“The gut is the second brain”, “the brain-gut connection”. Have you come across these  terms? Possibly yes and… quite a lot. This relationship has gained a lot of focus in the  last few years. You can find such connections almost anywhere and in a similar format.  You may begin to feel accustomed to such terms, but do you understand the  relationship? 

If you are not entirely certain, this blog might help answer your questions in a simpler  format. 

What is the Gut-Brain Axis? 

It is bidirectional communication through different channels within our body with the  help of different systems. We might even say that this communication is one of the most  frequent communications within the body, mainly mediated by the microbiome. 

The Microbiome 

Microbiome refers to the single-celled organisms (microbes) living in our guts, such as  bacteria, and fungi. In a healthy adult, good microbes are superior in number to harmful  microbes. These organisms help food digestion, the functioning of the gut, and more. 

But How? 

Currently, the dynamics of how the gut and the microbiome affect the brain have not  unfolded completely. However, thanks to the increased attention diverted to this area of  research, there is an increased number of published papers each year. Based on recent  research, the gut and its microbiomes exert their effects together mainly through four  pathways, which are : 

1. Neurological Pathway

2. Endocrine Pathway, 

3. Metabolic Pathway 

4. Immune Pathway 

1. Neurological Pathway 

This communication channel happens through the nervous system and its related  components. In neural communication, the gut microbiome communicates with neural  cells that directly reach the brain. One of these nerves is the Vagus Nerve, responsible  for digestion, heart rate, and calming the body. When it is actively working, it allows  messages to be sent to the brain. Neurotransmitters enable the messages to be  delivered when used or activated; just like sending a message through the phone via  the ‘send’ button. Moreover, the gut microbiome also affects the nerve messages within  the gut itself.   

2. Endocrine Pathway 

This is the line of communication regarding hormonal activity and its feedback. So, how  does the gut affect the brain through this channel? Essentially, the microbiome has the  power to modify the availability of nutritional molecules. Depending on the bacteria’s  effect, this can activate certain mood hormones in the brain. For instance, this  microbiome can lead to increased availability of a molecule that can cause stress  hormones like corticosteroids from the brain. As a result of that activity, the person starts  to experience stress physically, mentally, or both. 

3. Metabolic Pathway 

The Metabolic Pathway is the pathway for chemical molecules that emerge as a result of  enzymic or digestive reactions. Here, chemical molecules are equal to the components  that remain from bacteria after they help food digestion. Those components are  called metabolites and are related to how the guts affect the brain. Among the 

metabolites, there are two important bacteria metabolites in the gut: short-chain fatty  acids (SCFA) and lipopolysaccharide (LPS). These are produced in the gut, by the  microbiome during food digestion. 


This helps protect the brain from inflammation and behaves as a brain hormone  (influencing our mood). SCFA can enter through the brain-blood barrier; a tissue  acting as a gatekeeper to protect the brain against any harmful particles. When  SCFAs enter into brain area, they act like the white blood cells in our body, by  destroying damaging materials. This protects the brain against developing brain  diseases like Alzheimer’s. Moreover, it regulates the production of serotonin i.e  the happiness hormone in the gut, where 95% of it is produced. 


Unlike SCFA, this damages the gut line, and consequently the brain. It can leak  into the body’s blood system, resulting in the production of antibodies to fight it.  Producing antibodies means having a special force of police aiming to catch one  specific person. This issue mentioned is also known as a leaky gut syndrome.  Studies also show that people with depression have a higher likelihood of an  increase in antibodies against LPS. 

4. Immune Pathway 

The Immune Pathway incorporates the communication between cells, tissues, and  organs like white blood cells and tonsils, against pathogens, and infections. The gut  microbiota is one of the parts of the system which influences inflammation metabolism  within the GI tract. For instance, in IBS, an unhealthy microbiome causes an immune  reaction in the gut tissue, causing activation of painful feelings in the guts. This impairs  the regulation of the intestines in people with IBS.

Tips For You 

1. Do something to release your stress 

2. Add probiotics and prebiotics to your diet 

3. Prefer unprocessed and healthy meals and snacks over junk and unhealthy foods 4. Do not use unnecessary medications unless prescribed by your doctor 

Thus, the gut affects the brain either positively or negatively through the help of the  microbiome (and the four main pathways). Which depends on how well you take care of  gut health. 

If you think that you can benefit from professional support on this issue you can reach  here.  

Eda Hayrula is an intern working under Willingness with a bachelor’s degree in  Psychology. Her interests in Psychology are gastrointestinal disorders, coping with stress,  psychosomatic disorders, and trauma.


Appleton J. (2018). The Gut-Brain Axis: Influence of Microbiota on Mood and Mental  Health. Integrative medicine (Encinitas, Calif.), 17(4), 28–32.  

The microbiome. The Nutrition Source. (2022, July 25). Retrieved August 5, 2022, from  https://www.hsph.harvard.edu/nutritionsource/microbiome/ #:~:text=The%20microbiome%20consists%20of%20microbes,symbiotic%20micro biota%20coexist%20without%20problems.  

Chakrabarti, A., Geurts, L., Hoyles, L., Iozzo, P., Kraneveld, A. D., La Fata, G., Miani, M.,  Patterson, E., Pot, B., Shortt, C., & Vauzour, D. (2022). The microbiota-gut-brain axis:  pathways to better brain health. Perspectives on what we know, what we need to  investigate and how to put knowledge into practice. Cellular and molecular life  sciences : CMLS, 79(2), 80. https://doi.org/10.1007/s00018-021-04060-w