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End the overwhelm.

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.

In particular, 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..

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.

my child will thrive village, community, facebook group

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  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


  1. Zoe

    Hi, I have a almost 2 yr old who has leaky gut. & im completely overwhelmed! Reading through your article has helped clear my head ready for the plan of attack!

    I was told from 2 different practitioners doing muscle testing of an outcome of leaky gut.

    My question is: how long does it take to heal a leaky gut?

    Thanks so much

    • Tara Hunkin

      Hi Zoe,

      I’m glad the article has helped you figure out your plan of attack! Your question is of course as all these things are child/person specific, depending on the history and severity of gut dysfunction.

      However, the gut lining itself regenerates very quickly when it is supplied with the right nutrients and the irritants are removed. I generally recommend no shorter than a 3-month healing protocol before trying to reintroduce foods previously sensitive to etc. For some, it will take longer and others will see symptom improvement much faster than months, however, it is important (especially if there are microbiome imbalances or gut infections that are needing to be eradicated) that you don’t let up too soon. Although the gut lining may be less leaky or healed, if we let up too soon the bacterial imbalances or gut infections can ramp up again!

      I hope this helps,

  2. Wiloria

    I was wondering what approach do I take? I messed up really bad bc my kids and I became very sensitive to many different foods and we started to do a lot better when I eliminated much of what we were eating but I kept falling and binge eating junk food as well as my babies now I’m struggling trying to fig.bout how to fix this and maintain bc our health is very poor due to my neglect and lack of consistency. our bodies are soooo fatigued and we are always sick…. It’s gotten to be too much and completely impossible to heal how can I fix our bodies after all the damage done it’s so depressing bc it’s so much work but it’s also depressing bc I feel like a complete failure in something so serious!!!!!

    • Tara Hunkin

      Hi Wiloria,

      First, you need to cut yourself some slack. As parents, we have our hands full, to begin with, and then taking on a healing diet on top of that is very challenging. This isn’t easy for anyone. All we can do is start fresh.

      It is very important to prepare both mentally and in the kitchen before taking a gut healing protocol on. Make sure it is good timing for you and your family, clear as many of the obvious obstacles (like don’t start just before a food-focused holiday or vacation) and depending on the age of your children. Speak with them about what you will be doing and why and set up a reward system for them and yourself!

      Then start at the very beginning…identify the irritants to the gut lining remove them and add in the healing nutrients and repopulate the gut with beneficial bacteria and yeast. I know this is a very simplified look and when there are a lot of food sensitivities it is very challenging, but it does work.

      I hope this helps…Tara

  3. Kate

    Hello I’m having a hard time working out what I can qctually feed my 1 year old. She has ezcema so I want to heal her gut.
    She’s off dairy I’m trying to get her off wheat/gluten and she never has deadly nightshade foods…

    I’m struggling with how to feed her as she’s fussy.. she would eat a risotto with salmon and veg but don’t know how to remove rice and replace it… I do roast chicken and veg and then I can’t work out other meals and also snacks. . Help …please.. x

  4. Isabel

    I love this information!!
    I have 2 questions, how much coconut oil and orégano oil can a child take? I have 2 (9 and 11).
    Thank you for this great información.

  5. Leslie

    I have a 20 month old child who has (sadly) developed leaky gut after trying so hard to avoid that from happening. After I stopped nursing him when he was about a year old, he began to develop chronic diarrhea and has now developed eczema. I am very upset and at a loss, because​ my child does not eat any junk food or consume any processed sugar (or even fruit juice!) He eats mostly all organic and non-GMO. Our foods are all whole foods, and yet he continues to be sick. We are going for a stomach scope in a couple of days, so I am hoping we may get an answer. I am going to try bone broth this week for him to see if it will start to heal him. Can I add a collagen supplement to the broth for extra healing? Also what is a good probiotic for children that does not contain dairy (he is allergic)?


    • Natalie

      BioGaia for Kids is dairy free probiotic. we also done the CNS FoodScan test to establish the problem food and lots we wouldn’t never have imagined were problematic. She was already dairy, Soy, Egg and Wheat free but now we have a huge amount to tackle and we are about to embark on the healing process, fingers crossed! We are struggling with coming to terms with the amount she cannot eat, all of her favourite things, she is only 19 months (Non verbal) so we can’t even explain to her 🙁 Good luck to you x

  6. Sue

    vould you write up a typical daily protocol including supplemenrs to work with pleas

  7. Gercorless

    Just woundering how long does it take to clear all the bad stuff out of the gut and heal the leaky gut. One year into it now . I know it takes different amount of times for different children but just woundering how long at most have you seen it takes.

    • Nancy

      We did GAPS Diet very strictly for 5 years and saw little to no improvement. We did the Intro Diet part of GAPS for about the first year. We worked with a GAPS practitioner as well, who is a Certified Nurse Practitioner and did all the aforementioned testing and then some. Cut to 4+ years of expensive testing and supplements and we are almost exactly where we were when we started. We still entirely avoid wheat/gluten but did start adding in some other foods like soaked/fermented oatmeal, potato, rice, soaked/sprouted chick peas, etc. My daughter was 7 when we started and she’s now 12. Her issues were not as bad as mine to start off, and she is still bad. I found that I have to avoid high FODMAP foods, of which many of them are on the GAPS Diet, even in the first stages, such as onion and garlic which are highly touted. Those foods are like poison to me, and still are. It is very disheartening, to say the least.

  8. Alina K

    Hi, my 16 month old has had eczema and allergies to dairy, eggs, wheat, soy, and nuts. I’m wondering on how you have a baby eat sauerkraut kind of food. He refuses to eat anything like that. Plus his teeth are coming in late so he can’t even chew that well. Any suggestions?
    Thank you! much appreciated!

  9. Claudia

    My 3 year old has eczema, dairy, egg, peanut and wheat allergy. In regards to L-glutamine to repair gut lining is there a specific brand I should use? What is the recommended dose for a 3 year old?

    • Oksana

      We use Designs for Health L-G – 1 daily for our 4 year old, commended by our Dr.