The Gut as Our Second Brain? How the Gut Microbiota Affects Mental Health

The intestines are sometimes referred to as the “second brain” because they contain the enteric nervous system, an extensive network of neurons located within the walls of the digestive tract. This system regulates intestinal movements, the secretion of digestive substances, and blood flow, among other functions. Many of these processes can occur independently of direct instructions from the brain. However, the term “second brain” is a metaphor. The intestines do not possess consciousness or the ability to think, but they have their own nervous system that works together with the central nervous system.

Communication between the gut and the brain takes place through the gut-brain axis. This involves neural connections, hormonal signals, immune responses, and substances produced during metabolic processes. The vagus nerve plays an important role in transmitting information between internal organs and the brain. Communication occurs in both directions. Mental health can influence digestive function, while signals originating in the gut participate in regulating processes throughout the body.

Many people experience this connection in everyday life. Before an important examination, job interview, or public presentation, abdominal cramps, nausea, or a sudden urge to use the bathroom may occur. Stress affects intestinal motility and sensitivity to stimuli. This relationship can be particularly pronounced in people with chronic gastrointestinal symptoms. Pain, bloating, and changes in bowel habits can, in turn, increase psychological distress, interfere with daily functioning, and worsen anxiety.

Research on the gut-brain axis has focused considerable attention on the gut microbiota. This is the community of microorganisms inhabiting the digestive tract, consisting primarily of bacteria but also viruses, fungi, and other microbes. These microorganisms help break down dietary components, produce various substances, and regulate immune responses. The composition of the microbiota varies between individuals and changes in response to diet, age, medications, previous illnesses, and many other factors.

Gut bacteria produce short-chain fatty acids, including butyrate, which is an important energy source for intestinal epithelial cells. They also participate in the metabolism of tryptophan, an amino acid used by the body to produce serotonin. Research suggests that microbial metabolites may influence intestinal barrier function, immune responses, and processes involved in communication between the gut and the nervous system. The significance of these mechanisms in the development of mental disorders remains under investigation.

There are particularly widespread misconceptions about serotonin, often referred to as the “happiness hormone.” It is estimated that approximately 90% of the serotonin in the body is produced in the digestive tract, mainly by enterochromaffin cells in the intestinal mucosa. However, this does not mean that serotonin produced in the intestines directly improves mood. Serotonin does not freely cross the blood-brain barrier, and the serotonin involved in neurotransmission in the brain is produced locally. Therefore, the claim that increasing intestinal serotonin automatically improves psychological well-being is incorrect.

Could the composition of the microbiota be associated with depression? Observational studies have identified differences between the gut microbiota of people with depression and those without the condition. These differences involve, among other things, the presence of certain bacterial groups and metabolic processes occurring in the intestines. However, no single characteristic microbiota profile has been established that could be used to diagnose depression. It also remains unclear to what extent the observed changes contribute to the development of the disorder and to what extent they are its consequences. Depression can affect appetite, diet, sleep, physical activity, and medication use, all of which can alter the intestinal environment.

Similar relationships are being investigated in anxiety disorders. Animal experiments have shown that changes in the microbiota can influence stress-related behaviors. In humans, the findings are less conclusive. Chronic anxiety has complex underlying causes, and its development depends on interactions between biological, psychological, and environmental factors. At present, it cannot be concluded that disturbances in the microbiota independently cause anxiety disorders.

The relationship between the gut and mental health is particularly evident in patients with irritable bowel syndrome (IBS). This condition belongs to the group of disorders of gut-brain interaction. It is characterized by recurrent abdominal pain associated with changes in bowel movement frequency or stool consistency. Some patients also experience anxiety or depressive disorders, while stress can aggravate gastrointestinal symptoms. Treatment of IBS may therefore involve several approaches, including dietary modifications, pharmacotherapy, and appropriately selected psychological interventions. One method with demonstrated effectiveness is gut-directed cognitive behavioral therapy.

Growing interest in the microbiota has led to research into psychobiotics. This term refers to interventions targeting the microbiota that may have beneficial effects on psychological functioning. Researchers most frequently investigate probiotics, which are live microorganisms that provide documented health benefits when administered in adequate amounts. Scientists are examining whether selected bacterial strains can support depression treatment, reduce anxiety symptoms, or influence the body’s response to stress.

Clinical trial findings have been mixed. Some studies have observed reductions in depressive symptoms following the use of specific probiotic preparations, particularly as an adjunct to antidepressant treatment. Other studies have found no significant differences compared with placebo. Interpreting these findings is challenging because studies differ in the bacterial strains used, dosages, duration of supplementation, and participants’ health conditions. It cannot be assumed that every probiotic available at a pharmacy will have a similar effect on psychological well-being.

The Canadian Network for Mood and Anxiety Treatments (CANMAT), an organization that develops treatment recommendations for mood and anxiety disorders, has evaluated the available research on microbiota-targeted interventions in people with depression. According to its recommendations, probiotics may be cautiously considered as a third-line adjunctive treatment, particularly for patients who have responded inadequately to antidepressant medications. However, the authors emphasize the limitations of the available evidence and the lack of justification for routinely recommending probiotics to everyone with depression. There is also insufficient evidence to support prebiotics, synbiotics, or fecal microbiota transplantation as standard treatments for depression.

Can improving dietary habits have a positive impact on mental health? Research suggests that a properly balanced diet may support depression treatment and improve overall well-being. The Mediterranean diet has attracted particular attention because it is rich in vegetables, fruits, whole grains, legumes, nuts, olive oil, and fish. This dietary pattern provides fiber and nutrients necessary for proper bodily functioning. It may also benefit the intestinal environment, although it remains unclear how much of the observed mental health benefits can be directly attributed to changes in the microbiota.

Fermented foods such as kefir, natural yogurt, and fermented vegetables can also be included in the daily diet. Some contain live microorganisms, but fermentation alone does not mean that a product has scientifically established probiotic effects. The same applies to supplements. Preparations differ in their composition and properties, and research findings concerning one bacterial strain cannot necessarily be applied to others. Probiotics are generally well tolerated by most healthy individuals, but particular caution is required in patients with severe immune system disorders or serious illnesses.

Medications, particularly antibiotics, can also influence the composition of the microbiota. Their use sometimes leads to substantial changes in intestinal bacterial populations, which may persist after treatment has ended. However, this does not mean that antibiotics automatically cause depression or anxiety disorders. In bacterial infections requiring treatment, the benefits of appropriately selected antibiotic therapy usually outweigh the associated risks. Changes in the microbiota are not a reason to discontinue medications prescribed by a doctor without medical advice.

The growing popularity of this topic has led to the introduction of commercial gut microbiota tests marketed as a way to identify the causes of mental health problems. However, there is currently no clinically validated microbiota test capable of diagnosing depression or anxiety disorders or determining the appropriate psychiatric medication. Nor has a single ideal microbiota composition common to all healthy individuals been established. Interpreting the results of such tests without adequate scientific evidence may lead to unnecessary supplementation, restrictive diets, and expenses that provide no proven health benefits.

Does health begin in the gut? Proper digestive function is important for the entire body, and microbiota research demonstrates how complex its connections with the nervous system are. However, there is no scientific basis for attributing depression or anxiety disorders exclusively to gut health. Mental health depends on numerous interconnected factors, and the microbiota is one area that may contribute to the development of new treatments in the future.

Supporting gut health through a varied diet, adequate fiber intake, regular physical activity, and sufficient sleep is a sensible part of preventive healthcare. People with chronic gastrointestinal symptoms should receive appropriate diagnostic evaluation and treatment, particularly when these symptoms are accompanied by anxiety, low mood, or impaired daily functioning. For depression and anxiety disorders, treatments with established effectiveness, including psychotherapy and appropriately selected pharmacotherapy, remain the foundation of care. Interest in the gut-brain axis is scientifically justified, but many promising discoveries still require confirmation in clinical trials.

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