The connection between the microbiome and depression

The condition of the intestinal microflora directly affects the nervous system and our behavior. How is it possible? We will explain all the details in the following article.

The connection between the microbiome and depression

Last update: November 17, 2022

More and more studies are showing how closely the gut and the emotional world are connected. The microbiome affects mental health and when it’s out of balance, certain abnormalities can promote depression. Today we invite you to learn more about this very interesting topic.

The enteric nervous system (ENS) in the gut, which is also known as the “gut brain”, controls various neurotransmitters such as serotonin or norepinephrine, among others. Up to 95% of the happy hormone serotonin is made in the gut.

The microbiome: what is it?

The term “microbiome” (also microbiota or formerly gut flora) describes all the microorganisms in the body, with the majority of these bacteria found in the gastrointestinal tract. We are talking about 100 trillion microorganisms, including more than 400 species of bacteria, fungi, viruses, protozoa and other microbes. Microorganisms in the intestine perform extremely important functions, among others the following:

  • digestion and absorption of nutrients
  • Synthesis of vitamins K, B5, B8 (biotin) and B9 (folic acid)
  • Absorption of iron, calcium and magnesium in the intestine
  • Synthesis of short-chain fatty acids (SCFA)
  • Neuroendocrine regulation (gut-brain axis)
  • modulation of the immune system
  • Energy-homeostasis
  • Barrier function against pathogens
  • Synthesis of neurotransmitters
  • regulation of intestinal transit

The microbiome and depression: what’s the connection?

Various studies suggest this communication between the microbiome and the brain is two-way. The nervous, endocrine and immune systems are involved in this communication.

Microorganisms in the intestine produce substances that can pass through the intestinal epithelium into the blood, through the blood-brain barrier and into the brain. The opposite process also takes place: the nervous system acts on the intestinal bacteria and modulates them.

For example, we know that until 95% of serotonin is produced in the gut. This neurotransmitter is essential for mood regulation. Other important players in gut-brain communication are short-chain fatty acids (acetate, propionate, and butyrate), hormones like cortisol, and neurotransmitters like GABA.

Changes in the microbiota

The microbiome can be thrown out of balance by a variety of factors, including poor diet, antibiotics, chronic stress, lack of exercise, or lack of rest. In the case of depression, certain abnormalities of an imbalanced microbiota have been observed in various studies. However, the gut and the emotional world interact, meaning that depressive states can alter the microbiome. This creates a cycle as these changes then negatively affect the emotional state of the affected person.

What to do to support a healthy microbiome?

There are many external stress-producing factors beyond our control: crises, pandemics, accidents or deaths. These are predisposing factors that can promote depression. However, we also have many ways to protect ourselves, on an emotional and physical level. The following factors are particularly important to ensure a balanced microbiome:


I generally recommend it unprocessed, anti-inflammatory foods, such as vegetables (chard, purslane, basil…), nuts and seeds (almonds, sunflower seeds, pumpkin seeds…), pseudocereals (amaranth, quinoa…), fish, eggs and fresh grass-fed meat . Industrially processed foods and alcoholic and sugary drinks are not recommended.

The following foods are particularly important:

  • Fermented foods (yogurt, kefir, sauerkraut…)
  • Foods rich in polyphenols (vegetables, herbs, fruits…)
  • Foods with a high fiber content (whole grains, legumes, nuts and seeds…)

antibiotics and probiotics

Taking antibiotics disrupts the balance of gut bacteria. For this reason, probiotics are increasingly recommended when antibiotics are prescribed. Quality is important here as there are significant differences.

You should consider, among others, the following quality criteria:

  • contained bacterial strains
  • Number of bacteria (at least 109 KBE)
  • Safety (international certification GRAS status)
  • Ability to reproduce (even after therapy)
  • Stomach and bile acid resistance
  • temperature-dependent stability (the product should be stable at room temperature for as long as possible)

chronic stress

Chronic stress not only burdens the psyche, but throws the microbiome out of balance. Find ways to manage stress: Mindfulness, meditation, walks in the woods or sports can help you do this.


Exercise and sports not only reduce stress. They also favor the diversity of the bacterial world in the gut. At the same time, you prevent diseases such as colon cancer, obesity, anxiety and depression.

sleep quality

When you have trouble sleeping for a long time, many bodily functions change, including digestion. This causes long-term damage to the gut microbiome. Follow healthy sleep hygiene and healthy lifestyle habits. If you have chronic sleep disorders, you should definitely seek medical help.

The microbiome and depression: final thoughts

More and more research is showing a connection between the microbiome and depression. It is therefore important to actively improve those factors that we can influence. By building a healthy microflora, you can not only prevent mood disorders, but you can also improve your immune system and overall health.

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