The Second Brain: How Stress Affects the Gut-Brain Axis

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The Second Brain: How Stress Affects the Gut-Brain Axis

Understanding how the gut functions as a sort of "Second Brain."
Millions of neurons run between your gut & brain, and we now understand that digestive system has the ability to communicate with the rest of your body. Dr. Doni explains how your gut works, and why it's called our "second brain."

Millions of neurons run between your gut and brain, and we now understand that digestive system has the ability to communicate with the rest of your body. Dr. Doni explains how your gut works, ways to optimize its performance, and improve your overall health.

Understanding how the gut functions as a sort of "Second Brain."

Digestion Junction, what’s your function?

When I think about gut health, I immediately relate it back to internal and external stressors. In fact, since our understanding of the gut and microbiome has expanded, we’ve also realized that it’s actually our second brain. Now that we know that our brain isn’t the only organ handling stress, we can see the direct effect that stress has on the digestive system.

Digestion is the process of your body breaking food down into the smallest form of carbohydrates, protein, and fat. It does this so that nutrients can be absorbed through the intestinal walls into your body. These nutrients feed your cells and provide energy for everything you do. The body also uses these nutrients for the growth and repair of cells. The digestive system is also home to our amazing gut bacteria.

The digestive system has the ability to communicate with the rest of your body via signals from hormones, neurotransmitters, nerves, the immune system, and the gut bacteria. When the gut is stressed, these messages are sent throughout your body. That’s why it is so important to address your gut health first and foremost.

When working properly, your digestive system is performing amazing feats every day!

Microbes, Enzymes & Stomach Acid, Oh My!

First things first, let’s talk about three, often forgotten, star players of your digestion. A.K.A. your Pancreas, Liver and the Gallbladder.

1. Pancreas

The pancreas makes and secretes enzymes into the small intestine. There are three main types of digestive enzymes, coinciding with the three types of nutrients our body uses. Proteases are responsible for breaking down proteins into small peptides and amino acids. Lipases digest fat into fatty acids and glycerol. Finally, amylases turn carbohydrates into simple sugars.

When your stress level is high, the pancreas is less able to make enough digestive enzymes. This leaves food not completely digested, making it less likely you’ll absorb nutrients and vitamins from your food. It also makes you susceptible to food sensitivities where the the undigested food triggers an immune response.

There are genetic influences on the ability to make digestive enzymes, as well. Lactose intolerance and fructose intolerance are good examples of this, where the undigested sugars then cause bloating.

The pancreas also makes insulin, the hormone that tells cells to take in glucose from the blood, and glucagon, a hormone that tells the liver to make glucose if blood sugar levels are dropping.

2. Liver

The liver has many functions, but two of these functions specifically serve the digestive system. It 1) creates bile, and 2) processes the blood containing freshly absorbed nutrients (and anything else) from your small intestine. The liver manages excess carbohydrates in the blood by turning them into cholesterol or stored fat, which can lead to fatty liver.

The liver is also responsible for detoxification. There are two phases of converting toxins into a form that can be effectively eliminated. The toxic metabolites travel in the liver’s bile to be transferred out of the body in the stool.

3. Gallbladder

This pear-shaped “reserve” sits under your liver and stores the bile produced by the liver. Bile travels to your intestines during mealtime to digest fats. This is particularly important because it ensures that bile is present at the time you eat, making it possible for you to absorb fats and fat soluble vitamins.

Gall stones can sometimes form in the gall bladder. Potential causes: Stress and toxin exposure; a diet high in dairy products, gluten, and fried foods; nutrient deficiencies, such as vitamin B6 and choline; and genetic tendencies.

The Five Stages of Digestion

Did you know that the gastrointestinal tract is actually a long tube that starts at your mouth and ends at your anus. Here’s another fun fact: This tube can actually be up to 30 feet long in adults, WHOA!

This length allows cells to be broken down over a series of stages. This helps ensure that the most nutrients are absorbed – and that anything not serving your body gets eliminated.

Here are the five stages food and liquid must take as they make their way your system. Each are influenced by stress:

1. Mouth

Did you know that your saliva actually helps to break down what you’re eating? Not only does saliva moisten the mouth and food you consume, it also contains enzymes called amylase, electrolytes, and other various antibacterial compounds that begin the process of breaking down carbohydrates. So by chewing your food slowly, you can actually give your saliva the time it needs to aid in the digestive process. It also sends signals to your stomach and intestines to get ready to digest.

Plus, when you swallow, you stimulate your vagus nerve. This brings your body out of sympathetic “stress mode” and into “digest mode.” Eating quickly and on-the-run means less signaling to your body that you are eating. This can lead to less effective digestion, less absorption of nutrients, and more likelihood of food reactions, gas, bloating, and tummy trouble in general.

2. Esophagus

The esophagus connects your mouth to your stomach, through an opening in the diaphragm. Your stomach sits right under the diaphragm, unless you have a hiatal hernia, in which case the stomach is caught up in the diaphragm a bit. This can cause reflux, choking, or a feeling like your food gets stuck. It can often be resolved with deep breaths before and after you eat.

At the end of the esophagus is the lower esophageal sphincter (LES), which is a muscle that contracts, to prevent reflux of stomach contents. Interestingly, protein in the meal signals to the LES to close, whereas other substances, like peppermint and coffee, signal to the LES to open. So by eating protein with each meal, you can prevent reflux.

3. Stomach

The stomach, shaped similar to a sac and lined with strong muscles, makes hydrochloric acid, which digests protein in particular. It also makes mucus to protects the stomach lining from being damaged by the acid. When stressed, mucus production is reduced, making stomach ulcers and gastritis (stomach inflammation) more likely.

Once its work is done, the stomach releases the contents into the duodenum, the first part of the small intestine.

4. Small Intestine

Hormonal signals tell your pancreas to release the enzymes into the duodenum to help break down the remaining fat, protein, and carbohydrates. At the same time, the gallbladder releases bile produced by your liver and further break down the fats into a form that can be absorbed.

The walls of the next two sections of the small intestine, the ileum and jejunum, are folded into sort of “ruffles”called villi. These “ruffles” creates more surface area for digestion and absorption of nutrients and vitamins. These nutrients must travel through the cells making up the walls on the intestine in order to get to blood vessels on the other side, and into your body.

The cells of the small intestine are amazing. First of all, there are enough cells in the small intestine to cover the surface area of a tennis court. What’s more, these cells are replaced every 72 hours! When we are stressed, glutamine, which is an amino acid and fuel for the small intestinal cells, is diverted to helping with stress. This can leave the cells less healthy, with spaces in between the cells. This outcome is referred to as intestinal permeability or leaky gut. We all have some degree of leaky gut, but the more severe, the more likelihood of food reactions and other major health issues like allergies, skin rashes, migraines, anxiety, weight gain, autoimmunity, diabetes, and more.

Keeping Bacteria in Balance

There are bacteria living in the small intestines, and it’s important to keep them in balance. If the bacteria overgrow – referred to as small intestinal bacterial overgrowth (SIBO) – they can cause bloating, burping, and a lot of discomfort. There are many potential triggers. For instance, SIBO is more likely to occur after a bout of food poisoning, the use of antibiotics, constipation, and over-consumption of carbs, sugars, fiber, and fermented foods. That’s right, eating too much of a good thing can cause your good bacteria to overgrow.

Hormones from the small intestines also send messages to the pancreas to make more insulin and less glucagon, based on the quantity of carbohydrate in your meal. This is how your body prepares to move glucose from the blood into your cells.

5. Large Intestine

The colon, or the large intestine, is an important final stage of digestion where water and electrolytes get absorbed into the body. Toxins, along with undigested fiber from food, get eliminated from the body at this point too. The muscles in the intestines ensure consistent movement of stool out of the body, optimally at least once or twice per day.

There are bacteria living throughout the digestive system, but the majority of the gut bacteria, which we call the microbiome, live in the colon. They help to digest fiber and other components of food, to make nutrients and small chain fatty acids (SCFAs), which are important for the health of our intestines and body in general. The gut bacteria also communicate with our immune system and nervous system. They are greatly affected by stress, shifting optimal levels, and allowing the overgrowth of less healthy bacteria which produce toxins.

Toxins from bacteria (called LPS) and toxins (such as estrogen metabolites) that came from the liver in the bile can be absorbed back into the body, especially if the bowels are not moving regularly. This is not preferred because it can lead to inflammation and higher toxin (and estrogen) levels in the body.

The whole digestive process takes about 6 to 8 hours from the time you eat to your food passing through your stomach and small intestine. Once your meal enters your large intestine, it takes another 36 hours or so for further digestion, absorption of water, and finally elimination of undigested waste.

The Gut-Brain Axis

Interestingly enough, it’s actually only been in recent decades that studies have shown the direct cause and effect relationship of our gut on our brain and health. This is what we call the gut-brain axis.

And, in fact, with increased understanding of the role the microbiome plays in this communication pathway, it is now more specifically called the gut-brain-microbiota axis. Of the trillions of bacteria living in the intestines, it is not about any one type, but the overall balance and diversity of these bacteria that seem to foster health. They feed off the food we eat, so in that way, we determine the health of our microbiome by what we feed them. The preferred bacteria prefer vegetables, fruits (berries in particular), nuts, seeds, and minerals (like calcium).

Gut bacteria are greatly affected by stress, both past and present, and both emotional and physical stress. Pesticides, molds, and medications all disrupt the careful balance of gut bacteria, leaving you vulnerable to them sending “stress signals” from your gut to your brain (and your whole body).

Actually, there is evidence that shows a direct correlation to anxiety, depression and other psychiatric conditions. Further exemplifying the effect that – yes, you know what I’m about to say – stress has on our digestive function and microbiome composition, and in turn our central nervous system.

These stress signals come in the form of actual toxins produced by the bacteria – referred to as LPS – which can cross the intestinal lining and enter your blood stream. Imbalanced gut bacteria also shift our immune system to be more inflammatory, plus they cause leaky gut, which allows the inflammation to spread throughout the body. And they send stress signals via the vagal nerve, as well as through shifts in neurotransmitter and hormone levels, all of which activate the HPA (hypothalamic pituitary) axis, our stress response system.

Communication Pathways of the Second Brain

Let’s look into these communication pathways more specifically.

1. The Vagus Nerve & Nervous System

This is the biggest (and literally longest) nerve that connect your gut and brain, and it sends signals in both directions. It is part of the autonomic nervous system, which means it responds to stress signals in the body. When we are relaxed, the vagal nerve signals in support of digestion. When we are stressed, the vagal nerve shuts off digestion.

“Vagal tone” is the responsiveness of the vagal nerve to stress. Having good vagal tone is more associated with health, because it means your body responds to stress, and also relaxes when not stressed. Low vagal tone, in one study in particular, is more associated with irritable bowel syndrome (IBS) and Crohn’s disease. With low vagal tone comes higher inflammation and adrenaline, both of which send more stress signals from the gut to the nervous system. Disruption in the microbiome further affects vagal tone.

There are ways to support vagal tone, including:

  • Deep breathing or meditation
  • Swallowing (even when not eating)
  • Singing, gargling, laughter
  • Getting a massage or acupuncture
  • Doing hydrotherapy or biofeedback like Heartmath therapy for emotional processing of stress
  • Rebalancing your gut microbiome (more on that soon).

three ways our brain and gut are connected

2. Neurotransmitters

Neurotransmitters are chemical messengers that connect your brain and gut, and are responsible for mood, energy, focus, and sleep. And while we may associate our brain being wrought with emotions, our gut is actually responsible for producing many of these substances, like serotonin, that influence how we feel. In fact, 90% of serotonin is produced in the gut.

Your gut bacteria produce a neurotransmitter called gamma-aminobutyric acid (GABA), which is directly related to feelings of fear and anxiety. It’s what I refer to as your “stress buffer.” Without enough buffer to stress, you’re likely to feel every stress. So those butterflies you feel in your stomach when you’re nervous? Yeah. That’s a real thing!

3. Your Immune System

Your gut and its microbiome also play a critical role in your immune system and inflammation by either increasing or decreasing inflammatory cytokines (the messengers in the immune system). Any stressors in your past or present can lead to inflammation and its associated health issues, such as depression. There are even links to Alzheimer’s disease.

Imbalanced gut bacteria also increase leaky gut, making it more likely that inflammation and toxins from the bacteria, as well as from food sensitivities, will be able to cross the intestinal lining and make its way to your nervous system.

4. Hormones (Endocrine) and Growth Factors

The digestion and the gut bacteria can also influence hormone levels and growth factors, particularly in those in the nervous system. First of all, even if stress was first perceived by the amygdala and hypothalamus, causing an increase in cortisol, decreased digestion of food and a less optimal diversity of bacteria…the disruption in the gut then sends a cortisol signal back to the brain, creating a vicious cycle of stress. If you’re interested in learning more about how our noggin responds to stress, and the HPA axis, read my last blog here.

Additionally, certain gut bacteria themselves have been shown to decrease leptin function in the brain, a hormone that manages hunger and metabolism. They also decrease brain derived neurotrophic factor (BDNF), a growth factor in the brain associated with healthy brain cells. These hormone shifts can lead to cravings, decreased memory, and weight gain.

Interestingly, most of the same things that improve vagal tone also improve BDNF levels and help with stress recovery, so it’s possible reverse the effects of stress with essential self-care I’ll discuss below.

First, let’s review ways to know whether an imbalance gut-brain-microbiota axis is influencing your health.

10 Signs We Need to Talk About Your Gut

The scary truth is that we should all be talking about our gut, even when it may not seem like it’s necessary. This is because of a simple fact: We all experience stress. Therefore, we all are at risk of imbalanced gut bacteria, leaky gut and inflammation. Ultimately making it impossible for our digestive system to perform at it’s best 24/7.

Even a “mild”, relatively unnoticeable sensitivity to gluten or taking antibiotics can severely impact your gut and actually manifest in other areas. So really, if you aren’t getting signaled by your gut that something is off, it doesn’t guarantee that your gut is on the right track. In fact, that just may mean there’s a communication breakdown entirely, and your gut is unable to signal to you. Assessing your gut health is actually a critical step in addressing other health issues.

Here are some of the most common signs that we should schedule time to talk about your gut:

1. High Stress Levels

Whenever cortisol, your body’s main stress hormone, is too low or high then it decreases your ability to digest food. This means that you aren’t producing enough of those wonderful enzymes and acids to help your gut break down and absorb nutrients from your meal. At the same time, the undigested food can leak through your intestinal lining, triggering food sensitivities, and overfeed gut bacteria, leading to dysbiosis (an imbalance in the gut bacteria).

2. Irritated Stomach or Intestines

This can show up in many forms: gas, bloating, constipation, diarrhea, heartburn, stomach pain, or even colitis. An imbalance gut will have a difficult time processing foods and eliminating waste. Food sensitivities and dysbiosis develop, along with leaky gut, spinning a perfect storm of stomach trouble and more stress.

3. Skin Irritation

Inflammation in the gut caused because of a poor diet, food sensitivities, and dysbiosis may be linked to leaky gut. In turn, this can manifest through irritating skin conditions, like rosacea or eczema.

4. Autoimmune Conditions

An imbalanced gut has been shown to trigger autoimmune diseases where the body attacks itself rather than harmful invaders.

5. Unintentional Weight Changes

Gaining or losing too much weight without having made any changes to your diet or exercise habits is also a tell-tale sign of an unhealthy gut.

6. Food Sensitivities

Food reactions are the result of leaky gut allowing undigested food to get across the intestinal lining, triggering an immune response that can spread throughout your body.

7. Food Cravings

Poor diversity and quality of gut bacteria can cause food cravings. For instance, if you maintain a diet that is high in processed foods and added sugars, then there will be lower levels of good bacteria in your gut. These imbalances will lead you down a vicious cycle of increased sugar cravings, which will then damage your gut even further if those urgings prove to be too irresistible. High amounts of refined sugar have a direct link to the levels of inflammation you feel in your body.

8. Sleep Disturbance & Constant Fatigue

As I mentioned before, the majority of the body’s serotonin is in your gut. Serotonin is not only in charge of your mood, but it is also responsible for producing melatonin. Melatonin is the hormone that signals to your body and brain that it’s time to rest and prepares your body and mind for sleep. Additionally, food sensitivities, leaky gut, and imbalanced gut bacteria call all influence sleep and cause fatigue.

An unhealthy gut can absolutely be a contributing factor into poor sleep. Untreated this can lead to insomnia and/or chronic fatigue. Read more about ways to improve your sleep hygiene here.

9. Fertility Issues

While it may not be the first thing you think of, more and more studies are making connections between the microbiome and ability to conceive a pregnancy.

10. Anxiety, Depression, Decreased Memory and Migraines

Bringing it back to the brain, even if your gut feels fine, if you are experiencing mood or memory issues, or pain related to your nervous system, such as migraines, then I encourage you take a closer look at your gut health.

What YOU can do today!

Healing Leaky Gut with Dr. Doni WilsonI actually had to battle with my own set of digestive issues and let me tell you, it was not easy. Today we are actually really lucky because testing has come SUCH a long way. There are many ways you can begin this process and be your own advocate. But it is challenging to go the road alone. And why do that when you have me? I’ve built my whole practice around this! And if that’s not enough, take it from someone who has gone it alone and has been able to help others instead. You’re worth investing in, especially when it comes to your health. Here are some ways you can make changes right away.

Schedule a Consult

Contact me if you are interested in working together by phone or video (or in person if you are nearby), so I can help you with health panels that help us understand your body, as well as diet changes and supplements that make sense specifically for your case, to heal your gut.

Food Sensitivity Test

This panel will check for both IgG and IgA antibodies to 96 of the most common foods, including gluten and dairy products. It is a blood test completed with a finger prick that you can do at home.Diet change and stress reduction is always the first step; supplements can speed up the process, but without lifestyle changes they won’t be a “magic bullet” for you. You can do a TEST AT HOME FOR FOOD SENSITIVITIES WITH THIS HOME TEST KIT. Discover which foods to eliminate and get a sense of your leaky gut levels!

Stress Remedy Program

stress, stress remedy, leaky gut, probiotics, recipe planner, enzymesYou may also want to consider following my guided program, the Stress Remedy Program, to assist with exactly this situation—healing Leaky Gut. YOU CAN LEARN MORE ABOUT THE STRESS REMEDY PROGRAM HERE.

Leaky Gut Program

leaky gut, digestion, healingIf you’d like to find out whether you have Leaky Gut and have my help with addressing it, you may want to check out my LEAKY GUT SOLUTIONS PROGRAM. It includes consultations, the food sensitivity panel that I mentioned above, and support for implementing dietary changes and integrating supplements to help heal leaky gut.

Boost What Your Mama Gave You

Whether you get it from me or somewhere else. It’s so important that you choose high quality supplements. It is simply not worth taking a supplement from a company that is not holding themselves to high standards of testing and review. And you definitely don’t want supplements to have a long list of unnecessary “other ingredients” that may even aggravate Leaky Gut, such as sugar, sorbitol, and/or gums and waxes. You can find what I consider to be top quality supplements at my store.


What they are and what they do: Probiotics help repopulate your large intestines with good bacteria with the hope that they will stabilize the balance of bacteria, promoting the growth of helpful bacteria and preventing the growth of abnormal bacteria, yeast and parasites. It’s important to take it slow and easy when introducing bacteria to your gut. When unhealthy bacteria (and yeast) die, they can release toxins that make you feel worse.

I recommend a dairy-free probiotic containing a mix of Lactobacillus and Bifidobacteria as a good place to start when addressing the gut-brain axis.

Who should avoid them: Anyone who doesn’t feel well after taking probiotics should start by healing their digestion before taking probiotics. If you have histamine intolerance, be sure to stay away from Lactobacillus acidophilus. And if you feel know you have an imbalanced microbiome (SIBO for example), start with a bacillus formula instead, such as Megaspore, and begin with small, every other day dosing.


What they are and what they do: Prebiotics provide food for the bacteria living in your gut, helping them flourish. Probiotics are often made of a form of carbohydrate or fiber such as fructo-oligosaccharides (FOS), larch arabinogalactans, or inulin.

Who should avoid them: People who react negatively to probiotics, fiber and/or FODMAPs. You may need to start by healing your digestion and perhaps taking probiotics prior to adding in prebiotics.

Digestive Enzymes

Because stress reduces the production of enzymes, taking digestive enzymes can be a huge help when it comes to healing the gut-brain-microbiota axis.

I’m here for you!

Believe me, I understand that this can all see overwhelming. Healing the gut takes time, diligence and consistency. I know you can do it because I did it and thousands of patients I’ve guided have done it too. Sometimes it can feel like climbing a mountain, but when you get to the other side, you’ll be so glad that you did it. Don’t give up!

Wellness wishes to you, as always!

–Dr. Doni
29th July 2020


  1. Kelly, Kennedy, Cryan, Dinan, Clarke and Hyland. Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disordersFront Cell Neurosci. 2015; 9: 392.
  2. Pellissier S, Dantzer C, Mondillon L, et al. Relationship between vagal tone, cortisol, TNF-alpha, epinephrine and negative affects in Crohn’s disease and irritable bowel syndrome. PLoS One. 2014;9(9):e105328. Published 2014 Sep 10. doi:10.1371/journal.pone.0105328
  3. Schéle E, Grahnemo L, Anesten F, Hallén A, Bäckhed F, Jansson JO. The gut microbiota reduces leptin sensitivity and the expression of the obesity-suppressing neuropeptides proglucagon (Gcg) and brain-derived neurotrophic factor (Bdnf) in the central nervous system. Endocrinology.
  4. Liang, Wu and Jin. Gut-Brain Psychology: Rethinking Psychology From the Microbiota–Gut–Brain Axis. Front Integr Neurosci. 2018; 12: 33.
  5. Askarova, et al. The Links Between the Gut Microbiome, Aging, Modern Lifestyle and Alzheimer’s Disease. Front. Cell. Infect. Microbiol., 18 March 2020 |
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