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The Brain-Gut Connection: Resetting and Rebalancing

Naturopathic doctors are holistic practitioners and see the body with all its connections. We believe the basis of all disease and illness begins in the gastrointestinal tract and the organs of detoxification. After all, if the entire tube from your mouth to your rear end is considered the outside of your body, the only way you have access to the food you eat is through the processes of digestion and absorption.

If you are experiencing bloating, gas, heartburn, constipation, or diarrhea, your body is not functioning as efficiently as possible. These are warning signs that something is off; either the digestive process has been compromised, or the wrong bacteria have taken up residence there—or both. These signs are often ignored or begin to be considered “normal.” Many people go about their day thinking their symptoms are linked to something they ate. Often, this could be true. However, it likely also has to do with an imbalance in gut bacteria.

70% of Your Immune System Lives in Your Gut

The bacteria in our gut should be given much more credit than we allow them. They are an important part of our digestive system, but an even more important part of our immune system. There is a delicate balance of good and bad bacteria living within us. The good ones fight for us and protect us. The bad ones ferment foods and release gas.[1] They create digestive inflammation and ultimately result in disease. These bad bacteria are introduced through the foods we eat, the places we travel, the medications we take, etc. Every day, we come in contact with bad bacteria, but as long as we have enough of the good ones, we are able to fight them off. When our immune systems become weak, the bad bacteria start to outnumber the good ones—and we’ve got ourselves a problem.

Your Second “Brain” Is in Your Gut

If you have ever felt the sensation of “butterflies in the stomach” before a presentation, you are already aware of the brain-gut connection. The nerves that originate in our brain travel through our spinal cord to every corner of the body. When our brain interprets a stressful situation, that same stress signal fires through every nerve, and the entire body responds. During your presentation, this may show up as an urgent need to run to the washroom. Your palms may become sweaty and start to shake. All the while, your heart

is pounding in your chest, and you are convinced the audience can tell how nervous you are. These thoughts act as a positive feedback loop, enforcing and escalating the physical side of the stress response. Your brain is stressed, and your gut knows it.

Outside of presentations, many experience a generalized form of anxiety that exists all day. Anticipation for a stressful workday can present itself as bloating, diarrhea, nausea, and lack of appetite in the morning. Anxiety before bed can include a racing mind and physical restlessness, despite feeling exhausted. In these situations, the nervous system is on overdrive. Your mind has interpreted a dangerous situation, and your nervous system is poised and ready to run.

The same thing happens when we feel depressed. We may have negative thoughts in our brain, but our bodies experience fatigue, low motivation, pain, lack of appetite, and insomnia. It’s not just in your head: It’s in your whole body.

The Brain Can Influence the Gut, and the Gut Can Influence the Brain

Let’s talk food: Food is our fuel, and we are only capable of doing what our dietary fuel allows. When we eat poorly, we provide our bodies with inflammatory compounds instead of nutritious vitamins. These inflammatory compounds travel through our bloodstream and can build up in any part of the body. After one large and unhealthy meal, we won’t notice much. But if this poor dietary habit becomes a regular occurrence, inflammatory compounds can overwhelm our ability to clear them out. They begin interfering with regular processes and can show up in very interesting ways. Inflammation in the muscles and joints can appear as arthritis, stiffness, and pain. On the surface of the skin, inflammation looks like eczema and acne. Around the digestive tract, bloating and gas become the norm. But when these inflammatory compounds overload into the brain, we can experience brain fog, poor concentration, anxiety, and depression.

Resetting Brain and Gut Communication


Your body knows what to do; it just needs a bit of help to get started. In order to reestablish communication between the brain and gut, we first must begin by cleaning out the bad bacteria and resetting the balance of good and bad. Pharmaceutical antibiotics can be very harsh on the system and kill both good as well as bad bacteria. They specifically kill only bacteria and can be helpful in very severe cases of intestinal bacterial overgrowth. Yeast is a fungus that can grow anywhere in the body and is usually kept under control by our bacteria.[2] After antibiotic use, we lose our ability to control the yeast, and it tends to overgrow. Natural antimicrobials are a better option in this case, as they will gently eradicate bad bacteria as well as yeast.

In the meantime, we must address diet and identify foods that are contributing to inflammation. You may consider yourself a healthy eater, but your immune system ultimately makes the decision as to what is

right for you. Remember that food sensitivities are different from food allergies: An allergy may present itself immediately, whereas a sensitivity will create a delayed reaction that is hard to link back to what you ate. An elimination diet or food-sensitivity test can be very helpful in determining where to begin.


The process of digestion is a series of reactions that take place like a domino effect. When we see or smell food, we begin to salivate. This stimulates the production of stomach acid, which gets our stomach grumbling and increases our appetite. As soon as we start eating, a specific profile of digestive enzymes is released in response to the amount of carb, fat, and protein in the meal. When we eat too quickly or don’t chew our food well, these signals get confused and happen all out of sequence. We can end up with bloating, heartburn, burping, and stomach cramping.


Once we have cleaned out unwanted organisms from the gut, we can now begin to rebuild it.

“Probiotics are helpful, but the quality of the probiotic will depend on its variation and inclusion of specific strains of bacteria.”

Probiotics are not the only solution, however: Amino acids, antioxidants, anti-inflammatories, and vitamins all play a large role in reestablishing the ecosystem.


To reset brain-gut communication, we cannot be successful until we acknowledge the power of the mind. Arguably, this is the most important step—and easily the most challenging. We cannot change our stresses, but we can change our perception of them. We hold the power to determine how much we let our stresses affect us and impact our health. When we let our minds get the better of us, we create anxiety, lose sleep, and make poor decisions.

Becoming aware of negative self-talk and the physical symptoms associated with stress can alert us to how often this process takes place. Only then can we begin to create change and allow our bodies to heal in a top-down approach.


  1. Fooks, L., R. Fuller, and G. Gibson. “Prebiotics, probiotics and human gut microbiology.” International Dairy Journal, Vol. 9, No. 1 (1999): 53–61.
  2. Mayer, F., D. Wilson, and B. Hube. “Candida albicans pathogenicity mechanisms.” Virulence Journal, Vol. 4, No. 2 (2013): 119–128.

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Krysten DeSouza, ND, is a Mississauga naturopathic doctor with a special interest in anxiety disorders and mental health.