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Leaky Gut Not Healing? 7 Tips To Heal Your Leaky Gut

Healing your leaky gut is a journey full of ups and downs, it’s not always an easy straight line for gut recovery. There are a lot of pitfalls and mistakes that can be made along the way. If you are new to this journey, hang in there because it does get easier with time. If you are like most of my patients, you are probably struggling with many overlapping health problems, in other words, problems outside the gut like thyroid problems, adrenal fatigue, and hormone imbalances. These areas all impact how a leaky gut heals. But, if you understand this from the very beginning, you will have a better idea of the healing journey and what to expect. Because it is a journey, there is no quick 30-day leaky gut fix or magical protocol that works for everyone.

Depending on what kind of shape your gut is in, and what you are dealing with, It could easily take a year or longer. Healing a Leaky gut is going to require you to be super intentional with how you treat your body, and what you put into your body. I always recommend that you work with a functional medicine doctor who will be able to see all the pieces of your health puzzle, order you the correct functional lab tests, and help heal your gut faster than trying to do this on your own.

So, in today’s article, I want to review some of the most common reasons your leaky gut is not healing as well as some tips to help it heal faster.

Leaky Gut Not Healing?

1. Lectins And Leaky Gut

So, when someone has a leaky gut and it just doesn’t seem to be healing, sometimes we need to consider Lectins. Lectins are a type of protein found in many plant-based foods, such as legumes, grains, and nightshade vegetables. They are a natural defense mechanism in plants and can bind to carbohydrates on the surface of cells, including the lining of the gut. Healing a leaky gut can be more challenging for Vegans and Vegetarians who depend on many lectins as a protein source. The highest concentrations of lectins are found in foods like legumes, grains, and nightshade vegetables. Soybeans, Red Kidney beans, Peanuts, Wheat, Potatoes, and Tomatoes are some of the foods with the highest lectin levels.

How Lectins contribute to “leaky gut” or increased intestinal permeability:

1. Disruption of tight junctions: Tight junctions are the protein structures that seal the gap between cells in the gut lining. Lectins, particularly those with high binding affinity to carbohydrates, can interfere with the integrity of these tight junctions, causing them to become looser and allowing substances to pass through more easily aka Leaky gut

2. Inflammation and immune response: Lectins are known to activate the immune system and trigger an inflammatory response. Chronic inflammation in the gut can lead to damage of the intestinal lining and compromise the functioning of tight junctions.

3. Direct damage to the gut lining: Certain lectins, such as those found in wheat (gluten) and legumes (phytohemagglutinin), have been shown to have a toxic effect on the cells lining the gut. This can lead to cell damage and disruption of the barrier function of the intestines.

It’s important to note that while lectins might contribute to the development or worsening of leaky gut in some individuals, the extent to which they play a role can vary widely among individuals. Additionally, the impact of lectins can be influenced by factors such as individual tolerance, gut health, and overall diet.

Leaky gut not healing? die off

 2. Die Off and It’s Connection To Leaky Gut.

During bacterial die-off or “Herxheimer reaction” in the gut microbiome, there is a significant reduction in the population of certain microorganisms, often in response to antimicrobial treatments or changes in the gut environment. While this is a good thing, this die-off can lead to a release of toxins, heavy metals, and metabolites from the dying microorganisms. This die-off reaction can impact how your leaky gut heals or why your leaky gut is NOT healing.

Here are some key points about what happens during a die-off in the gut microbiome, how to prevent it, and how it affects someone who is trying to heal a leaky gut.

1. Increased toxin release: As the microbes die, they release toxins and byproducts into the surrounding environment. These substances can include lipopolysaccharides (LPS), histamines, ammonia, and other potentially harmful substances. The sudden release of these toxins can overwhelm the body’s detoxification systems and lead to a temporary increase in their levels in the gut and bloodstream. This can be a reason why your leaky gut is not healing or why healing slows down.

2. Inflammatory response: The release of toxins and byproducts during a die-off can trigger an inflammatory response in the gut. This immune response is part of the body’s defense mechanism against the foreign substances released by the dying microbes. Inflammation can manifest as symptoms such as bloating, gas, abdominal discomfort, diarrhea, or constipation. Inflammation by itself can cause a leaky gut. When the intestinal lining becomes inflamed, the tight junctions, which are proteins that hold the cells of the intestinal lining together, can become compromised. This compromises the integrity of the intestinal barrier, leading to increased permeability and allowing substances that should be confined to the gut to leak into the bloodstream. So the increased Inflammation can be a reason your leaky gut is not healing.

3. Temporary worsening of symptoms: In some cases, die-off reactions can temporarily worsen existing symptoms or cause new symptoms to emerge. This is often referred to as a “healing crisis” and can include a range of symptoms such as fatigue, brain fog, headaches, skin rashes, joint pain, or mood changes. These symptoms are thought to be a result of the body’s response to the increased toxic load and inflammation. Here are some additional articles on Die Off. 

Why Your Leaky Gut is Not Healing… Stress

3. Stress Leading to High Cortisol 

Stress can play a significant role in the development and exacerbation of leaky gut, also known as increased intestinal permeability. Here’s why stress and digestion don’t place nicely together. There are two branches of our Nerve system, the Sympathetic Nerve system and the Parasympathetic Nerve system. Digestion is coordinated by our Parasympathetic nerve system. The stress response causes our adrenal glands to produce cortisol.  High levels of cortisol shut down digestion and absorption. Rather than being in a parasympathetic state (Rest and Digest), during times of stress and high cortisol your body is now locked in a Sympathetic/ Fight or Flight state. (*)

How Stress Affects Leaky Gut

  1. Increased inflammation: Chronic stress triggers an inflammatory response in the body. Inflammation can disrupt the integrity of the intestinal lining and weaken the tight junctions between the cells, allowing substances to leak out and into the bloodstream.
  1. Changes in Gut Microbiome: Stress and high cortisol negatively affect the balance of beneficial and harmful bacteria in the gut. An imbalance in the gut microbiota, known as dysbiosis, can contribute to intestinal permeability.(*)
  1. Decreased blood flow to the gut: During high-stress situations, the body’s “fight or flight” response diverts blood flow away from non-essential functions, including digestion. Reduced blood flow to the gut can impair the gut’s ability to repair and maintain the integrity of the intestinal lining. (*)
  1. Impaired digestion and nutrient absorption: Stress can disrupt the normal digestion and absorption of nutrients. When digestion is compromised, larger undigested food particles can enter the bloodstream and trigger an immune response, promoting a leaky gut.
  1. Altered gut-brain axis: The gut and the brain are connected through the gut-brain axis.(*) Stress can disrupt the communication between the gut and the brain, affecting gut function and leading to a leaky gut.
  1. Mast cells are also affected by both acute and chronic stress. Anatomic connections between mast cells and enteric nerve fibers have been demonstrated in human gastrointestinal mucosa and are known to increase with inflammation.(*)

The mast cell–enteric nerve association provides a physiologic means for bidirectional communication between the central nervous system and intestinal tract through which stress may influence gastrointestinal function.

As stress has been shown to induce mast-cell activation, mediators released secondary to an external stressor may affect motility, visceral sensitivity, and gut barrier function.(*)

Leaky Gut Not Healing- It might be food allergies

4. Food Allergies and Food Sensitivities

Food allergies and food sensitivities can contribute to a leaky gut.(*) When you have a food allergy, your immune system recognizes certain food proteins as harmful invaders and initiates an inflammatory response to neutralize them. This immune response can damage the intestinal lining, leading to gaps between the cells that line the gut wall.

Both food allergies and food sensitivity will cause your body to react negatively to those specific foods, triggering an immune response and inflammation in the gut. For this reason, if you have a leaky gut and it’s not healing, it might be time to consider food allergies and food sensitivities as a reason your leaky gut is not healing.

Managing food allergies through avoidance of trigger foods, gut-healing protocols, and immune modulation strategies can help minimize the impact of food allergies on leaky gut and support overall gut health.

Not only can Food allergies and food sensitivities contribute to a leaky gut, but having a leaky gut can also be causing your food sensitivities. Either way, you must find out what you are sensitive to.

Food Allergy or Food Sensitivity- What’s the Difference?

Food allergy symptoms are immediate reactions (think hives, watery eyes, sneezing, or swelling of the tongue), while food sensitivity symptoms (headache, bloating, acne, and more) can be delayed. Since food sensitivity symptoms may not show up until hours or days later, it’s hard to detect them without a food sensitivity test.

If foods do show up on your lab results, you may have to eliminate those foods for a couple of months while healing your gut. Once you do that, you can try to reintroduce them. If you still show symptoms, longer periods away from those foods may be necessary until your gut fully heals.

Leaky Gut Not Healing? Medications that cause leaky gut

5. Your Medications

Medications are the double-edged sword of our modern world. Some are life-saving and non-negotiable. Yet the very medications you are taking could be the reason you have a leaky gut in the first place. Medications that cause a leaky gut include;  antibiotics, oral contraceptives (birth control pills), and NSAIDs.  Imagine trying to heal a leaky gut when you are taking these medications on a daily weekly basis. Let’s review each of these medications and how they may be a reason why your leaky gut is not healing.


Antibiotics are one of the most over-prescribed medications. Nearly half of all outpatient prescriptions are unnecessary, according to the CDC.1 They work by blocking bacterial processes by either killing the bacteria or stopping them from multiplying. Unfortunately, antibiotics cannot tell the difference between the “bad” bacteria causing an infection and the “good” bacteria that belong in your gut. As the number of good bacteria in your gut decreases, you become susceptible to gut infections including Candida overgrowth and SIBO, which can contribute to leaky gut and interfere with leaky gut treatment.

Oral Contraceptives

Oral contraceptives or birth control pills contain synthetic hormones such as ethinyl estradiol and norethindrone, which are not recognized or broken down by the body in the same way natural estrogen is. Birth control pills disrupt the gut microbiome, and cause not only SIBO but an overgrowth of yeast known as Candida. Candida, a type of yeast that is commonly found in the gut microbiome. Candida can contribute to a leaky gut when its growth becomes imbalanced.

When Candida overgrowth occurs, it can damage the intestinal lining and contribute to increased intestinal permeability. Candida has been shown to produce toxins and enzymes that can break down the gut barrier, leading to gaps between intestinal cells and allowing harmful substances to pass through into the bloodstream. For these reasons, if your leaky gut is not healing, you may need to consider another form of contraception.


Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly used to manage the pain and inflammation (swelling and redness) associated with some types of arthritis (such as rheumatoid arthritis) and other musculoskeletal disorders. NSAIDs are also used to treat non-inflammatory conditions such as migraine, period pain, and postoperative pain.

Some commonly used NSAIDs include:

  • aspirin (such as Disprin)
  • ibuprofen (such as Nurofen)
  • naproxen (such as Naprosyn)
  • diclofenac (such as Voltaren)
  • celecoxib (such as Celebrex).

Nonsteroidal anti-inflammatory drugs (NSAIDs), such as ibuprofen and aspirin, are known to have potential negative effects on the gastrointestinal tract, including contributing to a leaky gut. NSAIDs can cause a Leaky gut in a few ways. 

1. Disruption of the Gut Barrier: NSAIDs can damage the mucosal lining of the stomach and intestines, leading to increased intestinal permeability. This damage can weaken the gut barrier, allowing harmful substances such as bacteria, toxins, and undigested food particles to pass through the intestinal wall and into the bloodstream.

2. Inhibition of Prostaglandins: NSAIDs work by inhibiting cyclooxygenase enzymes (COX-1 and/or COX-2) in the body. While this action can reduce inflammation and pain, it can also hinder the production of prostaglandins that help protect the gut lining and maintain its integrity. A decrease in prostaglandins can make the gut more vulnerable to damage and impaired barrier function.

3. Alteration of Gut Microbiota: NSAIDs have been shown to disrupt the balance of beneficial bacteria in the gut microbiome. This dysbiosis can contribute to inflammation, oxidative stress, and further damage to the intestinal lining, potentially leading to a leaky gut.

Next time you think about taking NSAIDs for headaches, menstrual cramps, fever or chronic pain, keep in mind that they may be one of the reasons you have a leaky gut or why your leaky gut is not healing.

Best probiotics to Heal A Leaky Gut

6. Probiotics

While probiotics won’t cause a leaky gut, choosing the right probiotic can help dramatically speed up the healing process. When it comes to taking the best probiotics for a leaky gut, there are a few considerations I want you to be aware of.

The first is strain selection. Different probiotic strains can have varying effects on gut health. Some strains are better at improving a leaky gut than others. So for this reason, It is important to choose probiotics that have been studied for their benefits in supporting gut health and gut barrier function.

  • Studies show that various species of Lactobacillus, such as Lplantarum 299v, Lrhamnosus GG, and Lacidophilus DDS-1, are especially beneficial probiotics for a leaky gut.
  • Probiotics can exhibit anti-inflammatory properties against TNF-α or IL-6 [*].
  • They can also strengthen the mucosal barrier [*] and reduce intestinal permeability, upregulating Tight junction proteins [*].
  • And probiotics can increase butyrate-producing species [*].

These factors combine to result in greater integrity of the intestine, making probiotics a fantastic therapy for reducing leaky gut [*].

Now If your leaky gut is due to SIBO (small intestinal bacterial overgrowth) you may want to avoid lactobacillus-based species and lactic acid-based probiotics. These probiotics could potentially cause more bacterial overgrowth. In cases with someone who has SIBO, It is typically recommended that you start with soil-based probiotics or spore-based probiotics like Bacillus strains.

Leaky Gut Not Healing- it could be fermented foods

7. Fermented Foods

You’ve probably heard countless sources say fermented foods are a gut’s best friend. Here’s why we need to be careful of cookie-cutter medicine and healthcare practitioners and nutritionists who don’t personalize their treatments. What’s good for one person, may not be good for the next. This is why I recommend you always work with a Certified Functional Medicine Practitioner and get the proper testing!

In individuals with histamine intolerance or MCAS, consuming high-histamine foods, including some types of fermented foods, can trigger symptoms such as headaches, hives, and digestive issues, and potentially contribute to the development or exacerbation of leaky gut.

Some fermented foods that can be high in histamine include aged cheeses, sauerkraut, kimchi, yogurt, and kefir. Histamine in these foods can be released during the fermentation process and can accumulate if the person lacks sufficient levels of the enzyme diamine oxidase (DAO), which is responsible for breaking down histamine in the body.

For individuals with histamine intolerance and leaky gut, its often helpful to reduce or avoid high-histamine fermented foods and other histamine-containing foods to manage symptoms and support gut health

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