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Leaky Gut Protocol- Don’t Make These 8 Common Mistakes

Leaky Gut Syndrome can be at the core of many different conditions, including skin disease, a compromised immune system, food allergies, digestive problems, ear infections, depression, autoimmune diseases or any common health condition that comes from a state of chronic inflammation. The Leaky Gut 4R Protocol addresses some of the root causes of a leaky gut and helps support healing.  The problem is that people can make a lot of mistakes when it comes to following this leaky gut protocol. In today’s article, I’m going to review some of the most common leaky gut 4R protocol mistakes I see being made.

Leaky Gut Protocol Don’t Make these 8 Mistakes

8 Mistakes When Following A Leaky Gut Protocol

Healing your damaged gut is a journey full of ups and downs and it’s not always an easy straight line for recovery, in fact, most times it’s not. There are a lot of pitfalls along the way as well. 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. There are many underlying health issues that can complicate treatment for leaky gut. But if you understand this from the very beginning, and you understand that healing a leaky gut is a process that wont be fixed overnight, you will have a better idea of what this healing journey looks like. Because it is a journey, remember, there is no quick 30-day fix or magical leaky protocol that you will read about on the internet. Avoid these kinds of Quick fix 30 day programs as they are nothing more than a scam.

Depending on what kind of shape your gut is in, and whats causing your leaky gut, It could easily take a year or longer. Now when I say “heal” your gut, I’m not talking about feeling better. When I say healing your leaky gut, I’m talking about testing for a leaky gut, identifying the kind of leaky gut you have (Trancellullar vs Paracellular) and then retesting. On retesting for leaky gut, your lab results are now normal. So this is how I define healing and within this process, there are many leaky gut protocol mistakes made.

Healing a leaky gut is going to require you to be super intentional with how you treat and what you put into your body. I always recommend that you work with a Certified Functional Medicine Doctor who will be able to connect the many dots and the root causes. So, let’s get into The 8 most common mistakes People Make When following a leaky gut 4R protocol.

Leaky Gut Protocol- 1. Not Understanding the Role Lectins Have with Leaky Gut

1. Not Understanding the Role Lectins Have with Leaky Gut

So, number one is not understanding the role lectins have with leaky gut. 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

There are several ways in which lectins may 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.
  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 those found in Beans, Nuts, and Seeds (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 and cause a sudden release of histamine from cells located in the gut lining.

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.

Leaky Gut Protocol Mistake #2

2. Ignoring or Not Recognizing “Die Off”

Many patients nowadays are self-treating, meaning they are following some recommendations they find on the internet and are not under supervision. While its great to have this information, the problem that many people run into is when they experience a die-off or “Herxheimer reaction”, they dont know what to do. If you dont know what to do or how to recognize die off, it might be best to work with someone who has experience in this area before attempting a 4R gut healing protocol.

During a die-off, 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 metal overload, and metabolites from the dying microorganisms are now entering your bloodstream at higher levels than your body is accustomed to.

Here are some key points about what happens during a die-off in the gut microbiome and what you can do to minimize die-off:

There are three main things I want you to remember about die-off and its connection to a leaky gut and what you should do if you begin to experience a rapid die-off.

  1. Increased toxin release: As the microbes die, they release toxins and byproducts into the surrounding environment. These toxic substances can include lipopolysaccharides (LPS Toxins), 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.
  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. Gut Inflammation can manifest as symptoms such as bloating, gas, abdominal discomfort, diarrhea, or constipation.
  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.

Learn more about the symptoms of die-off associated with SIBO, Parasites, and Candida here

It’s important to note that while die-off reactions can be unpleasant and uncomfortable, they are typically temporary and a sign that the body is responding to changes in the gut microbiome. If you begin to experience die-off, it’s important to take certain steps.

One thing you want to make sure is that you are having a minimum of two bowel movements per day. We need to keep things moving and we need to make sure nothing is slowing down our elimination pathways.

The next thing you want to make sure you are doing is taking a binding agent that has Zeolite, activated Charcoal, and fulvic acid. The breakdown of unwanted microorganisms and biofilms can lead to the release of harmful LPS toxins (lipopolysaccharides), heavy metals, and organic compounds like glyphosate.

This is where binding agents play a star role as they can help “mop up” these unwanted compounds. I can’t overstate the importance of staying hydrated and making sure that you are having a minimum of two bowel movements per day. If your die-off symptoms are taking a toll on you, rather than stopping all your supplements cut them in half for a week or two. This is usually all you need to do to help your liver catch up with its workload.

Learn more about Die Off in my Die Off series.

  • Part I Recognizing Symptoms of Die off,
  • Part II The Real Reason for Die-and How To Prevent it,
  • Part III How To Best Manage Symptoms of Die Off.

Leaky Gut Protocol- Mistake 3

3. Eating On The Run or During Stress

Number three on my list of common Mistakes Made Following A Leaky Gut Protocol is not paying attention to WHEN you’re eating. Here’s what I mean by that. Digestion is coordinated by our Parasympathetic nerve system specifically the Vagus Nerve. Eating when you are on the go or under stress, is one of the worst things you can do when you have a leaky gut. Stress is one of the main causes of a leaky gut. That’s because when your stress response kicks in, your digestive process slows down to a crawl. Rather than being in a parasympathetic state, during times of stress, you are now locked in a Sympathetic/ Fight or Flight state. I recommend these vagus nerve exercises and this Ileocecal valve release technique to everyone who has any kind of motility disorder.

Stress can impact the permeability of the gut in the following ways:

  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.
  2. Altered gut microbiota: Stress negatively affects the balance of beneficial and harmful bacteria in the gut. An imbalance in the gut microbiota, known as dysbiosis, can contribute to intestinal permeability (Leaky Gut).
  3. 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.
  4. 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.
  5. 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 potentially leading to a leaky gut.
  6. 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.(*) High cortisol levels from emotional stress will also affect Mast Cell stability.

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.(*)

If interested in learning more about the effects of stress and digestion you can check out this article- 

Leaky Gut Protocol Mistake 4

4. Not Testing For Food Sensitivities

Not only can Food sensitivities contribute to your 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 allergies and food sensitivities are not the same. The elimination diet that many doctors recommend to patients is great for identifying food allergies but it’s not going to work when it comes to food sensitivities or food intolerances. Here’s why…. Food allergies are immediate reactions, and food sensitivities and food intolerances are delayed reactions, meaning that you eat something this morning but it doesn’t start causing problems for two days.

Remember, food allergy symptoms are immediate reactions (think hives, watery eyes, sneezing, changes in blood pressure, heart rate, or swelling of the tongue), while food sensitivity symptoms (headache, bloating, Brain fog, acne, and more) can be delayed. Food sensitivity/Intolerance symptoms may not show up until 72 hours later, it’s hard to detect them without a food sensitivity test.

If foods do show up on your food sensitivity test, you will have to eliminate those foods for a couple of weeks or a couple of months while healing your gut. Once you do that, you can try to reintroduce them.

How Food Sensitivities Can Lead to Leaky Gut:

  1. Immune response: When you consume a food that you’re sensitive to, your immune system may react by releasing antibodies and inflammatory molecules. This immune response can damage the intestinal lining, compromising its integrity and contributing to a leaky gut.
  2. Inflammation: Food sensitivities can cause chronic inflammation in the gut. Inflammation, in turn, weakens the tight junctions between the cells of the intestinal lining, making it easier for substances to leak through.
  3. Altered gut microbiota: Food sensitivities can disrupt the balance of beneficial bacteria in the gut, leading to dysbiosis. An imbalance in gut bacteria can contribute to increased intestinal permeability.

It’s important to note that while food sensitivities can contribute to leaky gut, not all cases of leaky gut are caused by food sensitivities. Leaky gut can have various underlying factors, including chronic stress, certain medications, infections, and other digestive disorders.

Leaky Gut Protocol Mistake 5

5. Taking Medications That Damage and Cause Leaky Gut

Another mistake when following a leaky gut protocol is not considering your current or past medications. Medications are the double-edged sword of our modern world. Some are life-saving and non-negotiable. Yet there are other gut-damaging medications such as antibiotics, oral contraceptives (birth control pills), and NSAIDs that can do more harm than good and get in the way of fixing a leaky gut. Learn more about medications and Leaky Gut here.


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 also disrupt your internal balance of Candida by causing something called estrogen dominance – meaning too much estrogen in the body. Candida cells can permeate your gut lining, causing a leaky gut.


NSAIDs such as Advil and Motrin work by stopping your body’s production of a chemical called prostaglandins. (*) They do this by blocking cyclooxygenase (COX) enzymes. These enzymes produce prostaglandins, that cause inflammation, pain, and fever. The problem with blocking prostaglandins with NSAIDS is that these prostaglandins also protect your stomach and intestinal lining. This is how and why NSAIDs can damage your gut, cause liver inflammation, and derail your leaky gut treatment.

Antidepressants Including SSRIs

As research continually unfolds the intricate relationship between the gut and the brain, the concept of gut dysbiosis and its influence on mental health has garnered increasing attention. Antidepressants, commonly prescribed to address mood disorders, have been found to negatively impact the delicate balance of gut microbiota, leading to gut dysbiosis.(*)

Studies have shown that antidepressants, particularly selective serotonin reuptake inhibitors (SSRIs), affect the composition and diversity of gut microbiota. These medications, designed to alter neurotransmitter levels in the brain, can adversely impact the gut microbiome, leading to dysbiosis, leaky gut, and many other problems related to the gut. Essentially these antidepressants are acting like antibiotics and these changes in gut microbial populations can influence not only digestive health but also mental health outcomes.(*)

Learn more about the different medications that Cause Leaky Gut here

Leaky gut Protcol Mistake 6

6. Taking the Wrong Probiotics

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 have been shown to enhance the integrity of the intestinal barrier, while others may not be as effective for a leaky gut. Some species are great for depression and anxiety and others not as great. So for this reason, It is important to choose probiotics that have been studied for their potential benefits in supporting gut health and gut barrier function or whatever ails you.

Studies show that various species of Lactobacillus, such as Lplantarum 299v, Lrhamnosus GG, and Lacidophilus DDS-1, Lrhamnosus GG, are the probiotics that are especially beneficial for leaky gut. Studies show that may increase mucin expression and secretion by goblet cells as a mechanism to enhance barrier function and pathogen exclusion by limiting bacterial movement through of the mucosal layer [,,].

Studies show that various species of Lactobacillus, such as Lplantarum 299v, Lrhamnosus GG, and Lacidophilus DDS-1, increase mucin expression and secretion by goblet cells as a mechanism to enhance gut barrier function and pathogen exclusion. They do this by limiting bacterial movement through the mucosal layer [,,].

Probiotics and Leaky Gut

Taking the Right Probiotic Strains when you have a leaky gut can be magical, the wrong kinds of probiotics can set you up for failure. I alway recomend a Functional Stool Test when working with patients who have leaky gut. Among the main effects of probiotics include;

  • Probiotics also help modulate intestinal permeability affecting the mucus, epithelium and microbiota.
  • Help regulate intestinal transit
  • Probiotics can exhibit anti-inflammatory properties against TNF-α or IL-6 [].
  • They help in the production of short-chain fatty acids and vitamins
  • Providing enzyme digestion activities for the degradation of undigested fibers and the neutralization of xenobiotics.
  • They can also strengthen the mucosal barrier [] and reduce intestinal permeability, upregulating Tight junction proteins [].
  • 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 complicated by bacterial overgrowth aka SIBO, you will want to make sure you read your probiotic Label. Certain lactobacillus species  could cause more bacterial overgrowth. Make sure you know what kind of lactobacillus strains you are taking. In cases with someone who has SIBO, It is typically recommended that you stick to soil based probiotics or spore based probiotics like Baccillus strains

If you have SIBO I recommend you watch/Read this article on Best Probiotics When You Have SIBO

Until your leaky gut treatment is complete and you fix your leaky gut, I recommend soil-based probiotics which can bypass your small intestine and colonize your colon and large intestine instead.

Leaky Gut protocol Mistake 7

7. Eating Too Many Fermented Foods

You’ve probably heard countless sources say fermented foods are a gut’s best friend. The truth is that when you introduce fermented foods into your gut microbiome, it can be a game of Russian roulette. Fermented foods contain live bacterial and yeast cultures, you don’t know exactly what kind of bacteria or yeast those fermented foods contain or how much of those bacteria and yeast are present. This might be ok for someone without a leaky gut, But, it could be a deal breaker and leaky gut protocol mistake for some. I recommend you take my quiz to see if your symptoms line up with histamine MCAS.

You can take my free Histamine intolerance MCAS Quiz here

Instead of eating fermented foods, here’s what I recommend, if you have SIBO or Candida overgrowth, you should WAIT until after you fix a leaky gut to eat fermented foods. The other issue with fermented foods is they contain high levels of Histamine.

Here’s why this may be important to you, If you are someone who has Inflammatory Bowel disease, there is a very good chance you are also dealing with histamine intolerance to a degree.

Histamine intolerance is a condition in which the body has difficulty breaking down and metabolizing histamine properly as a result people with histamine intolerance have excess histamine in their body and too much histamine can contribute to a leaky gut.

It turns out that within the gut lining, in the mucosal layer are Mast Cells. These Mucosal mast cells are important regulators of the gut barrier ().

Histamine Can Cause Leaky Gut

High levels of histamine can contribute to a leaky gut in several ways:

  1. Inflammatory Response. High levels of histamine in the body can trigger an immune response, leading to chronic inflammation. This inflammation can affect the gut lining and disrupt the tight junctions between the cells, compromising the integrity of the intestinal barrier.
  2. Mast cell activation: Histamine acts as a signaling molecule released by mast cells, which are immune cells involved in allergic reactions. Increased mast cell activation can result in the release of more histamine, leading to further inflammation and potential damage to the gut lining.
  3. Enzyme deficiency: In individuals with Leaky Gut, there may be a deficiency or dysfunction in the enzymes responsible for breaking down histamine, such as diamine oxidase (DAO) or histamine N-methyltransferase (HNMT). This can lead to an accumulation of histamine in the body, potentially contributing to gut inflammation and heightened intestinal permeability.

In order to best manage histamine intolerance and reduce the risk of leaky gut, you may want to read this article. The last on my list of mistakes being made when following a Leaky Gut Protocol is not eliminating gluten long enough.

Leaky Gut Protocol Mistake 8

8. Not Completely Eliminating Gluten and Dairy

The last mistake I see many people making when following a leaky gut protocol is that once they start feeling better, they start allowing gluten to creep back up and into their diet. Here’s something interesting.

A study was just performed assessing the impact gluten has on people with celiac disease, people with non-celiac gluten sensitivity, and people with no reported reaction to gluten whatsoever.

The researchers found that ALL participants experienced leaky gut changes after exposure to gluten. Not some of the participants but all of them. SoIt doesn’t matter if you have Celiac disease, Non-Celiac Gluten Sensitivity (NCGS), or wheat allergy, Eating gluten allows the tight junctions to open up. Remember your tight junctions are what keeps your gut barrier healthy like a mesh cloth rather than a chain-linked fence and Gluten can trigger zonulin release, widening those tight junctions.

People Who Read Today’s Article 8 Mistakes People Make When Following a Leaky Gut Protocol Recommend the following


4 Step Protocol For Healing A Leaky Gut and Eliminating Parasites


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