood, sleep, appetite, and pain perception.
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GABA (gamma-aminobutyric acid) — an inhibitory neurotransmitter that contributes to reducing anxiety.
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Dopamine — involved in motivation, reward, and cognitive function.
Immune Mechanisms
Imbalance in microbiota (dysbiosis) can increase intestinal permeability, leading to systemic inflammation. Inflammatory cytokines can cross the blood-brain barrier and alter neuron functioning, affecting mood and behavior.
Endocrine Mechanisms
The microbiota influences the hormonal stress response, regulating the hypothalamic-pituitary-adrenal (HPA) axis. Microbial imbalance can raise cortisol levels, amplifying stress responses, anxiety, and vulnerability to depression.
Metabolic Mechanisms
The microbiome participates in fat and carbohydrate metabolism, producing SCFAs that regulate energy balance and modulate inflammation. These metabolites affect neurons and brain function.
The Microbiome and Mental Disorders: Evidence and Examples
Modern research demonstrates a direct link between changes in the microbiome and various mental health conditions. The table below summarizes the key findings:
| Mental Condition | Microbiome Changes | Possible Mechanisms | Supporting Evidence |
|---|---|---|---|
| Depression | ↓ diversity, ↓ Bifidobacterium, Lactobacillus | Increased inflammation, reduced serotonin synthesis | Cross-cultural studies show correlation between dysbiosis and depression severity |
| Anxiety Disorders | Altered Firmicutes/Bacteroidetes ratio | Impaired HPA axis regulation, ↑ cortisol | Probiotics reduced anxiety in clinical studies |
| Autism | ↓ Bacteroidetes, ↑ Clostridia | Effects on metabolites influencing behavior | Microbiota transplantation in animals altered behavioral patterns |
| Schizophrenia | ↓ diversity, ↑ pro-inflammatory strains | Neuroinflammation, dopamine metabolism impact | Some antipsychotics affect microbiome composition |
| Stress | Dysbiosis, ↓ beneficial strains | HPA axis-dependent | Animal studies show correlation between microbiome and cortisol levels |
Depression and Anxiety
Most studies agree that patients with depression exhibit reduced gut microbial diversity. Beneficial bacteria such as Bifidobacterium and Lactobacillus are often present in lower numbers. These microbes are involved in neurotransmitter synthesis and maintaining an anti-inflammatory environment.
Animal experiments show that transplanting microbiota from depressed individuals into healthy animals induces anxiety- and depression-like behaviors. This suggests that microbiome changes are not merely a consequence of illness but may play a role in its development.
Autism and Behavioral Disorders
Research in autism spectrum disorders (ASD) shows specific microbiome changes in children. Dysbiosis is associated with gastrointestinal symptoms and may exacerbate behavioral and emotional difficulties. Small clinical trials indicate that modulating the microbiome with specific probiotic strains can improve behavioral measures in children with ASD.
Schizophrenia and Cognitive Impairment
Patients with schizophrenia often have reduced microbial diversity and increased pro-inflammatory bacteria. Evidence suggests that inflammation and neurotransmitter imbalance (especially dopamine) contribute to cognitive deficits and psychotic symptoms. Some antipsychotic drugs also modify microbiota, which may influence symptomatology.
Practical Approaches: Therapy and Prevention
Probiotics and Prebiotics
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Probiotics — live microorganisms that positively affect the microbiome.
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Prebiotics — dietary substances that promote growth of beneficial bacteria.
Clinical studies show that certain probiotic strains can reduce anxiety and depression, particularly in mild to moderate cases. While not a replacement for psychotherapy or medication, they represent a promising adjunct therapy.
Diet
A diet rich in fiber, vegetables, fruits, whole grains, and fermented foods promotes beneficial bacteria and reduces inflammation. The Mediterranean diet, for example, is associated with lower risk of depression and anxiety.
Antibiotics
Long-term antibiotic use can alter the microbiome and temporarily affect mental health. This factor should be considered in chronic treatment plans.
Personalized Medicine
Microbiome sequencing technology allows for individualized approaches: predicting mental health risks, selecting diet or probiotic interventions, and integrating data into treatment plans.
Future Directions
Microbiome science is rapidly evolving. Key research areas include:
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Identifying specific strains that influence stress and mood.
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Studying the role of viruses and fungi, not only bacteria.
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Understanding microbiome effects on neuroplasticity and cognition.
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Conducting long-term clinical trials on probiotics for mental disorder prevention.
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Investigating the impact of early-life nutrition (breastfeeding, complementary feeding) on microbiome development and future mental health.
The microbiome is not a peripheral factor but a central component of the complex biological system linked to brain function and mental well-being.
Key Takeaways
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The microbiome affects mental health via neurochemical, immune, and endocrine pathways.
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Microbiome alterations are linked to depression, anxiety, autism, schizophrenia, and stress.
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Probiotics, prebiotics, and diet can improve mental state as adjuncts to therapy.
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Personalized microbiome analysis opens opportunities for individualized mental health care.
Conclusion
The microbiome is a key factor in human mental health. The gut-brain axis demonstrates that diet, microbiota, and immune function are directly connected to emotional and cognitive states. Microbiome modulation using probiotics, prebiotics, and dietary strategies represents a promising complement to traditional therapy. Ongoing research promises new individualized approaches for diagnosing and supporting mental health, making medicine more personalized and scientifically grounded.
