The Gut-Brain Axis 


The frequent bittersweet feeling that humans experience, best described as ‘butterflies’, is a scientifically justified phenomenon, which began merely as a “gut feeling”, and is now saving countless lives.  


Microbiology, the study of all living organisms, too small to be seen with the naked eye, is in my opinion, one of the most outstanding breakthroughs in human anatomy, physiology and pathology.  


The humble human digestive tract home to over 100 trillion commensal microorganisms, is at the core of optimal human health. This magnificent coexistence and the gut-brain axis, discovered in 1960, has since rightfully evolved into one of the most fundamental aspects in determining health and disease across all human beings.  


The Digestive System: Anatomy   





Small intestines (duodenum, jejunum, ileum)  

Large intestines (cecum, colon, rectum, anus)  


Acessory organs:  





Adipose tissue (fat tissue)  


The Structure of the Digestive Tract:  


1) Mucosa layer: (inner layer) 

Mucous epithelium 

Lamina propria 

Muscularis mucosa 


2) Submucosa layer: (middle layer) 


3) Muscle layer (muscularis): (outer layer) 


Two types of GIT muscles:

Skeletal muscle and Smooth muscle 


1) Skeletal muscle (voluntary control) = swallowing & defecation (mouth, pharynx, upper oesophagus & anal sphincter). 

2) Smooth muscle (involuntary control) = the rest of the GIT. 

The smooth muscle has 2 layers: 

Inner, circular muscle 

Outer longitudinal 


The enteric nervous system: 


The human gut contains a specific nervous system known as the enteric nervous system. These nerves can be found along the entire digestive tract from the oesophagus to the anus and acts as the gut's “brain”. The network of neurons in the gut is as plentiful and complex as the network of neurons in our spinal cord (more than 100 million nerve cells). Due to this plexus of nerves humans feel their emotions in their gut, often described as a “gut feeling”.   


The Enteric Nervous System is arranged in 2 plexuses: 


1. Myenteric plexus:

A network of sympathetic and parasympathetic nerves between the circular and longitudinal muscles of the muscularis layer (controls gut motility). 

2. Submucosal plexus:

A network of sympathetic and parasympathetic nerves between the muscularis and submucosal layers (controls digestive secretions). 


The gut’s brain functions independently to the rest of the nervous system however, it is regulated by the Autonomic Nervous System (ANS).   


The Autonomic Nervous System is made up of:  


Sympathetic nerves  

Parasympathetic nerves 


Functions of the Autonomic Nervous System:  


Controls the speed at which food moves through the gut. 

Controls the secretion of acid in our stomach (HCL).  

Controls the production of mucus on the intestinal lining.  


1) PARAsympathetic Nervous System: (rest and digest) 

Increases muscular activity (gut motility) 

Increases digestive secretions  


2) SYMpathetic nervous system: (fight and flight) 

Decreases muscular activity (gut motility) 

Decreases digestive secretions 


The HPA axis and the gut:  


The HPA axis (hypothalamic-pituitary-adrenal axis), which is our internal stress response system, is another mechanism by which the brain can communicate with the gut to help control digestion through the action of hormones. 


Stress and Digestion:  


Stress triggers our sympathetic nervous system (fight or flight) and the HPA axis (high cortisol) which causes the following changes to occur:  


Increased heart rate (to increase the circulation of blood and adrenaline) 

Increased breathing rate (to increase oxygen)  

Pupil dilation (to enhance vision – especially in the dark)  

Sweat production (to regulate energy)  

Slows down non-essential functions: digestion (to conserve energy)  

Speeds up essential functions: diverts blood to the heart and skeletal muscles (to fight or flight/ run)  


Both the fight and flight response and HPA axis our vital mechanisms, which can save our lives in acute situations of immediate danger. However, civilised societies have developed so rapidly, that our current “stressors” are completely different from those of our ancestors. Our human brain has not been able to adapt and evolve at the same pace and therefore, cannot distinguish the difference between a physical threat, such as being chased by a wild animal versus modern-day perceived stress such as financial debt.  


When a person becomes chronically stressed, which means that they are in a constant state of fight and flight, due to the many stresses we have today, they may start to experience a variety of digestive complains such as pain, bloating, diarrhoea, constipation and other discomfort. 



Gut-Brain axis:  


The gut-brain axis is a bidirectional link between the central nervous system (brain and spinal cord) and the enteric nervous system (gut brain). The vagus nerve is one of the largest nerves in the human body and connects the gut to the brain, which allows them to communicate bidirectionally (sends signals in both directions).  


How does the gut and the brain communicate? 


Neurotransmitters (pertaining to the nervous system)  

Neuroendocrine hormones (pertaining to the endocrine system)  

Cytokines (pertaining to the immune system)  


These compounds are produced in by many different types of cells: 


Nerve cells of the brain and gut  

Gut cells  

Microbes living within the large intestines 

Immune cells  

Adrenal glands (HPA axis - neuroendocrine hormones) 


Some of the most important compounds made in the gut inlcude: 

(which directly influences the brain) 


Serotonin: involved in regulating sleeping, appetite and mood. 

GABA: involved in mitigating anxiety and stress.  

SCFA (butyrate, propionate and acetate): involved in regulating memory and learning processes. 


The gut microbiome:  


The microbiome refers to the microorganisms inhabiting the large intestines of the human gut. There are 10x more microorganisms living in the human gut than human cells which makes up our entire anatomy! 


Why are these microorganisms so important? 


The gut microbiota stimulates enteroendocrine cells = cells in the digestive system which produce vital hormones known neuropeptides.  

The gut microbiota is involved in tryptophan metabolism = a type of amino acid which is converted into serotonin. (95% of serotonin is made in the gut!) 

The gut microbiota is largely involved in human immunity = The GALT (gut associated lymphoid tissue) makes up 70% of the body’s immune system.  

The gut microbiota maintains the integrity of the intestinal lining = and is therefore protective against leaky gut, which has been directly linked to anxiety and depression. 

The microbiota has been shown to produce the following neurotransmitters; GABA, serotonin, dopamine as well as SCFAs (small chain fatty acids).  




Dysbiosis refers to an imbalance between the ‘good’ and ‘bad’ microorganisms living in the gut. Dysbiosis is a negative term which describes a compromised microbiome, with low numbers of beneficial bacteria and higher numbers of pathogenic bacteria. Since the microbiome is an ecosystem, every organism which inhabits the human gut has to fight for space, food and survival. Many factors can reduce the number of good bacteria and when this happens, the bad bacteria, like the opportunistic that they are, steal the space and food, making the environment even more unfavourable for the good ones to survive.   


Dysbiosis is associated with highly prevalent disorders in today’s society, such as allergies, autoimmune diseases, metabolic disorders, digestive disorders (IBS) and neuropsychiatric disorders (anxiety and depression).  


How does dysbiosis occur? 



Antibiotics cannot distinguish between the good and bad bacteria residing in the human gut. Frequently prescribed broad-spectrum antibiotics are non-selective, killing all bacteria including the good bacteria, allowing pathogenic microbes an opportunity to take over the fragile ecosystem and thrive. 


Other factors which may lead to dysbiosis include; C-section birth, bottle-fed, long term medications (pain killers, oral contraceptive pill etc.), stress, smoking, alcohol and recreational drug misuse, diet and lifestyle and pollution.