The 4 Ways the Gut & Brain Connect

Updated: Jan 7

The gut-brain connection (sometimes referred to as the ‘Gut-Brain Axis’) is the link between our brain and our enteric nervous system. The enteric nervous system is a group of 200-600 million neurons in our gut. These make up our body’s ‘second brain’.

Pretty cool, huh?

Research over the last 20 years is showing a clearer and clearer link between gut health and brain health. And our gut and brain are linked in more ways than one.

How does the Gut-Brain Connection Work?

There are 4 ways that the gut and brain connect:

  1. The Vagus Nerve

  2. The Gut-Brain Immune Connection

  3. Gut Permeability

  4. Neurotransmitter Production

For example, if our gut microbiome - the collection of around 100 trillion bacteria, fungi, parasites, etc. found in our gut - is out of balance, our gut will not be able to produce neurotransmitters and hormones that support brain function and positive mood. This is significant considering our gut produces around 90% of the serotonin and 50% of the dopamine that our brain uses. It also produces GABA as well.

If our intestines are overgrown with bad bacteria, fungus, or parasites that have overwhelmed our good gut bacteria, then these species can release toxins that impact our psychological health dramatically, including mental illness such as depression, anxiety, and even schizophrenia.

If our diets are low in prebiotic foods, such as vegetables and mushrooms, then the good bacteria populations (probiotics) in our gut will not be fed. Also, if we eat diets low in probiotic foods, such as kimchi, kombucha, kefir, and even small bits of healthy, organic soil, then our gut cannot repopulate its beneficial bacterial species (known as probiotics).

Probiotic foods contain these probiotic bacteria, and we rarely, if ever, get enough of these foods in a westernized diet. Prebiotics are the fibers and other nutrients contained in vegetables and other natural foods that feed probiotics, and only 1 out of 10 adults get adequate servings of fruits and vegetables per day. In fact, on average Americans consume around only 16 grams of fiber per day, whereas our hunter-gatherer ancestors consumed around 150 grams of fiber per day.

Boy, did they feed their probiotic gut bacteria.

At the same time, if our diets are high in bad fats, sugar, artificial sweeteners, and toxins like pesticides, then this can cause further damage to our gut, giving ‘opportunistic species’ the opportunity to grow and overtake our gut and GI tract. Opportunistic species include microorganisms like candida, H. pylori, C. Diff, and other bacteria, fungi, and parasites.

This does not begin to address nutrient absorption. Vitamins, minerals, amino acids, enzymes, and phytonutrients all work together to support proper brain function. As well as of course protein, fat, and carbohydrates, but those are less interesting. All this, however, does not account for the nutrients or interactions with food that we do not yet know about - and that category is likely a lot bigger than we can imagine.

If our intestines, liver, kidneys, gallbladder, or pancreas are not functioning properly, or are overwhelmed by toxins from toxic foods or the environment, then we will not be able to properly absorb and use micronutrients to support our mental health.

Given the fact that neurotransmitters (happy chemicals in our brains) are made in part from amino acids, B vitamins, and bacteria, it is absolutely crucial that the organs in our gut are functioning properly and we are eating plenty of foods dense with vitamins, minerals, etc. But also, we then must be absorbing those nutrients properly.

After all, we are not what we eat. We are what we absorb.

The brain and body are one and the same. They are not separate. If we want a healthy brain, we must have a healthy gut.

Now that my lengthy tangent is over, let’s discuss the 4 specific ways that the gut and brain are connected so that we can understand how this relationship functions and why this connection is so significant.

1: The Vagus Nerve of the Gut-Brain Axis

Perhaps the best known connection between the gut and the brain is the vagus nerve. The vagus nerve is a conglomerate of 200-600 million different nerves that stretch from our gut (the enteric nervous system) to our brain. The enteric nervous system is the mass of neurons that are all throughout our small and large intestines, liver, gallbladder, pancreas, kidneys, stomach, and esophagus.

These nerves notify our brain when things are going well in the gut or when something is wrong. This occurs in part via physical sensations and mental distress. They also make us aware when things are going well - such as that feeling of “ahhh” you get when your gut and digestion are on point.

As a multiplicity of studies are now showing, this group of neurons is quite literally our body’s 2nd brain. When things are going poorly in our gut, such as increased intestinal permeability (“leaky gut”), this can be directly linked to depression, anxiety, bipolar, etc.

Fun fact, we also have a third brain located in our heart, which is composed of around 44,000 neurons. Not a huge amount, but still significant and certainly fitting when you consider cultural phrases such as “my heart aches” or feeling “broken-hearted.”

So, back to the vagus nerve. Via this conglomerate of nerves, the gut talks to the brain and the brain to the gut. Gut bacteria, fungi, and parasites within our gut microbiome send chemicals (good or bad) via this pathway to the brain.

When our gut is filled with pathogenic bacteria, fungi, or parasites, we may experience anxiety, depression, schizophrenia, or other mental illnesses due to the harmful neurotoxins which are excreted by pathogens.

But really, it’s not these little guys’ fault. it’s just in their nature.

On the other hand, we may experience good feelings, such as those that come from Lactobacilli and Bifidobacteria. These probiotic bacteria are some of the most powerful and beneficial to our brain. Among other things, Lacto and Bifido make neurotransmitters for our brain. These neurotransmitters lift us up and make us feel good. Lacto and Bifido are responsible in part for the synthesis of dopamine, serotonin, and GABA. Lacto and Bifido can be consumed in multiple fermented foods - kimchi, sourdough bread from starter, kvass, raw sauerkraut, kefir, raw apple cider vinegar - as well as probiotic supplements.

If you’d like to begin using a probiotic supplement that contains these probiotic bacteria, Mood+ by Garden of Life is one that my wife began using for her mental health that has worked very well for her over the last several months. She notices a very immediate change when she is taking it vs. when she is not. Though, that immediate difference in mental stability could be due more to the Ashwagandha (an herbal adaptogen) in the supplement than anything else. Which is great! Either way, it is still a high quality probiotic supplement and seems to do very well in assisting with people’s mental health.

2: The Immune Connection Between Gut & Brain

When there is a flare up of the immune system in the gut, it causes the immune system throughout the rest of the body to go on high alert. This includes the immune system in the brain. In part, this is because the gut houses a majority of our immune system (around 80%), so when our gut is on high alert then the body is ready to act. This can often put us in a state of ‘flight-or-flight’, rather than ‘rest-and-digest’.

When our gut is unhealthy, and even leaky, the immune system throughout our body and brain will be on high alert. ‘Leaky gut’ occurs when the tight junctions in our gut become weak and damaged. This can allow proteins, bacteria, etc. into other parts of the body where they can have an ill effect on our health. This then instigates an immune response in that part of the body, causing inflammation which is the body’s protective response to invaders. This can occur in the brain just the same as it can in other areas of the body.

This is significant when you consider that brain-specific immune cells outnumber our brain cells 3 to 1. If these immune cells are on high alert and triggering inflammation to protect us from intruders, chances are we will be suffering negative mental reactions which could include anxiety, depression, bipolar, etc.

We need probiotic gut bacteria to protect the lining of our gut and act as the “bouncers” of our immune system, so that our gut lining will remain strong and in tact, preventing pathogens from exiting our gut into other areas of the body (such as our brain). Our gut bacteria enhance and assist our immunity in profound ways, including creating vitamins, regulating our metabolism, and defending against bacteria and pathogens.

Bad bacterial overgrowth causes a weakening of our gut lining, as they release toxins and burrow into the lining of our gut. This is why we must have an ample amount of probiotic bacteria, such as Lactobacilli and Bifidobacteria, to protect our gut. Read more about this in the next section.

3: Healthy or Unhealthy Gut Permeability

We have microscopic junctions in the wall of our intestines. These junctions are meant to allow tiny amounts of particles out into our bloodstream for necessary purposes. In the case of increased gut permeability, or “leaky gut”, these tight junctions become more permeable and their gaps expand.

This occurs when our gut wall becomes damaged or weakened due to inflammation or bad bacterial/fungal overgrowth. This can occur due to gut exposure to environmental toxins such as pesticides or antibiotics as well as because of a diet filled with pro-inflammatory foods. These foods include sugar, artificial sweeteners, preservatives, gluten, or conventional dairy or meat.

If you’d like to learn more about what foods or toxins are inflammatory and cause leaky gut and ‘gut dysbiosis’ (the overgrowth of bad gut bacteria/fungi), read my article What Kills Good Gut Bacteria.

So, what happens when our gut becomes leaky? Well, things get dicey. Proteins, bacteria, fungus, and parasites can escape into our bloodstream from the gut and enter other areas of our body including the lungs, muscles, organs, and the brain. When this happens, it is associated with mental illnesses including anxiety, depression, and schizophrenia. It is also associated with thyroiditis, asthma, diabetes, and other autoimmune conditions.

The Leaky Gut / Blood-Brain Barrier Relationship

If we have ‘leaky gut’ then this can let pathogenic bacteria, fungi, or parasites into our brain. If these pathogens cross our blood-brain barrier, they can cause harm by releasing harmful neurotoxins.

As it turns out, when we have a diet high in inflammatory foods or are exposed to too many toxins like aluminum, glyphosate, or mercury that cause leaky gut (which we are all exposed to each day in the U.S.), then we are also prone to experience what is referred to as “leaky brain” at the same time.

While it may sound like a strange term, leaky brain simply means that our blood-brain barrier (the barrier that keeps toxins and pathogens out of our brain) becomes “leaky” or weak, and is not as adept at keeping out the bad guys. As you can imagine, this can lead to severe mental health complications.

If we have a leaky gut, there is a good chance we may have a leaky brain as well. This is simply because the environmental toxins that cause leaky gut often cause leaky brain as well.

When these bacteria, fungi, and parasites enter our brain, they cause the immune system in our brain to turn on and attack. Our immune cells cause inflammation in the brain, a reaction that is meant to contain the pathogens and protect the rest of the brain and body from the infection while the immune system handles the intruders.

So, in addition to the neurotoxins released by pathogenic bacteria, fungi, etc., the inflammation produced by our immune response has also been clearly linked to mental illness. But our immune system is only trying to protect us - it’s better than allowing these pathogens to roam free.

It is important to note that toxins such as glyphosate and aluminum are readily able to pass through the blood brain barrier. Our immune system can handle some of these intruders, which is why we have so many immune cells - they outnumber our regular cells. But, when our diets are filled with an abundance of unhealthy foods and a shortage of healthy ones, then our immune system is compromised and it begins to struggle to fight. Add in the constant onslaught of toxic chemicals being sprayed on our food and toxins we are exposed to in the water supply, in our air, and in our have a breeding ground for mental and physical illness.

The Link Between Mental Illness and Food Sensitivities

If we want to overcome mental illness, we must constantly fill our diet with healthy, whole fruits and vegetables (especially vegetables - a LOT of them). Probiotic foods are also very important for overcoming mental illness. We must also minimize our consumption of processed and packaged foods, processed sugar, unhealthy saturated fats and vegetable oils, gluten, and also conventional dairy and meat.

Man, easier said than done. Am I right?

Depending on who you are though, one or several of these foods could be playing a very large role in your mental illness.

For me, I used to suffer with severe anxiety and some challenging depression. I stopped eating all foods with processed white sugar and all dairy as well 6 years ago. When I quit eating these foods, I experienced an immediate transformation in my mental health. Within 2 weeks, I was no longer experiencing the severe anxiety and addiction cravings I had been going through for years, my energy was ways up, and the regular OCD thoughts and behaviors I had dealt with dissipated drastically.

Later on, I stopped consuming gluten. OCD thoughts and behaviors improved even further within just 3 days of making this change.

It is extremely important to also say that several years leading up to these diet changes I had been making progress in my spiritual life and improving my mental health through cognitive behavioral strategies. There is no substitution for spiritual and cognitive-behavioral work. No matter how great your nutrition is, you can still be miserable if you do not grow a deep spiritual connection to yourself and Higher Power and learn to change your perception of life and those around you.

My diet is certainly more restricted than ever, and that presents challenges. But, when I experienced such powerful benefits, the sacrifice seems small in comparison. I’m not saying this will work for you, but you could give it a try and see what happens.

Everyone’s bodies and brains are different. Foods that contain dairy, sugar, artificial sweeteners, and gluten have been researched in thousands of case studies and laboratory studies. Many people experience substantial reductions in their mental illness when they alter their diet. They may have a food sensitivity that has been causing the severe mental illness, as food sensitivities (which are similar in ways to allergies) can affect someone mentally just the same as physically.

On the other hand, we are well aware that these foods are strongly linked to inflammation, and so it makes sense that going off of them would bring an improvement in mental health.

I believe there are many who have no idea these foods are affecting their mental health, due to a lack of knowledge and the fact that they eat these foods every single day, so they would never know the difference.

4: The Production of Neurotransmitters in the Gut

One of the most fascinating and powerful parts about the gut is that it is the place where a majority of our neurotransmitters are produced. Neurotransmitters are the brain chemicals that determine our mental state. Our gut bacteria are involved in the production of many of these neurotransmitters, especially serotonin, dopamine, and GABA. These neurotransmitters are all produced by Lactobacilli and Bifidobacteria probiotic strains.

Lactobacilli and Bifidobacteria probiotic strains are found in foods like kimchi, raw sauerkraut (fermented cabbage), milk and coconut kefir, and fermented vegetables such as carrots, cucumbers, and radishes. They can also be found in high-quality probiotic supplements. Below are the neurotransmitters that are produced in part by Lactobacilli and Bifidobacteria probiotics.


Serotonin is the neurotransmitter (or “happy chemical”) in our brain that gives us a feeling of peace, completeness, and well-being. Around 90% of the serotonin produced in our body is produced in our gut by our Lactobacilli and Bifidobacteria probiotics (beneficial gut bacteria). Without an adequate amount of these bacteria, we will likely be unable to produce and absorb enough serotonin. Depletion or malabsorption of serotonin is well-known as one of the fundamental reasons for depression.


Approximately 50% of our dopamine is produced in our gut. This is the neurotransmitter responsible for causing feelings of accomplishment, purpose, and pleasure. Depletion or malabsorption of dopamine is a fundamental reason for addiction and anxiety. Like serotonin, Lactobacilli and Bifidobacteria produce dopamine.


GABA is the neurotransmitter that gives us feelings of calm, ease, and causes us to have that “chill out” feeling. I have not been able to find a study that specifies exactly how much GABA is produced by gut bacteria, but research shows that it is produced in part at least by Lactobacilli and Bifidobacteria, just the same as serotonin and dopamine. Perhaps there is a study out there I was unable to locate or we just aren’t sure what percentage of GABA is produced in the gut yet.

Mood+ by Garden of Life is a quality probiotic supplement that has made a real difference for my wife. Perhaps it could for you too!

If you’d like to learn more about how neurotransmitters are made in the gut, click here.

If you’d like to know how to spot a high quality probiotic supplement, click here.

Check out the articles below if you’d like to know more about the gut-brain axis:

How to Heal the Gut to Improve Mental Health + Supplements I Recommend

Why Healing Your Gut Heals Your Brain

How Your Gut Health Influences Your Mental Health

What Kills Good Gut Bacteria: Gut Microbiome & Mental Health

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