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How High Cortisol and Stress Shuts Down Digestion, and Affects Your Gut Microbiome

The link between stress, digestion, and your gut microbiome has received significant attention in recent years. Our bodies have a remarkable response to stress known as the “fight or flight” response. When activated, our adrenal glands will release a variety of stress hormones, including cortisol. While cortisol is crucial for short-term stress responses, ongoing chronic stress, can lead to high levels of cortisol and all the problems that go along with it.

In today’s article, I will explain exactly how stress and high cortisol cause various problems related to digestion. I will also explain how stress and cortisol can negatively affect the gut microbiome. Lastly, I will review some important nutritional and lifestyle tips to alleviate the impact that this stress has on your digestion and gut microbiome.

The Consequences of High Cortisol on Digestion

We’ve all experienced that feeling when we’re nervous: an upcoming interview, a school presentation in front of our peers, where we feel like we are being judged, those jitters that we feel in the pit of our stomach are proof that our brain and gut are connected. It’s no surprise that the gut is often referred to as the second brain because it has a nervous system with more neurotransmitters than the brain’s central nervous system.

The Centers for Disease Control and Prevention of the United States estimates that stress accounts for around 75% of all doctor visits (*) and this level of stress extends to primary care doctors. Studies show that stress and burnout among primary care doctors is 50% to 80%.(*)

These patients and primary care doctors report having heart problems, an upset stomach, ulcers, insomnia, fatigue, back pain, and headaches, among other complaints. Stress also increases your risk of diabetes, especially in overweight individuals.

One of the biggest problems I see with my patients who have Leaky Gut, IBS, or IBD, and SIBO is a history of a lifetime of stress and anxiety. Those are always the common denominators. “When we’re stressed, our brain activates the sympathetic nervous system.

The sympathetic nervous system is our flight-or-fight response: it prepares the body to protect itself against imminent danger by conserving functions that aren’t immediately needed for survival. That makes sense right? Our innate wisdom of the body prioritizes what needs to be done here and now.

As part of this fight or flight response, under stress, your brain will send a signal to your adrenal glands instructing them to pump out a hormone called Cortisol and adrenaline. During this fight or flight response, (Stress response) If it doesn’t help you run faster, run longer, or fight harder, it will take a back seat and that includes almost every aspect of digestion. Digestion does not take center stage when you are under stress. You see our Digestion, is run by another part of our nervous system known as “Rest and Digest” It’s better known as our Parasympathetic Nerve System.

Stress and gut Microbiome

How High-Stress Levels Alter The Gut Microbiome

High cortisol can induce negative changes in the gut microbiome, the community of microorganisms living in our intestines(*). Remember when our body perceives stress, our adrenal glands begin to secrete Cortisol. High cortisol levels can alter the balance of gut bacteria, favoring the growth of harmful microbes like Streptococcus, and Escherichia coli while reducing the populations of beneficial bacteria like Lactobacillus and Bifidobacterium.(*) This imbalance in the gut microbiome, known as dysbiosis, can further compromise the integrity of the intestinal barrier and exacerbate a Leaky Gut.

The combination of increased gut permeability due to changes in tight junction function and alterations in the gut microbiome composition can create a vicious cycle in which stress contributes to Leaky Gut, and Leaky Gut, in turn, can perpetuate chronic stress and inflammation in the body.(*) The consequences of stress-induced leaky gut extend beyond digestive issues and can have far-reaching effects on overall health, including immune dysfunction, systemic inflammation, and the development or exacerbation of various chronic diseases.

Stress and Leaky Gut

High Cortisol, Stress, And Leaky Gut

Stress can significantly impact the integrity of the intestinal barrier and contribute to the development of a Leaky Gut.(*) When we experience stress, whether it be acute or chronic, our bodies respond by releasing cortisol, the primary stress hormone. High levels of cortisol in the body can lead to changes in the gut environment that affect the tight junctions between cells in the intestinal lining. These tight junctions act as gatekeepers, regulating the passage of molecules and substances into the bloodstream.

Under conditions of chronic stress, the continuous presence of high cortisol levels can disrupt the normal functioning of the intestinal barrier. Cortisol has been shown to increase gut permeability by affecting the proteins that make up the tight junctions, making the barrier more permeable.

Normally, the intestinal barrier acts as a selectively permeable membrane, regulating the passage of nutrients while keeping harmful compounds out of circulation. However, under conditions of chronic stress and sustained elevation of cortisol, the integrity of this barrier can be compromised.

This increased permeability allows for the passage of larger molecules, such as toxins, undigested food particles, and bacteria, from the gut into the bloodstream. As these substances leak into the circulatory system, they can trigger an immune response and system inflammation throughout the body. Learn more about common causes of Leaky Gut here.

Stress, High Cortisol, And Vagus Nerve Function

Stress and high cortisol impact many areas of digestion and we can’t talk about the effect of stress on digestion without talking about the Vagus Nerve. If you never heard of the Vagus Nerve here is a little refresher on why it’s important for digestion. The vagus nerve plays a crucial role in the bidirectional communication between the gut and the brain, forming a key component of the gut-brain axis and it plays a major role in digestion(*). As the longest cranial nerve, the vagus nerve extends from the brainstem to various organs in the body, including the heart, lungs, and most importantly, the gastrointestinal tract. Its intrinsic connection to the gut makes it a vital player in regulating digestion, gut motility, immune responses, and overall gut health.(*)

One of the primary functions of the vagus nerve concerning gut health is its role in modulating the parasympathetic nervous system, which is responsible for promoting rest, relaxation, and digestion.

The Mighty Vagus Nerve

The vagus nerve helps to stimulate the release of

  • Stimulates organs of digestion to release enzymes
  • Stimulates or increases gut motility,
  • Stimulates and plays a role in appetite,
  • Regulates intestinal inflammation-maintain a balance between pro-inflammatory and anti-inflammatory pathways
  • Enhances nutrient absorption.

All of these functions are essential for maintaining a healthy digestive system (*). By activating the parasympathetic response, the vagus nerve promotes optimal gastrointestinal function and supports overall gut health.

Additionally, the vagus nerve regulates gut-brain communication, influencing mood, emotions, and stress responses. Through its connection to various brain regions, the vagus nerve can transmit signals related to gut health and overall well-being. This communication pathway is pivotal in linking gut dysfunction with conditions such as anxiety, depression, and mental health disorders, highlighting the interconnectedness of the gut and brain in maintaining holistic health.(*)

Research has shown that the vagus nerve can sense and respond to signals from the gut microbiota, influencing brain function and behavior.(*) The vagus nerve is activated by several neurotransmitters produced by the gut microbiota. This highlights the importance of a healthy gut microbiome in promoting optimal vagus nerve function and overall gut-brain axis balance.

Enhancing vagus nerve tone can be accomplished by correcting intestinal dysbiosis, and improving short-chain fatty acids, prebiotics, and probiotics. If you have gut issues you will want to learn ways to stimulate this vagus nerve to support your gut microbiome, digestion, and motility. You can do this with specific exercises known as vagal nerve exercises.

Stress and High Cortisol Can Shut Down The Vagus Nerve 

Remember the Vagus nerve represents the main Nerve of the parasympathetic nervous system, and this parasympathetic nerve system, everything from our mood oversees, immune response, heart rate, and yes digestion! Think of your Vagus nerve as the connection between the brain and the gut. When stress hormones like cortisol run high, they put a block on the Vagus nerve.

High levels of Stress hormones, like cortisol and adrenaline, decrease blood flow to the digestive system including the stomach… this in turn causes less Hydrochloric acid production in the stomach. Well….. (HCL) Hydrochloric acid is needed to digest fats and proteins. If you decrease Hydrochloric acid (HCL) production this is going to put the brakes on the digestion of proteins and fats. Now stop for a moment and think, “What might be the consequence of poor digestion of proteins and fats?”

If you said bloating, gas, belching, feeling full all the time, food allergies, skin conditions, and toxicity,  you would be exactly right. When stomach acid is decreased, due to high cortisol levels, the overall pH of the stomach rises, in other words, it becomes more alkaline, and bacteria that are normally killed by acid, begin to proliferate. This is one of the ways people get infected with H.pylori and other pathogenic bacteria.

Follow these 5 tips to improve low stomach acid

Stress Stomach Acid and Acid Reflux

Stress, High Cortisol, And Acid Reflux

While we are on the topic of bacteria let’s review how stress can cause or exacerbate Acid reflux. Once these bacteria begin to take over and colonize your gut, you can get an enormous amount of gas that builds up pushing against a sphincter called the lower esophageal sphincter, or the LES for short. The LES prevents the contents of the stomach from coming back into the esophagus. This is what we call acid reflux. Acid reflux is caused by a LES (lower esophageal sphincter) that’s not working the way it’s supposed to. It’s not creating a nice tight seal between the stomach and esophagus.

If you have acid reflux you most likely have an infection with H.pylori, you could have a problem with not enough acid in your stomach, you could have a problem with LES and you could have too much cortisol shunting blood away from your stomach and reducing acid production.

Stress can slow down the emptying of the stomach, causing food and stomach acid to remain in the stomach for a prolonged period. This delay can increase the pressure in the stomach, leading to the reflux of acid into the esophagus.

Hopefully, you can now see that simply taking antibiotics and antacids does not fix the root cause of Acid reflux. If you don’t ask the right questions, you will never get the right answers.

Bloating and Stress Can Cause SIBO

High Cortisol And The Gut Microbiome

High cortisol, caused by prolonged stress, can also have dire consequences on your gut microbiome. These changes often show up as Small Intestinal Bacterial Overgrowth (SIBO). SIBO is a condition characterized by the overgrowth of bacteria in the small intestine. Normally the small intestines do not have the same kind of bacteria that the large intestines do. But once the bacteria from the large intestines move up and colonize the small intestines, they begin to rob nutrients from you, while producing hydrogen or methane gas. We can thank stress and high cortisol levels for this.  High cortisol levels can cause Small Intestinal Bacterial overgrowth (SIBO). High cortisol is not the only cause of SIBO and changes to the gut microbiome, but when cortisol levels run high, it can make treatment and relapse rates a bit of a challenge.

There are many factors behind SIBO. Some of the factors include a high sugar diet, a bout of food poisoning, motility issues, hormone imbalances, neurotransmitter imbalances, and certain medications that can disrupt this balance, allowing bacteria to proliferate in the small intestine. SIBO can manifest through symptoms such as gas, bloating, diarrhea, fatigue, and skin issues like rosacea. But let’s talk about bloating and SIBO.

Being bloated all the time causes a malfunction in another valve called the ileocecal valve. The Ileocecal valve is another valve- This one is between the small intestines and the large intestines. If you are bloated all the time, your IC valve stays open, and this is how we develop bacteria overgrowth in the small intestines. When the IC valve stays open, bacteria from the large intestines, move up and take residence in the small intestines.

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Fight or Flight Digestion and Our Gut Microbiome

There are a few more things I want you to know about stress, high cortisol, and the microbiome. When the HPA axis is we get a surge of cortisol and adrenaline released into our system. Let’s review the consequences.

  1. Alteration to the gut microbiome
  2. We get changes in the permeability- The gut becomes more leaky, and this can be a biological door into colorectal cancer, autoimmune diseases, and several chronic health problems caused or exacerbated by a Leaky Gut. (*)
  3. Thinning of the gut lining (*)
  4. Decreased mucous production. Mucous not only forms a physical barrier the mucous layer of the gut is the home for a major part of the immune system. (*)
  5. Decreases SIgA Levels(*)

Sadly, early events in our life that kept us in this fight or flight state, program the HPA axis- for all these consequences. This becomes one big problem that snowballs into even bigger problems. This is the connection between stress, and how high cortisol affects digestion and various problems in the gut.

Tips To Alleviating Stress Improve Digestion and Improving Your Microbiome

Tips To Alleviating Stress, Improve Digestion, and Improving Your Gut Microbiome

Whether you have been diagnosed with anxiety, panic disorder, or some other condition, it should be quite clear that balance needs to be reestablished between your sympathetic and parasympathetic nervous system

To have a positive impact on digestive symptoms, we want to activate the parasympathetic nervous system, which is the body and brain’s rest and digest response—it undoes what the sympathetic nervous system does.

When the parasympathetic nervous system is activated, your body becomes calm, your heart rate goes down, and your gastrointestinal system functions as it should.

If this is something you want to learn more about “How to activate your Vagus Nerve” I recommend that you read the article I wrote on Vagus Nerve Exercises.

Remember This About The Effects Of Stress on Gut Health, Digestion and Motility

So a few things to remember and a few recommendations when it comes to dealing with stress and gut/digestive problems. Too much stress and high cortisol can have numerous implications for our digestive health. Symptoms like bloating, constipation, heartburn, and stomach pain may be a sign that you are more stressed than you might think.

If you have infections that keep coming back, SIBO that doesn’t improve, or a leaky gut that never heals, and when I say Heals- I mean you tested for it, you identified it through testing, you treated it and now you retested, and the testing shows the problem is gone. That’s what I mean when I say heal.

If you’re not healing (based on retesting) it might be time to look at your adrenal glands and how they are one of many root causes that are causing you to plateau.

Well, there you go! I hope today’s video, helped you understand another piece of the puzzle on how stress affects the gut and perhaps why you’re not getting better despite changes in your diet, medications, and or supplements. You need to know the “WHY”

If you have questions about today’s video, the best way for me to answer them is for you to drop a comment below.

If you have questions about becoming a patient and learning more about my BIG picture you can visit my website lastly, after you give today’s video a thumbs up I recommend that you watch this video next.

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  4. The Gut-Brain Connection- Learn How to Harness this Powerful Connection.
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