Leaky Gut, Chronic Disease, and Long Term Health

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Leaky Gut

This blog discusses the very important health issue of leaky gut. You will learn:

  • What is the gut & the gut microbiome 
  • What is leaky gut, its symptoms and why it matters for your long-term health
  • What is the problem with chronic inflammation and its link to leaky gut & chronic disease
  • What are the causes of leaky gut and how do we test for leaky gut

‘All disease begins in the gut’. – Hippocrates, c. 460-370 BC, over 2,000 years ago

What exactly is The Gut?

The gut is our digestive system. You may also hear it called the digestive tract, the gastrointestinal or GI tract. The gut extends from the mouth, through the esophagus, stomach, small intestine, pancreas, liver, gallbladder, colon and finally rectum or anus. 

What is the Gut Microbiome?

The gut contains a microbiome. The microbiome is the collection of trillions of microorganisms (bacteria, fungi and viruses) that live in the gastrointestinal tract. Most of these microbes live in the large intestine. 

The gut has the largest number and diversity of microbes. The gut bacteria composition changes across the digestive tract. In the stomach and small intestine, there are relatively few species of bacteria. 

There are a small number of core microbial species shared by most people. Beyond that, populations of microbes can differ quite a lot from person to person. Within one person, the microbial populations stay fairly constant over time. Changes can occur due to changes in lifestyle, diet and age.  

The microbiome is extremely important for health and well-being. It influences metabolism, nutrition, physiology and immune function. In fact, 70-80% of immune cells reside in the gut. This means that the health of the immune system depends on the health of the gut.

Even in healthy people, the microbiome has both beneficial and pathogenic gut bacteria. In a balanced gut microbiome, the beneficial bacteria outweigh and keep the harmful bacteria under control. If the harmful pathogenic bacteria become too plentiful, then a condition called dysbiosis results. 

Imbalances in the gut microbiome is linked to gastrointestinal (GI) conditions such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), dysbiosis, gut infections and many others. The microbiome influences health more widely and plays a role in diseases like obesity, type 2 diabetes, mental health issues, allergies, MS, neurological diseases, skin issues and more.

What is Leaky Gut?

Leaky gut is also known as intestinal permeability. It is a condition in which the gut lining becomes permeable or ‘leaky’.

The digestive system breaks down food and absorbs nutrients from the food. It is a barrier which controls what can enter the bloodstream. The mucous lining of the gut is designed to absorb water and nutrients from food that can then pass into the bloodstream. The lining is meant to be protective and non-permeable. This means that nothing extra should pass through, either from the gut into the body or vice versa. 

Tight junctions are proteins in the gut lining. They are tiny openings that allow nutrients and water to pass through into circulation in the body. They prevent harmful or toxic substances from entering the bloodstream. In the case of leaky gut, the tight junctions have loosened, allowing substances that should not pass through the gut lining to do so. This is permeability of the gut. 

Once tight junctions are loose and the gut is permeable, it literally means that there are leaks in the gut lining. Damaging things like toxins, bacteria and molecules of partially digested food can leak through.  These things are meant to stay in the gut to be metabolized or else eliminated through stool. If they get into the bloodstream, they can cause problems by triggering inflammation. 

As inflammation spikes within the gut, it disrupts the gut bacteria and negatively shifts the health of the microbiome. This creates a vicious cycle that worsens leaky gut, which further affects the microbiome.

This inflammation can trigger the immune system to launch an attack. Once the gut is permeable, these substances pass though frequently, which triggers frequent immune system reactions, which can cause widespread inflammation and an over-reaction of the immune system. This inflammation and over-active immune system can become chronic if the leaky gut is not healed.

What are Symptoms of a Leaky Gut?

  • A burning feeling in the gut
  • Painful indigestion 
  • Diarrhea
  • Gas and bloating from fermentation by overgrown bacteria
  • Low energy from the reduced ability to draw energy from food
  • Sensitivities, intolerances or issues that prevent eating a wide variety of foods

Why is it important to Treat Leaky Gut? What happens if the Gut is Leaky?

Leaky gut may be responsible for many health issues. These can be minor (bloating, cramps, fatigue, food allergies and sensitivities, gas and headaches) to much more serious issues like autoimmune conditions, depression and other mood disorders, diabetes, inflammatory bowel disease and MS. 

Many diseases are linked to having a leaky gut. The full list is not entirely known, but some of the diseases that are rooted in leaky gut include any autoimmune disease like Lupus, Type 1 Diabetes, Celiac disease and others. Allergies, arthritis, asthma, autism and gut issues (examples include Crohn’s disease, inflammatory bowel disease, irritable bowel syndrome, ulcerative colitis and others), food allergies, intolerances or sensitivities or multiple food and chemical sensitivities, schizophrenia, skin issues and many other conditions or diseases. 

The Consequences of Leaky Gut for Long Term Health

Chronic inflammation: What is Wrong with Chronic Inflammation?

Inflammation is the body’s response to eliminate foreign unrecognized substances by the immune system. Successfully clearing pathogens is how inflammation is resolved. 

Acute inflammation is when there is a response to a sudden and acute damage to the body, like cutting your finger. To heal the cut, the body sends inflammatory cells to the injury. These cells start the healing process. Once healed, the body stops sending inflammatory cells to the site of the injury. Unresolved acute inflammation can lead to chronic inflammation. 

Chronic Inflammation Leads to Chronic Disease

Chronic inflammation is closely associated with chronic diseases, cancers and aging (Mou Y, 2022). It causes pathogenic changes that happen in various chronic diseases. This includes things like slow tissue remodeling, organ dysfunction, autoimmune responses and cellular senescence. Cellular senescence is when cells age. Senescent cells stop multiplying but don’t die off when they should. They instead remain and continue to release chemicals that can trigger inflammation. 

Inflammation of this type that doesn’t resolve itself is called chronic inflammation or systemic inflammation. It can ultimately lead to chronic inflammatory diseases. In chronic inflammation the body continues to send inflammatory cells even when there is no outside danger. The immune system has gone into overdrive and overreacts. Inflammatory cells and substances start to attack tissue and cause inflammation that comes and goes. This can cause severe damage to tissue. 

Examples of chronic inflammatory diseases that can develop with chronic inflammation include Alzheimer’s, autoimmune diseases, asthma, cancer, heart disease, type 2 diabetes and others.

Leaky gut leads to a state of chronic inflammation. 

In some circles of conventional medicine, leaky gut syndrome is still considered a hypothetical condition and is not necessarily recognized as a medical diagnosis. In Functional Medicine, we know that increased intestinal permeability, or leaky gut, can be a significant health problem which plays a role in chronic inflammation, gastrointestinal disease, autoimmunity and other health conditions.


There are now over 100 known autoimmune or AI diseases (Autoimmune Association, 2023). Well-known examples include MS, Celiac, Type 1 Diabetes, Lupus, Hashimoto’s, Grave’s, Rheumatoid Arthritis, IBD, Crohn’s and many more. 

Leaky gut can be very harmful due to the connection between leaky gut and autoimmunity (or AI). As the gut becomes leaky and more toxins enter into circulation via the loosened tight junctions of the gut, the immune system is activated. It will mark these foreign invaders from the gut as dangerous and attack them. It will be called to do this over and over due to the leaky gut. The immune system will go into overdrive and can then start to be less precise. 

Autoimmune disease develops because the immune system gets triggered and goes into overdrive due to the constant perceived attack. This overreaction can eventually become chronic. 

Due to molecular mimicry, some of these foreign invaders start to look like the different tissues of the body. For example, the gluten molecule is similar to thyroid tissue. So, the immune system will start to attack ‘self’ or own tissue. This can happen to any organ of the body. If the immune system attacks the thyroid, then Hashimoto’s or Grave’s diseases can develop. If it attacks the joints, then rheumatoid arthritis can develop, if it attacks the myelin sheaths, then MS is a possibility.

Once a person has one AI disease, they become highly susceptible to developing a second AI disease. This is because they already have a leaky gut so a second or even third AI condition can develop. This is why it is CRITICAL to work on healing leaky gut.

How do you know if you have Leaky Gut? 

Leaky gut syndrome is a silent disorder. You don’t really feel anything in terms of symptoms. So, most people don’t know they have it until the intestinal lining is damaged. The symptoms of leaky gut syndrome can be a bit vague and they can vary from person to person. The main symptoms of leaky gut can include:

  • A burning feeling like an ulcer in the gut
  • Painful indigestion 
  • Gas, bloating or abdominal pain
  • Diarrhea and/or constipation
  • Poor immune function due to poor gut health
  • Headaches, brain fog and/or memory loss
  • Abnormal fatigue due to the reduced ability to draw energy from food
  • Nutritional deficiencies, resulting from the reduced ability to draw energy from food
  • Skin issues such as rashes, eczema, acne, rosacea
  • Strong carbohydrate or sugar cravings
  • Joint pain or arthritis
  • Mood swings, depression, anxiety, ADD or ADHD
  • Autoimmune disease

If you think you may have leaky gut syndrome, it is important to see a Functional Medicine doctor. In our clinic, we regularly work with people on improving gut health and resolving leaky gut.

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What are the Causes of Leaky Gut?

Leaky gut is caused by a combination of potential triggers that cause the gut to become leaky or permeable. These triggers include:


Diet is one of the biggest factors in leaky gut syndrome. The gut bacteria respond very quickly to changes in diet. An unhealthy diet can begin to damage the microbiome in as little as 24 hours, leading to dysbiosis (David LA, 2014). In contrast, diet can be very healing for a gut that has become leaky. Minor damage to the microbiome can be reversed in 2-4 days, by eating a healthy diet (David LA, 2014).  

Nutrient deficiencies, particularly in vitamin A, D and zinc, are also a factor and can increase gut permeability.

The foods to avoid because they cause leaky gut are:

  • Processed foods
  • Excessive sugar & artificial sweeteners, in particular sucralose
  • Dairy 
  • Excessive alcohol 
  • Processed seed oils and unhealthy fats 
  • Legumes
  • Soy
  • Raw vegetables can be harder to digest with gut issues like leaky gut
  • Other toxic/inflammatory foods: nightshades, eggs or GMOs
  • Any food to which a person has an allergy or intolerance is inflammatory

A Note on Gluten & Zonulin

Grains, and especially gluten, can be inflammatory and lead to leaky gut. This is not just a problem for celiac people or those with a gluten intolerance. Research shows that gluten creates leaky gut in everyone.  

This is because the protein called gliadin, found in wheat and gluten, increases another protein, zonulin. Zonulin weakens the tight junctions, causing the tight junctions of the gut to open. When gluten is consumed regularly, this zonulin-initiated opening of tight junctions is repeated over and over. This eventually causes the gut to become leaky.  

Gluten-containing foods are:

  • Grains such as wheat, spelt, rye and barley.
  • Foods made from wheat include all types of bread (unless labeled ‘gluten-free’), baked goods like cake, cookies, doughnuts, muffins, pies, pancakes and waffles. Pasta, cereal and crackers all have gluten as well. 
  • Gluten appears in unexpected foods like beer, gravy, soups, some pasta sauces or salad dressings. 

Going gluten-free initially requires some education to learn how to avoid all the numerous foods with gluten.


  • Pharmaceutical medications, including NSAIDS (non-steroidal anti-inflammatory drugs) like Ibuprofen, Motrin and Advil, steroids, the birth control pill and acid-reducing drugs like PPIs, contribute to leaky gut.
  • Chemotherapy and radiation therapies degrade the intestinal mucosa and contribute to leaky gut.
  • Antibiotics kill both good and bad bacteria in the gut, which can lead to an imbalance of bacteria and damage the gut lining.

Environmental Toxins & Chemicals

Environmental triggers are many-fold in today’s polluted world. They can come from the diet. Things like gluten, dairy, GMO’s, food additives, pesticides, chemicals used in processed foods and in processing, etc. can be a trigger that over-activates the immune system. 

According to the World Health Organization, there are now more than 160 million chemicals in use (WHO, 2022). One huge source of chemicals is personal care products and cosmetics. Personal care products are largely unregulated. The FDA does not require safety testing of ingredients in personal care products before they are used. 


Chronic inflammation is a big contributor to leaky gut, as it loosens the tight junctions. Chronic inflammation can be triggered by poor lifestyle habits:

  • Drinking too much alcohol
  • Being overweight or obese
  • Not exercising or exercising at maximum intensity too frequently
  • Being chronically stressed out
  • Smoking cigarettes
  • Not sleeping enough

Gut Issues

  • Pathogenic bacteria in the gut can also trigger zonulin, which will loosen the gut lining.
  • Gut conditions, like yeast overgrowth, candida, SIBO (small intestinal bacteria overgrowth), gut dysbiosis (when bad or toxic bacteria outnumber the good bacteria in the gut), parasites, other pathogens or other gut issues can all lead to intestinal permeability or a leaky gut.
  • Infections, such as H pylori, salmonella and E. coli, can damage the gut lining.

Chronic infections

Chronic infections can be the stealth cause of many health problems. Infections that are low level or undiagnosed can drain the immune system and allow it to get stuck in the ‘on’ position. If undiscovered, chronic immune activation and low-level inflammation over time damage the gut lining. Infections that can become chronic and are notoriously hard to diagnose include Lyme disease or any Lyme co-infections. Viral infections may be the issue. Viruses remain dormant in the body and can basically be reactivated at any point in time, particularly during times of stress. Shingles is an example, as it is the reactivation of the chicken pox virus. Mold illness, which can develop into CIRS (Chronic Inflammatory Response Syndrome) is another example. It can be hard to diagnose and can become a serious and chronic health issue. Other infections, like strep throat, can be low level and simply overlooked. The infections and their related toxins are damaging to the gut lining.


Stress has a negative and multi-pronged approach to damaging gut permeability (Madison A, 2019). Stress raises inflammation and gut barrier permeability. For example, two cytokines involved in immune and inflammatory responses, called IL-1 and IL-6, increase cortisol release (Obrenovich, 2018). Cortisol is the main stress hormone and contributes to gut leakiness. Stressed patients often have HPA axis dysregulation, resulting in elevated cortisol levels (Obrenovich, 2018).

A leaky gut allows bacteria to seep into circulation, producing an inflammatory response. This can further increase cortisol and weaken the gut (and other) barriers. Bacteria can leak through the stress-remodeled gut barrier, thereby boosting inflammation (Madison A, 2019). 

One study looked at difficult marriages as a chronic stressor (Kiecolt-Glaser JK, 2018). The couples in difficult marriages had greater gut permeability than their less hostile counterparts (Kiecolt-Glaser JK, 2018). The study concluded that a distressed marriage can promote a pro-inflammatory environment in the body through increased gut permeability. This would then impact the permeability of other barriers and fuel inflammation-related diseases and disorders (Kiecolt-Glaser JK, 2018).

Testing for Leaky Gut

There is no one perfect test to diagnose leaky gut syndrome. Diagnostic tests are not 100% accurate in confirming leaky gut, but they can give info on gut permeability, immune response or levels of inflammation.

A blood test or stool test can show signs of inflammation or damage to the gut lining. There is a zonulin test. Zonulin regulates the tight junctions of the gut lining and can be measured in the blood or stool. Zonulin antibodies can also be measured. 


  • The health of the gut microbiome is critical for overall health and immunity.
  • The gut can become leaky, meaning there are essentially tiny openings in the gut lining. This allows toxins and other unwanted substances to enter into the bloodstream.
  • Once this happens, the gut is now leaky or permeable. Leaky gut can lead to chronic inflammation. Chronic inflammation can lead to chronic diseases like autoimmune conditions, digestive diseases (IBD, IBS, etc.), Alzheimer’s, skin conditions and many others.
  • A leaky gut can develop from:
    • A poor diet
    • Gluten
    • Medications
    • Environmental toxins & chemicals
    • Inflammation
    • Gut issues
    • Chronic infections
    • Stress
  • Testing for leaky gut is not a perfect science. We can run a few tests to check or we can presumptively treat a leaky gut based on the symptoms picture of a person.

** Please stay tuned for our next Blog on Leaky Brain!  **

As always, please get in touch with us. If you or someone you know is struggling with cognitive or neurological symptomscontact our clinic today. We can work on any issue(s) and improve your health. Book a free health evaluation call with us today, to see how we can help you with your concerns. We can answer your questions and help you book an initial consult with one of the functional medicine doctors in our clinic.

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Dr. Miles has spoken for the following organizations:

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