top of page

The Gut Microbiome-the Key to Health and Cognition, Part 1

For decades, the traditional medical community has been treating ailments and mental health as unrelated issues. However, an overwhelming amount of evidence is now showing that the microbiome in our intestinal tract regulates a tremendous amount of our body AND mind. Dysbiosis, or an imbalance in the microbiome has now been linked to a wide variety of physical and mental health conditions, behavioral disorders, and learning challenges. This two-way communication is termed the "gut-brain axis"(Chen & Chen 2021).

What IS the microbiome? According to the Harvard School of Public Health, the microbiome includes "not only bacteria but fungi, parasites, and viruses. In a healthy person, these 'bugs' coexist peacefully, with the largest numbers found in the small and large intestines but also throughout the body." (The Microbiome, 2023). The human gut is home to over 2500 microbial species and 90% come from four types.

These gut microbes or "microbiota" are involved in digestion, activation of our immune system, nutrient absorption, communication with the Central Nervous System, creation of neurotransmitters, synthesis of vitamins, regulation of the Vagus Nerve, and regulation of the entero-endocrine system.

An infant's microbiome starts with what they receive in utero. Mother's microbiome, infection, and medications taken during pregnancy all influence the baby's development. Babies are then exposed during delivery in the birth canal and through the mother’s breast milk. The fluids in the birth canal coat the baby as it passes through. What the baby is exposed to at this time completely depends on the mother's microbiome. Babies who did not deliver through the birth canal and/or did not breastfeed did not have the benefit of receiving these from their mothers and thus are likely to have gut dysbiosis from the onset.

Environmental exposure and diet can change the microbiome later. Environmental exposures include medications (particularly antibiotics), pesticides, food additives, heavy metals, chemical exposures, etc. Some studies have shown that antibiotics change the microbiota and thus lower the levels of amino acids such as tyrosine, tryptophan, and phenylalanine from which vital neurotransmitters are made (Chen, Xu & Chen, 2021; Gao et al, 2018).

Neurotransmitters are the chemical messages of the body and brain. They serve various functions and include GABA, dopamine, serotonin, acetylcholine, histamine, and others. These neurotransmitters basically help pass information from one cell to another and are necessary for everything our brain does-auditory and visual processing, speech production, memory, and executive function. The excitatory. neurotransmitters are glutamate, acetylcholine, histamine, dopamine, norepinephrine, and epinephrine. The inhibitory, or calming neurotransmitters are GABA, serotonin, and dopamine. The microbiota use these neurotransmitters to communicate with the central nervous system and they alter the synthesis and degradation of them as well.

Communication with the vagus nerve and thus the central nervous system happens in the lining of the intestinal wall, called the mucosal lining. Here, there are between 100 and 500 million NEURONS. The amount of information going from the gut to the brain is NINE TIMES the amount coming from the brain to the gut. So, having a strong mucosal lining is vital for this communication to occur. A very thin mucosal lining leads to something called "leaky gut". Now, not only can our gut not efficiently communicate with our brain via the vagus nerve, but proteins will sneak out the wall of the intestinal tract, triggering an immune response and mast cell activation.

The Vagus Nerve does not cross the intestinal wall. Rather, information is passed to it through the mucosal lining to those millions of neurons in the enteric nervous system.

If left unbalanced, gut dysbiosis can lead to diarrhea, colitis, Chron's disease, IBD/IBS, and diverticulitis, to name a few. It can also impact the blood-brain barrier and cause what is known as "leaky brain." In addition, it can cause learning problems and trigger the sympathetic nervous system (think Fight, flight or freeze ). Acetylcholine is the main neurotransmitter of the parasympathetic nervous system (think rest and digest). Depletion of acetylcholine can then result in our stress responses constantly being triggered.

If you or your loved one are struggling with attention, focus, behavior, speech, learning, mood, or motivation, it is highly likely that gut dysbiosis is highly involved.

In our next article, we will discuss how an infant's microbiome forms and its relationship to developmental delay, learning differences, and speech delay.


Ahn, J., & Hayes, R. B. (2021). Environmental Influences on the Human Microbiome and Implications for Noncommunicable Disease. Annual review of public health, 42, 277–292.

Chen, Y., Xu, J., & Chen, Y. (2021). Regulation of Neurotransmitters by the Gut Microbiota and Effects on Cognition in Neurological Disorders. Nutrients, 13(6), 2099.

Gao, K., Pi, Y., Mu, C. L., Peng, Y., Huang, Z., & Zhu, W. Y. (2018). Antibiotics-induced modulation of large intestinal microbiota altered aromatic amino acid profile and expression of neurotransmitters in the hypothalamus of piglets. Journal of neurochemistry, 146(3), 219–234.

The Microbiome (2023). TC Chan School of Public Health, Harvard University.

101 views0 comments

Recent Posts

See All


bottom of page