How To Fix Leaky Gut Naturally


If you’re having any kind of chronic inflammation, you should definitely be addressing your gut to be sure it is functionally optimally.

Did you know that technically the area from your mouth all the way through your gut is outside of your body? Our intestinal barrier is meant to selectively allow only certain nutrients to pass into the body. Leaky gut, or better known as increased intestinal permeability, is a condition in which the intestinal barrier “leaks” or allows more things to enter the body that shouldn’t.  The intestinal barrier becomes less protective against bacteria, parasites, and fungi, as well as food particles that are not completely digested.  When these allergens and antigens enter the body, they have the potential to illicit an immune response.

Many believe that leaky gut is the cornerstone of inflammatory conditions and autoimmune disease.  Even Hippocrates, who stated “All disease begins in the gut” over 2,000 years ago, knew that the gut plays a crucial role in total body health.

Leaky gut is associated with autoimmune diseases like type 1 diabetes, inflammatory bowel disease, rheumatoid arthritis, asthma, multiple sclerosis, chronic fatigue syndrome and depression. (R)

It’s no surprise that people with inflammatory bowel disease tend to have damaged intestinal barriers. (R) (R)  The goal with most chronic health conditions is to lower inflammation. Many cytokines, including tumor necrosis factor-a (TNF-a) and interferon-g (IFN-g), disrupt the intestinal barrier during active phases of inflammatory bowel disease. There are also mucosal mast cells release mediators that affect gut permeability, which include histamine, serotonin, leukotrienes, prostaglandins, IL-4, and TNF-a. (R)

The epithelial layer of the gut is the front line of the barrier, and is made of a single layer of cells linked together by tight junctions, and covered by two layers of mucus. (R) Tight junctions can be thought of the gate keepers in the intestinal tract, which allow nutrients to enter the body to be used for energy and metabolism.  When the gut is damaged, the tight junctions are not as good at keeping environmental antigens out of the body.

Environmental antigens that pass through a leaky gut can trigger local and systemic inflammation. (R)

Symptoms of intestinal permeability are wide and varied. Bloating, constipation, diarrhea, gut pain, and anything associated with an abnormal gut are common symptoms. The symptoms can be both local and systemic, which is why many people with leaky gut also have other symptoms, such as acne or eczema, headaches, and joint pain.

When the gut becomes leaky or more permeable, the gut itself can definitely become inflamed. However, leaky gut can contribute to inflammation in other organs, and may not necessarily cause inflammation in the gut. So, while you may not notice gut pain, you may notice joint pain which could be stemming from leaky gut.


Testing for Leaky Gut

Lactulose-Mannitol Test

A simple, affordable test is the lactulose-mannitol intestinal permeability test. You swallow two non-metabolized sugars, lactulose and mannitol. Lactulose and mannitol are then measure in the urine, and ratios between the two are assessed. 

LPS, Occludin, Zonulin, and Actomyosin

Cyrex Laboratories has one called Cyrex lab Array #2 that is a blood draw which measures lipopolysaccharides (LPS), occludin, zonulin, and actomyosin protein antibodies.


Causes of Leaky Gut

In short, these are the main causes: (R)

  • Intestinal inflammation
  • Stress
  • Nonsteroidal anti-inflammatory drugs (NSAIDs)
  • Alcohol
  • Cow’s milk intolerance (and likely any food intolerance, such as wheat)
  • Small intestinal bacterial overgrowth (SIBO)
  • Pancreatic insufficiency
  • Gut infections
  • Dysbiosis
  • Obstructive jaundice
  • Vitamin and mineral deficiencies


Wheat, Gluten, and Food Sensitivities


Zonulin is a protein in the body that increases intestinal permeability. It does so by binding and opening the tight junctions between epithelial cells in the gut.

Zonulin is found to be increased during acute phases of celiac disease, which then decreases when following a gluten-free diet. Persons with autoimmune conditions, such as type 1 diabetes, have also been found to have higher levels of zonulin. (R) (R)

The reason wheat is bad for inflammatory conditions is because it contains gliadin, which increases zonulin, which then increases intestinal permeability. This occurs whether someone has autoimmunity or not. (R)

Wheat also contains wheat germ agglutinin, which can cause inflammation, including histamine release from mast cells. (R)

If you have any type of chronic inflammation, wheat should be the first you get rid of.

If you’re sensitive to other foods, and you get inflammation from them, it could potentially lead to leaky gut.


Gut Bacteria

Our bodies contain roughly the same amount or even more bacteria cells than human cells. (R) This is kind of crazy to think about.

We need gut bacteria in order to thrive. They have the ability to regulate metabolism, immune function, and protect us from infection. Not only do we need gut bacteria in general, but we need the right amounts of good bacteria, and a disrupted microbiome is linked to many conditions, particularly autoimmune conditions. (R)

One primary reason why an unbalanced microbiome is linked with inflammatory conditions is due to bad bacteria increasing intestinal permeability.

There are actually quite a few things that can disrupt the balance of good bacteria to bad bacteria. Antibiotics are probably the most well-known cause of creating an unhealthy balance of bacteria in the gut. (R)

Just 3-4 days of antibiotic use causes a loss of diversity and shift in bacterial communities. After antibiotic treatment, some bacterial communities returne to their initial state, while others do not, leading to a disruption in the balance of the gut microbiome. (R)

Other causes include a diet low in fiber, high in processed and refined carbohydrates, as well as stress and infections. Infants that aren’t breast fed have been found to be at an increased risk of developing a disrupted microbiome.

A Western diet, which is highly processed, high in fat, and high in sugar, can be detrimental to the gut. (R)

Zonulin is dependent on gut bacteria. Probiotic supplements decrease zonulin, and improve intestinal permeability. (R)

Beneficial bacteria help prevent the colonization of pathogens by competing for space, nutrients, and they can release antimicrobials. Beneficial bacteria can also digest fiber and produce short-chain fatty acids. These short-chain fatty acids, such as butyrate, can be used for energy by the cells of the colon (colonocytes). (R)

Increasing the probiotics Lactobacilli and Bifidobacteria can help restore a healthy gut bacterial population. (R) Lactobaccilus plantarum, Bifidobacterium longum, and Lactobaccilus rhamnosus GG improve tight junction and intestinal barrier function. (R)

A diet high in saturated fat decreases Lactobacillus and increases Oscillibacter, which correlates with increased intestinal permeability. (R)

Helicobacter pylori is a gram-negative bacterium that increases intestinal permeability. (R)

Getting rid of infections, consuming probiotics, and maintaining a balance of good bacteria in the gut are crucial for maintaining a healthy gut.


Stomach acid reducing medications

The stomach is supposed to be acidic. It helps breakdown and digest the food we eat, and it also protects us by killing harmful bacteria before it has the change to find a new home in our gut. Chronic ingestion of acid reducing medications may lead to gut infections and bacterial overgrowth, (R) which may increase intestinal permeability



How to Fix Leaky Gut

*I recommend working with a qualified health professional before trying anything discussed here.

In short, here’s what you will need to do:

  • Remove intestinal pathogens
  • Restore a healthy balance of good bacteria with probiotics and fermented foods (if tolerated)
  • Heal the cells of the gut
  • Reduce stress
  • Eat more fiber (careful with SIBO)
  • Eat a diet that doesn’t cause you inflammation and provides adequate nutrition
  • Avoid proton pump inhibitors or H2 blockers, which decrease stomach acid and can lead to dysbiosis, overgrowth, and increased intestinal permeability
  • Don’t take NSAIDs and other medications that increase intestinal permeability, if possible
  • Stop taking antibiotics if you don’t need them – if you do need them, take probiotics during antibiotic treatment
  • Try supplements that lower inflammation and help heal the gut


Balance Gut Bacteria

Since we know that an unhealthy balance of intestinal bacteria can cause leaky gut, then we will need to create a health balance of them. If you have gut infections, I recommend working with a qualified professional to help you. Herbal antibiotics such as berberine, oil of oregano, and garlic are effective at killing off microbes.

You'll also need to consume probiotics. Fermented foods work well if you tolerate them, as do probiotic supplements. Be sure you are getting at least Lactobaccilus plantarum, Bifidobacterium longum, and Lactobaccilus rhamnosus GG, since these are great for gut health.

What’s the Best Diet for Leaky Gut?


The best diet for leaky gut and inflammation is different for everyone. The best way to figure out which foods are causing inflammation for you is an elimination diet. This is where you eliminate the foods that you think are causing inflammation for a certain amount of time; I would say at least 30 days. You then add back each food one at time, every 4-7 days. During this time, you’ll need to document and track your food intake, calories, nutrients, as well as symptoms pre-elimination, during elimination, and as you add back foods.

Luckily, there are a few different diets out there to at least get you heading in the right direction.

Here are some ideas:

  • Paleo Autoimmune Protocol/Low Lectin Diet (no grains, beans, legumes, nightshades, nuts/seeds, cow’s milk, eggs)
  • Low Histamine Diet
  • Low FODMAP Diet
  • Modified Vegan or Vegetarian Diet (no animal products, while also eliminating the most allergenic foods like wheat, nuts, seeds, etc.)
  • Bowel Rest - Intermittent Fasting or Liquid Diet

Which route you want to go with diet will depend on your individual preferences, knowledge about your own body, and ability to follow through.

Interestingly, most of the healing diets out there have some very common foods that are eliminated.  Wheat and grains are problematic for a lot of people with inflammation. Nuts and seeds are also a common problem for many, as well as cow’s milk, eggs, and beef. The removal of refined carbohydrates are also common in all diets to improve gut health, except for maybe liquid diets. Fiber is also important, since low fiber diets increase the amount of bacteria that degrade intestinal mucus, increasing susceptibility to damage. (R)

Obviously, no junk food is allowed.

Be sure to track you nutrient and food intake. It’s likely that you’ll need vitamin and mineral supplementation during the elimination phase, depending on how many foods you remove. It’s also a good idea to work with a qualified health professional, particularly if you’ve never done anything like this before.


Lower Stress

We all know stress is bad for health. Stress comes in all forms, not only psychological, but also chemical and physical. Stress activates mast cells to release inflammatory mediators. Mast cells are found in the gut, and stress can activate them, leading to intestinal barrier damage. (R)


Vitamin A

Vitamin A helps protect us from infection, and vitamin A deficiency and subclinical deficiency can alter the gut microbiome and lead to an increase in intestinal permeability. (R)

Be sure you are getting enough in your diet.


Vitamin D

Vitamin D protects the gut by increasing the expression of tight junction proteins. (R)

You can read more about vitamin D here.



Zinc deficiency has been shown to lead to intestinal inflammation and damage to the intestinal barrier. It also stabilizes mast cells. If you supplement with zinc, be sure you are consuming enough copper, as they need to be in balance. Zinc supplementation can lead to copper deficiency (R), so be careful.


Fiber and Butyrate

Butyrate produced by bacteria in the gut inhibit intestinal inflammation, reduce oxidative stress, and help maintain the integrity of the gut. Butyrate is produced by gut bacteria when they ferment or digest fiber. Both soluble and insoluble fiber are important for maintaining the health of the gut. (R)


Don’t Take NSAIDs

NSAIDs increase intestinal permeability within 12 hours, and increase inflammation in the small intestine within 10 days. (R)

If possible, avoid taking NSAIDs.


Don’t Drink Alcohol

Alcohol is bad for gut health. It can lead to an altered gut microbiome, bacterial overgrowth, and it increases gut permeability. (R) Avoid it, especially when you're trying to heal.


Exercise, But Not Too Hard

Exercise is important for health. However, too much exercise can increase intestinal permeability through increased oxidative stress and inflammation. (R)



In cells models, quercetin promotes tight junction proteins, which may help repair a leaky gut. (R)

I personally have found quercetin to be helpful for gut inflammation. Quercetin inhibits mast cells in the gut, and can help reduce inflammation. (R)  I can tell you from my own experience, that quercetin indeed works wonders for gut inflammation.


Digestive Enzyme Supplements

Betaine HCl and digestive enzyme supplements are commonly used to help breakdown and digest food.

An altered gut pH, and low production and release of digestive enzymes can play a role in malabsorption, food intolerance and allergy, autoimmune conditions, bacterial overgrowth, and gastrointestinal discomfort. Persons with pancreatic insufficiency tend to have an increase in intestinal permeability, and digestive enzyme supplementation can improve intestinal permeability. (R)

I prefer to get the body to make more stomach acid and increase its own digestive enzymes, if possible. One way that has helped me digest food is to chew on a piece of ginger before or during my meal.  This really gets the digestive juices flowing, and I find it helps increase digestion better than taking supplements.

If you want to go the supplement route, acid-stable fungal enzymes may be a better option than supplemental pancreatic enzymes, since the acid in the stomach can destroy most of the pancreatic enzymes. There are enteric coated pancreatic enzymes, but in people with pancreatic insufficiency, they might not be able to produce and release adequate sodium bicarbonate to dissolve the capsules. (R)



Omega-3 are well-known for decreasing inflammation, particularly in those with inflammatory conditions. (R)

Western diets typically comprise of too much omega-6 fatty acids, and too little omega-3 fatty acids, leading to a more pro-inflammatory body.

You should at least be getting the recommended amount of omega-3s in your diet. If your gut is inflamed, it’s likely that a higher intake of omega-3s could help. It can thin your blood though, so if you're bleeding, don't take too much.

I’m not entirely sure how I feel about fish oil, since it’s been found to be highly oxidized. That being said, I have found relief in the past for ulcerative colitis through fish oil supplementation. You can read more about fish oil here.

You can get enough omega-3s from actual food, such as salmon and flax seeds, which is what I recommend.



Curcumin has anti-oxidant and anti-inflammatory properties. In rat and cell studies, curcumin helps heal the gut and intestinal permeability. (R) (R) Curcumin can also thin blood like omega-3s, so be careful.


Slippery Elm

Mucus is important for protecting the gut lining. Slippery elm contains mucilage, which can help coat, soothe, and protect the digestive tract. It also has the ability to increase mucus secretion.  Know that slippery elm may decrease the absorption of medications, herbs, and nutrients. (R)


Coconut Oil/Medium Chain Triglycerides

Coconut oil contains medium chain triglycerides, which are beneficial for a number of reasons. The first is that they are easy to digest and do not require bile for digestion and absorption. (R)

In a damaged gut, and particularly for people with fat malabsorption, coconut oil and MCTs can be a good source of fat and calories. Coconut oil is also an antimicrobial, and has been shown to improve intestinal bacteria and health. (R)

Coconut oil is high in saturated fat, so for those who are sensitive to saturated fat, be careful on the amount you consume.



L-glutamine is considered a conditionally essential amino acid, because at times of great stress and injury, the body cannot make enough to keep up with the demands for repairing tissue. L-glutamine is used for fuel by colon cells, and used for repairing and maintaining the intestinal barrier. (R)

Glutamine is also needed for the production of secretory IgA. (R)

L-glutamine has a lot of science backing it up. If you tolerate it, then this is something that will likely help repair the gut. L-glutamine gave me a headache when I tried it a few years ago, but I may give it another shot at some point.



N-acetyl-D-glucosamine (NAG) is found in the intestinal mucus and secretory IgA, and can block the adherence of Candida albicans to the gut. NAG deficiency has been found in the mucin of persons with inflammatory bowel disease.  It’s possible that it could help. (R)