How the Gut Microbiome Affects our Brain

How the Gut Microbiome affects our Brain

What is Gut Microbiome?

Gut Microbiome copy

Considering the gut microbiome is the big topic in health and science recently, you may know that not all microbes are bad for us. While there are definitely pathogenic microbes like Staphylococcus aureus that causes food poisoning, at all times there are around 500 to 1000 different species of bacteria living in the human body. In fact, there are more bacterial cells in our body than human cells. The importance of their function is becoming more apparent as we learn new things about them.

In recent years, we have increasingly understood the contribution made by the gut microbiome not only in the regulation of host physiology, particularly metabolism and immunity, but also the Central Nervous System (CNS) and brain function. However, it’s hard to picture how tiny microbes in our gut, can contribute to our day to day cognition, health and well-being.


Brain Health

Brain HealthIt is estimated that 90% of our Serotonin is produced in the gut by microbes.1 Serotonin is an antidepressant neurotransmitter that helps with sleeping, eating, and digesting. Furthermore, Lactobacillus and Bifidobacterium, often found in probiotics supplements or food, produce Gamma-Aminobutyric Acid (GABA) – our chief inhibitory neurotransmitter.2 GABA helps inhibit or reduce the activity of the neurons or nerve cells and the dysfunction of GABA modulation has been found to lead to anxiety disorders.

So, we basically have this huge mass of little drug factories sitting in our gut, pumping out different substances that affect the brain. In fact, the gut and its microbes appear to affect the brain so much, that preclinical research in rodents suggested that certain probiotics have antidepressant and antianxiety effects. The study shows that the probiotic Bifidobacterium infantis had anti-depressant effect on par with that of the anti-depressant drug, Citalopram.3

The Good Gut

Scientists have observed that microbe-free mice living in sterile bubbles have a personality that is distinct from mice with gut microbes. Microbe-free mice were found to be more prone to taking risks and freely explore their environment. Risk taking might be good if you’re a young entrepreneur, but this kind of risks these mice engage in is only an excellent strategy for quickly getting killed by a predator. Not only are the mice unusually reckless, scientists also noted that these microbe-free mice have memory related defects. In the book, “The Good Gut” by Justin and Erica Sonnenburg, it describes how researchers put normal and microbe-free mice through some memory tests. It seems that microbe-free mice tend to forget things they saw just 20 minutes earlier. The forgetfulness in these microbe-free mice may be explained by a lower level of BDNF (Brain Derived Neurotrophic Factor). BDNF is a powerful protein, important for learning and memory. It stimulates the production of new brain cells and strengthens existing ones. Low levels of BDNF are also linked to depression and anxiety. 4,5

ConclusionMissing Microbes

In between 2010 and 2015, about 3600 related articles have been published on the topic of gut microbiome. At this point, saying the gut microbiome is important to health is an understatement. As Dr. Martin J. Blaser, MD, author of the book “Missing Microbes” put it, “losing your entire microbiome outright would be nearly as bad as losing your kidneys or liver”.

Unlike the kidneys or liver however, you can change the makeup of your microbiome with what you put into your mouth. I guess Hippocrates knew what he was talking about when he said, “All disease begins in the gut” and “Let food be thy medicine…”





  1. Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P, Ma L, et al. Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis [Internet]. Cell. U.S. National Library of Medicine; 2015 [cited 2018Aug21]. Available from:
  2. Yunes RA, Poluektova EU, Dyachkova MS, Klimina KM, Kovtun AS, Averina OV, et al. GABA production and structure of gadB/gadC genes in Lactobacillus and Bifidobacterium strains from human microbiota. [Internet]. Advances in pediatrics. U.S. National Library of Medicine; 2016 [cited 2018Aug21]. Available from:
  3. Desbonnet L, Garrett L, Clarke G, Kiely B, Cryan JF, Dinan TG. Effects of the probiotic Bifidobacterium infantis in the maternal separation model of depression. [Internet]. Advances in pediatrics. U.S. National Library of Medicine; 2010 [cited 2018Aug21]. Available from:
  4. Rogers GB, Keating DJ, Young RL, Wong M-L, Licinio J, Wesselingh S. From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways [Internet]. Advances in pediatrics. U.S. National Library of Medicine; 2016 [cited 2018Aug21]. Available from:
  5. Jiang H, Ling Z, Zhang Y, Mao H, Ma Z, Yin Y, et al. Altered fecal microbiota composition in patients with major depressive disorder. [Internet]. Advances in pediatrics. U.S. National Library of Medicine; 2015 [cited 2018Aug21]. Available from:


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