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Get a head start with my researched and field tested tool kit so that your child can thrive too.


The 3R Secret to Healing Your Child’s Leaky Gut

The 3R Secret to Healing Your Child's Leaky Gut - Remove, Repair and Repopulate

You've probably already heard the term leaky gut, but have you grasped the concept of what it really is? The mainstream media is buzzing these days with research on the micro biome (the trillions of microorganisms that reside in the gut) and how it is tied to our health. Not only do these microorganisms affect digestive health, but they also impact areas far removed from the gut. This article will discuss the 3R Secret to Healing your Child's Leaky Gut.

The balance of microorganisms in the gut has a powerful effect on the brain. This interaction is called the gutbrain axis, an area of great interest and research. As parents of children with neurodevelopmental disorders, the gut-brain axis is an important topic for us to pay attention to which is why it is important to know the secret to healing your child's leaky gut

The health of the gut is tied to our children’s overall health and wellness AND to their brain function. Let's skip the why for today and jump right into how to heal a leaky gut and optimize our child’s microbiome so they too can have the best chance at optimal brain function. So what is The 3R Secret to Healing Your Child's Leaky Gut?

in a nutshell
  • Leaky gut is likely an integral part of your child’s symptoms of autism, ADHD, or sensory processing disorder, as it impairs brain function.
  • In order to heal a leaky gut, you must remove the irritants, restore the integrity of the gut lining and repopulate the gut microorganisms.

What is Leaky Gut?

Let's start by revisiting the anatomy of the digestive tract, or gastrointestinal (GI) tract. Simply put, the digestive tract is a long tube that runs from one end of the body (mouth) the other (anus). The GI tract is built to receive, process and break down foods into usable nutrients. With the introduction of foods comes a reasonable amount of pathogens, which, in a healthy GI tract, are destroyed by stomach acid. Once food is digested in a complicated process that begins in the mouth and continues into the small intestine, nutrients are absorbed via the gut lining—the small intestinal lining in particular. This same gut lining is also designed to ensure that pathogens and waste materials remain in the digestive tract to be eliminated via the stool.

Essentially, digested food particles are small and harmless enough that they can pass through the digestive lining without a problem. In a healthy GI tract, larger undigested food particles, fiber, waste, and microorganisms are prevented from passing through the digestive lining.

Leaky gut occurs when the tight junctions of the gut lining in the small intestine, which function as “gate keepers” to allow only usable particles to be absorbed through the gut lining into the bloodstream, become weakened. This weakening opens the gates wide, allowing inappropriate substances to be “leaked” into the bloodstream, which can cause both obvious and subtle symptoms throughout the body and brain.

The 3R Secret to Healing Your Child's Leaky Gut

Step 1: Remove

In order to heal a leaky gut, you must first remove irritants—including any overgrowth of pathogenic bacteria, yeast or parasites—to the gut lining that are triggering inflammation and weakening the tight junctions.

Step 2: Repair

Once the irritants to the gut lining are removed, it is possible to support the repair of the lining with food, supplements, and digestive support.

Step 3: Repopulate

Typically, leaky gut goes hand in hand with dysbiosis (an imbalance of the bacteria and yeast in the gut). Repopulating the gut with a variety of beneficial bacteria through fermented foods and probiotics is crucial.

Remove the Irritants

The first step is identifying irritants that are contributing to the inflammation and weakening of the tight junctions in the gut. These are typically inflammatory foods and pathogens.

Remove inflammatory foods: 

Some foods are inflammatory to everyone. For example, processed foods, sugars and unhealthy fats (vegetable oils and animal fat of poorly raised animals) should be removed by everyone on the 3R program. Other foods are inflammatory to certain individuals due to an inability to properly digest them, or because of an allergy or intolerance to the food. These foods should be avoided in order to promote an environment of healing in the gut.

Remove pathogens:

An overgrowth of pathogenic bacteria, yeasts and parasites must be addressed to heal the gut. This can be achieved by using both foods and supplements.

Foods to help remove pathogens include:

  • Garlic
  • Oregano
  • Turmeric
  • Raw honey
  • Pineapple/bromelain
  • Coconut oil

Supplements to help remove pathogens include:

  • Enzymes to breakdown biofilm
  • Berberine
  • Oregano oil
  • Grape seed extract
  • Black walnut hulls
  • Wormwood extract
  • Cloves
  • Diatomaceous earth

In some cases, pharmaceuticals, such as the antifungal nystatin, may be necessary. This is something you can discuss with your practitioner.

Repairing the Gut Lining

Once gut irritants have been removed, the gut lining can be repaired. A healthy gut lining replaces its cells every seven days. This process is heavily dependent on a process called methylation (as I discussed in an earlier article), so you may also want to speak with your practitioner about methylation support.

Certain foods and supplements aid in restoring the integrity of the gut lining.

Foods to repair the gut lining:

  • Bone broth and meat stock
  • Aloe vera
  • Colostrum

Supplements to repair the gut lining:

  • L-glutamine
  • Collagen powder
  • Quercetin
  • Digestive supports: HCl with pepsin and/or digestive enzymes
  • Ginkgo biloba extract (GBE)
  • Vitamins A & C
  • Zinc
  • N-acetylcysteine (NAC)
  • Phosphatidylcholine
  • N-acetyl-D-glucosamine (NAG)
  • Gamma linolenic acid (GLA)

For more information on some of these supplements and related studies on their efficacy for healing leaky gut, read this article from the Natural Medicine Journal.

Repopulate the Microbiome

In order to heal the gut, the balance of beneficial-to-pathogenic microbes must be restored. This can be accomplished through food, supplements, and alternative therapies.

Fermented foods to repopulate the gut

  • Fermented vegetables (fermented pickles, sauerkraut, carrots, etc.)
  • Fermented dairy products, if dairy is tolerated (these need to be long ferments (24 hrs) which unfortunately are not typically available commercially. Fermenting your own dairy products is recommended.
  • If dairy isn’t tolerated, coconut yoghurt and coconut kefir are good alternatives.
  • Fermented drinks, such as water kefir and kombucha

When repopulating the gut, fermented foods are ideally part of your plan. Properly fermented foods have many more strains and volume of beneficial bacteria compared to only a few strains per probiotic supplement. It is an inexpensive way to repopulate the gut while crowding out the pathogenic microbes.

Supplements to repopulate the gut:

  • Probiotics (beneficial bacteria)
  • L. reuteri is a particularly beneficial strain for our children1
  • S. boulardii (beneficial yeast)

Alternate therapies:

  • Enemas using probiotics
  • Helminth therapy
  • Fecal transplant

Talk to your health practitioner about these alternate therapies, which can be helpful when other methods fall short.

Tests to Consider When Healing a Leaky Gut

Testing is not required to heal a leaky gut, but can shorten the path to healing. Certain tests are often able to identify particular foods and/or pathogens you need to address. In particular, the comprehensive stool analysis from some labs will identify specific antibacterial/yeast/parasitic agents that will be most effective.

Three tests to consider are:

1. Comprehensive Stool Analysis (CSA): Test to analyze the health of the gut through identification of both good and pathogenic bacteria, yeast and parasites. In addition, the CSA often provides markers of the immune function of the gut lining, inflammation and digestive function.

2. Organic Acids Test: Identifies metabolites in the urine that are the result of such things like yeast overgrowth, which is common in our children. This can be especially helpful if the stool analysis provides a false negative.  On occasion, the stool sample may not capture the yeast (as it can be protected by biofilms and not always present in the stool).  The Organic Acids Test is useful for not only identify gut issues but provides many other markers that are helpful in identifying the root issues for our children.

3. Food Sensitivity Test: There are many versions of food sensitivity testing available. Identifying which foods your child is sensitive to is key. In order to give the immune system a break, and in turn decrease inflammation in the gut so it can repair, food irritants need to be eliminated. Although there is a lot of debate over reliability, these tests can be a great help in addition to a food journal to identify which foods need to be avoided for healing to occur.

Develop Your Action Plan

1. Figure out what foods your child is sensitive to (either by analyzing their food journal for symptoms or through testing) and remove them completely from their diet for 90 days.

Grab Your Food, Mood, Sleep & Poop Journal Here!

2. Talk to your practitioner about the cost/benefit of getting a comprehensive stool analysis and an organic acids test for your child to see what pathogens might be lurking in their gut that need to be addressed.

3. Prepare or source gut-healing and probiotic foods.

4. Determine what additional supplements you may want to use and discuss with your practitioner.

Let me know if you have tried the 3R program in the comments below or in our Facebook group, the My Child Will Thrive Village. What did you find most beneficial? What were the effects? If you are considering this method, what questions do you have? I’d love to hear from you.


  1. Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in OffSpring, Buffington, Shelly A. et al.Cell , Volume 165 , Issue 7 , 1762 – 1775