The brain and gut are linked by a communication highway that can have serious implications in the emergence and treatment of many diseases.

By understanding the complexity of our body, we can make ourselves healthier and happier. This article investigates how the brain, gut and microbes work together to influence your health and mental health, before taking a look at what you can do to keep the cogs well-greased and disease at bay.

What is the gut-brain axis?

When I was a kid, my mum used to say “Eat well, so you can grow big and strong,” so I thought food was like bricks, building material for my body. Scientists would agree with my mum, but they'd also add (in a slightly ominous manner): “What you eat affects your whole body in different ways.”

The brain is the captain of the body and receives signals from the central nervous system (CNS). The lining of the gastrointestinal tract contains millions of neurons and nerve cells that produce an array of hormones; this is the enteric nervous system. It regulates gastrointestinal functions, and communicates with the Captain which is why often the gut is called the “second brain”.
Scientists discovered that gut microbiota can even exchange signals with the brain.

Like a chief engineer, the “second brain” reports on macronutrient content and calories. These signals travel from the gastrointestinal tract via the enteric nervous system to the central nervous system ending up in the brain.

This is called the gut-brain axis: a two-way communication system between the belly and brain that informs, directs and responds to each other’s signals. It is very important for maintaining homeostasis, the balance in and between physiological processes, and coordinating the work of our organ systems.

Your gut microbes influence disease

Unusual variations in the representation and abundance of gut bacteria are associated with diseases and symptoms that affect the digestive system and other parts of the body. For example, changes in the microbiome have been demonstrated in patients with seemingly unassociated conditions, ranging from allergies and autism spectrum disorder to cardiovascular disease and diabetes type II.

FACT ☝️ Specific neurodegenerative diseases, like multiple sclerosis or Parkinson’s disease, are also accompanied by problems related to digestive dysfunction.

Bacterial functions of the microbiome have been put forward as a possible axis for understanding the relationship between gut bacteria, mood and developmental disorders such as autism and depression. This is because some microbes can produce neuroactive compounds that cross the gut barrier and influence brain function.

Inflammation has been associated with depressive symptoms. This is because the activity of pathogenic microbiota can activate the immune system, leading to inflammation that also affects the central nervous system. Interestingly, research indicates that probiotics can significantly reduce depressive symptoms in the same way antidepressants do: by blocking inflammatory cytokines released by the body.

The answer is less clear-cut for autism spectrum disorders, but studies do indicate disturbances in the microbiome composition of patients. Exactly how these mechanisms work has yet to be discovered but probiotics, prebiotics, microbiome transplants and diet are all being considered as possible means to modulate these alterations.

I’m not sick, why should I care?

The body is a complex biological machine, and its systems do not work in isolation. There’s a reason why evolution saw fit to connect the gut to the brain and not your elbows or thumbs. Scientists are particularly interested in the bioactive compounds released by the gut microbiome and how they could be harnessed to treat disease.

“When you put something in your mouth, it will always have an effect on a number of the body’s systems.”

Miguel Toribio-Mateas,
nutritionist, clinical neuroscientist

It’s believed that a happy and healthy microbiome helps the gut-brain axis to function correctly, thus sustaining health. On the other hand, dysbiosis (abnormal alteration of the microbiota composition) induced by lifestyle factors, like poor eating choices and stress, is associated with obesity. This metabolic condition has also been shown to have adverse consequences on mood and cognition.

☝️Dysbiosis refers to an imbalance in the ecosystem of microorganisms that occupies a specific area of the body, like the skin or gut. In the case of intestinal dysbiosis, the communities of beneficial and benign bacteria that usually make up the microbiota are altered, leading to digestive symptoms and conditions.

A healthy diet rich in fibre, vegetables and fruit is the first step on the path to building a strong and varied ecosystem of microbes in your gut. Research indicates that microbiome diversity is a positive thing, while lack of diversity is associated with poor health and disease.

In fact, diversity in your diet with lots of plant-based options nourishes a broad range of gut microbes allowing them to perform many functions and take over from each other if something happens. This, in turn, contributes to epithelial gut integrity and immune homeostasis while allowing the gut-brain axis to communicate correctly.

Probiotic strains of Bifidobacterium and Lactobacillus, the bacteria you find in live cultured yoghurt, have been reported to improve mood and reduce anxiety symptoms in patients with inflammatory bowel disease. It has also been suggested that fermented products, such as kefir, kombucha, yogurt or kimchi may help improve cognitive functions, memory and focus while lowering stress.


Your body is a seamless supersystem of smaller systems that are intertwined at an intense level of complexity, even for scientists. Fortunately, the human brain is endowed with the capacity for self-reflection and common sense to help navigate the world we live in. So before you leave, check out the most important points of this article and make better choices for your health now.

1. Nothing works in isolation in the human body, all systems are connected.
2. The gut-brain axis connects the central and enteric nervous systems.
3. Digestive problems are found in diseases of other organs and systems.
4. Gut microbes produce compounds that may influence the gut-brain axis.
5. Dysbiosis has been detected in many non-digestive diseases and conditions.
6. Probiotics can be used in the treatment of depression.
7. A more diverse microbiome is associated with better health.
8. Lifestyle factors like diet and stress affect your gut microbes.
9. You can check your disease protection with our Microbiome Test