Healing Leaky Gut

Healing Leaky Gut

Healing leaky gut turned out to be the most difficult and the most rewarding step for our health. Learning how to heal leaky gut was expensive and time consuming. Stomach acid, hiatal hernias, digestive valves, diet, detoxification, drainage, and ‘bad’ bacteria in stool tests must also be addressed. Here is the content outline for those who like to skip around:
Healing Leaky Gut Can Mean Big Health Improvements

Leaky Gut Symptoms & Our Stories

Leaky Gut Tests: Western Medicine

Leaky Gut Tests: Alternative Medicine

How to Heal Leaky Gut

  1. Stomach Acid
  2. Hiatal Hernia & Digestive Valves
  3. Diet
  4. Detoxification
  5. Drainage
  6. Clearing the Stool Test
  7. Probiotics
  8. Parasites Make it Hard to Keep the Gut Healthy

Keeping the Gut Healed

Things That Didn’t Work

Practitioner Team




Healing Leaky Gut Can Mean Big Health Improvements!

Healing leaky gut was the first issue with which I became totally frustrated. No doctor or team of doctors, western or eastern, was able to guide us through the process. After several years and thousands of dollars, I realized the practitioners were putting various band-aids on symptoms. I finally decided to take time out of my too-busy life to get to the root of the problem. Fixing both the microbiome and function of the gut turned out to be the most difficult and the most important step for our family’s health. The symptom resolution we got from fixing our gut alone has been remarkable. Our oldest child had 90% of her symptoms (including Lyme symptoms) resolve when her gut was fully healed. The remaining 10% of her symptoms were resolved with parasite treatments.


This information is a summary of years of practitioner visits, thousands of dollars, and about 1 year full-time of my time. It took me that long to research, experiment, and debug. I finally figured out how to permanently shift the balance of microorganisms and how to heal leaky gut.


I feel so strongly about the importance of healing leaky gut that I also made an introductory video:



Leaky Gut Symptoms & Our Stories

Leaky gut symptoms range from autism and ADD/ADHD to nausea to abdominal cramps, constipation and diarrhea [1]. Below I have created my own list of symptoms. It is not a complete list, but rather a list of symptoms that our oldest child first experienced. I am making my own leaky gut symptom list because society often considers some of these ‘normal’ or rationalize ‘that’s the way s/he is’. I did this myself for many years. I wish I had pieced this all together years ago. These symptoms are mostly not well known or well documented. Anyway, on to the list:


  • Sugar cravings, flare-up in symptoms with carbs and sugar
  • Tummy aches
  • Skipping Meals, lack of hunger
  • Pale complexion
  • Vomiting
  • Weight loss
  • Bad moods, Moody
  • Failure to thrive (child), not growing, decreasing or low on the growth chart
  • Eczema, skin issues
  • Nausea
  • Blood in stool
  • Distended belly (also a symptom of parasites)
  • Food in stool, stool that looks ‘undigested’

Overall, our oldest child was struggling with these symptoms. There were days when her tummy aches were so bad that she couldn’t walk. Some days her moods were so bad that she didn’t smile or laugh.


A few years later, even after our oldest child had resolved most of these symptoms, our youngest child had more minor leaky gut symptoms. Her symptoms included:


  • Pale complexion
  • Loss of appetite
  • Tummy aches
  • Distended belly (again, also symptom of parasites)
  • Lack of growth

Even before any of these issues, our family ate healthier than anyone we knew. Our children were not allowed to eat processed foods or any food from preschool. We were dairy and sugar/carbs light. We were the family with the child at birthday parties who isn’t allowed to eat cake. Generally we ate a full GAPS / WAPF diet. I believe, but cannot prove, that our gastrointestinal (GI) problems stemmed from generations of poor diet, antibiotics, heavy metals, toxins, and chronic infections (bacteria, parasites, Lyme) that made each generation’s GI balance get worse and worse.


What about the younger child’s leaky gut symptoms years later? My opinion is that the gut needs to be monitored, because dysbiotic bacteria in the gut can always flare back up. I think it is impossible to get rid of dysbiotics completely, but I think it is possible to shift the balance. Keeping a healthy balance requires vigilance. Our younger child was struggling with Lyme disease, parasites, and heavy metal toxicity when her leaky gut symptoms appeared. Changes in the ‘terrain’ or environment caused the dysbiotic bacteria to flare up. We had to go back to the process of how to heal leaky gut with her. Since then we have cleaned up Lyme, parasites, and are in-progress on heavy metals. We haven’t seen another relapse of leaky gut symptoms.


The rest of the family did not have any obvious leaky gut symptoms, but we all did the same how-to-heal-leaky-gut protocol with our oldest child. This was both to support her and to prevent any future problems with the rest of us. The adults experienced increased energy, productivity and vitality. In hindsight, although we had no obvious leaky gut symptoms, we also had a significant increase in health from healing our guts.



Leaky Gut Tests: Western Medicine

A lot of time and money was spent going to gastrointestinal (GI) specialists and pediatricians all over the state of California with our oldest child. They did lots of tests, most of which were not really looking for leaky gut. Here’s what they found:


  • Endoscopy – Dinner in stomach from the previous night -> low motility. Diagnosed with ‘gastritis’. Endoscopy is done under general anesthesia. It was useless in our case, but might be useful if you suspect a structural deficiency like a twisted intestine.
    Endoscopy Photos

  • Barium drink study – Small hiatal hernia, consistent with chiropractic findings. No other issues.
  • H-pylori & Giardia & Parasite tests – all repeated multiple times, all negative, although now I know that these are hard to catch with Western tests.
  • Abdominal Ultrasound – normal
  • Blood in Stool

Overall the conclusion was to give her pain pills for the tummy aches, and probiotics and digestive enzymes to help with motility. Note that this child had been on probiotics since birth. However, the probiotics had inulin / FOS, which in hindsight was probably not the best idea. Inulin and FOS are great if there are no dysbiotic bacteria; otherwise they tend to feed them instead of the ‘good guys.’


We came to the end of the road where the GI specialists from some of the best universities in the country couldn’t help us. I asked about changing diet, and they said that wouldn’t help. After exhausting all options here, we started looking at what alternative medicine could offer.



Leaky Gut Tests: Alternative Medicine

Microbology and Yeast Stool Test Results Example

Doctor’s Data Microbiology & Yeast Stool test results showed dysbiotic levels of Hemolytic Strep, E.coli, Klebsiella, Pseudomonas,Saccharomyces cerevisiae, and Citrobacter freundii. Some of the members of our family also had no beneficial Lactobacillus, and were low on other beneficials as well. These stool tests we repeated at Genova and the results were basically the same as the Doctors Data results.


I prefer the Doctor’s Data stool test over Genova for two reasons:


  1. It’s cheaper.
  2. It cultures the dysbiotic bacteria against both ‘Natural Antibacterials’ and ‘Prescriptive Agents’. This gave me the best ideas for what antibacterials might work. In my experience, their culture suggestions were good ones. The only missing piece was cultures for dysbiotic E. coli. An example of culture suggestions can be found on pages 2-4 of this Great Plains Microbiology Example Report.

I am not a huge fan of Doctor’s Data in general because of their rude and unhelpful attitudes. If I could do it over again, I would do the stool tests with Great Plains Laboratory.
Is a microbiology and yeast stool test really a leaky gut test? Not directly, but indirectly. If there are dysbiotic or ‘bad guy’ bacteria and yeast in large quantities in the gut, then food is not properly being digested. The combination of undigested food and dysbiotic bacteria means that there are most likely holes in the gastrointestinal lining.

After lots of money and years spent doing microbiology and yeast stool tests, I actually do believe in the consistency of these tests. I also want to point out that elimination of our oldest child’s symptoms was concurrent with her having a clear stool test.
Bioset and ZYTO testing also showed dysbiotic bacteria along with food (wheat, sugar, etc.) & environmental sensitivities. Generally we tended to test sensitive to foods that we had recently eaten. This is also not a direct leaky gut test, but is an indicator of leaky gut.

Parasites are also another indicator of leaky gut. Parasites can eat and attach to the intestinal lining.

How to Heal Leaky Gut

We got rid of all the dysbiotic gut bacteria and had a full colonization of beneficial bacteria in our stool tests in about 4 months. This is what I call ‘Clearing the Stool Test’ and it was a huge turning point for our oldest child’s health. About 90% of her symptoms resolved once we cleared the stool test. This includes many of the symptoms that we associated with Lyme disease and autism, not with necessarily with the gut. The remaining 10% cleared with parasite treatment. I now consider the question ‘How to heal leaky gut?’ equivalent to the question “How to clear the microbiology and yeast stool test?”


We tried all kinds of things over many years to clear up our stool tests. Supplements. Acupuncture. Chiropractic. Energy Treatments on ZYTO. We were never successful until we figured out the following items. The ordering of the topics below is prioritized from most helpful to least helpful.


This is the ‘healing leaky gut’ list I wish I had many, many years ago. We had to figure out all of these steps by trial and error, brainstorming and debugging. And never giving up. Tens of thousands of dollars and many years later, we have healed our gut and have no more leaky gut symptoms. Healing leaky gut was not easy. But well worth it.


The rank-ordered ‘How to Heal Leaky Gut’ list, from most helpful to least helpful:

1. Stomach Acid

I have observed that when we have leaky gut symptoms, we often aren’t producing enough stomach acid. Our family took the Stomach Acid Assessment, and sure enough our oldest child with GI symptoms was the only one who failed. A few years later, our youngest child started having leaky gut symptoms. Sure enough, she then failed the Stomach Acid Assessment.


Is stomach acid really essential to healing leaky gut? If we aren’t producing enough stomach acid, then the whole rest of the digestive process is thrown off. This leads leading to malabsorption, malnutrition, and vitamin and mineral deficiencies. Stomach acid is also our first line of defense against bacteria, parasites and viruses in our food.


I spent many days researching what to do about low stomach acid. My conclusion was to supplement stomach acid using Betaine Hydrochloric acid (HCL) with pepsin. I asked a few practitioners about this and got varying opinions. The main concern seemed to be that stomach acid is supplemented, then the body will stop producing it. However, there were no other methods suggested to increase stomach acid.


It made sense that stomach acid is needed to fix digestion, nutrient deficiencies, GI symptoms, and bring one to an overall healthy state. I theorized that proper digestion might ‘reboot’ their system to start producing stomach acid again on it’s own. So I decided to give it a try. We stayed on HCL until the majority of their GI symptoms resolved (including a Clear Stool Test). This took about 3-4 months each time.


Then we went off of the HCL for a week and re-did the stomach acid test. After this time, we passed the stomach acid test. Being an engineer, I repeated the stomach acid tests a month later and still they passed.


My hunch is that HCL helps reset the pH in the stomach & upper bowel, which helps kick out the bad guys and helps good guys (like Lactobacillus) take over. HCL in combination with supplements like grapefruit seed extract (see below) to kick out bad guys and probiotics to help colonize good guys seemed to be the formula.


Here’s my summary: Once the body has reached the new ‘operating point’ then the stomach starts producing it’s own HCL. I think of the HCL as a temporary crutch to ‘jump start’ the whole digestive process.


To dose the amount of HCL, we found a few options:


  • Home muscle testing. I don’t have a video on HCL specifically, but below is a video showing how I tested and dosed my husband on probiotics.
  • Give HCL pills one at a time and wait 5 minutes between pills until the tummy burns or hurts.
  • Give HCL pills one at a time, wait, and then re-do the stomach acid test. We do this first thing in the morning, just like the Stomach Acid Assessment.

Even our young children (ages 3 & 4 at the times of GI distress) needed quite a bit of HCL. The dosing ended up being about 3-4 pills (500mg each) in their cases. I have heard of cases where much more has been used. In addition to HCL, both of our children went on digestive enzymes (Klaire Vitalzymes). We didn’t notice much clinical difference with the enzymes, but from my experience, it seemed like if we weren’t producing enough HCL then we were probably also not producing digestive enzymes. I think the enzymes were helpful but not essential like the HCL.

2. Hiatal Hernia & Digestive Valves

Whenever we had leaky gut symptoms, we also usually had hiatal hernias, Houston valve and/or ileocecal valve issues. We never had any obvious hernia or valve symptoms. It only occurred to me to go to the chiropractor because I thought we might have some spinal misalignments that might be impacting our digestion. I had no idea about hernias, Houston Valves or Ileocecal Valves, and how essential they are to healing leaky gut!!


We were lucky to have gone to a chiropractor who could diagnose and treat hiatal hernias & digestive valves. We stumbled across this very important piece of the GI puzzle. Chiropractically resolving the hernia and valve issues offered some immediate relief to symptoms – the children usually started eating more and complaining less of tummy aches. In hindsight, I am suspicious (but cannot prove) that dysbiotic bacteria actually caused the valve and hernia problems. This would mean that the hernia and valve issues were a leaky gut symptom rather than a cause.


We have always gone to our chiropractor for help with hernia & valve issues. What does a chiropractic adjustment of hernias and valves look like? I did find a few videos that demonstrate some basic techniques. I cannot comment on the accuracy of these videos personally, but they are similar in nature to what we experience at our chiropractor. This is one case where I actually recommend finding a chiropractor who is skilled at these adjustments.


Hiatal Hernia Self Adjustment

Your Houston Chiropractor Dr. Gregory Johnson Treats Hiatal Hernia

Your Ileocecal Valve and how to close the Ileocecal Valve
The following video has a water technique starting at minute 1:00 that we’ve found pretty effective for home use. We actually do it jumping instead of dropping the heels:
How to Fix a Hiatal Hernia

3. Diet

Healthy Snack for Soccer Team
Changing our diet to support the changes we were trying to achieve in our digestive tract was a big deal. I’m now convinced that without the diet changes, we never would have been successful in healing leaky gut. It was one of the most difficult things we had to do, but it majorly changed our health.


Gluten-free, diary free wasn’t enough. Grain free didn’t work either. We had to adopt an even more restrictive diet to make the conditions in our digestive tract unfriendly to the dysbiotic bacteria. We needed an ‘autoimmune Paleo’ which is no fruit, sugars (including honey, stevia, etc), grains, dairy or nuts. Basically meats, green veggies, and cabbage family became our staples. We also stayed away from sweet vegetables, like carrots, sweet potatoes and squash. More details, tips and practical information can be found in the best diet for health section of this site.


Dr. McBride of the GAPS diet recently started recommending a 30-day ‘fast’ of bone broth and pureed meats. She experienced that many people have guts that are so broken that her previously-recommended GAPS diet isn’t enough. We did this twice for other reasons after we already had a clear stool test. Our results with this broth & meat fast were amazing – clinically we were doing great. Our immune systems really started working, and our oldest child really started to fight Lyme – a positive CDC Western Blot antibody test!
In hindsight, I would’ve fasted first to get us to the finish line faster. (Note: I’m the kind of person who likes to solve problems as fast, simply, and economically as possible. I want to get back to living and working ASAP!!!) I’m honestly not sure that we “suffered” any more on the fast than we did by just eliminating those food groups.
More details on our experience with the 30-day fast are in the article “Fasting to Heal Leaky Gut”.


Changing the diet may sound easy. It is actually really hard. Sugar is the most addictive legal drug on the planet. Society doesn’t support people who don’t feed themselves (and their children!) sugar and alcohol. More tips for mentally preparing and dealing with diet changes can be found in the best diet for health and social and emotional aspects of healing sections.


We went through massive brain fog and withdrawal as things died off and our bodies switched from metabolizing sugars to metabolizing fat. The Drainage and Detoxification sections below were essential to support our dietary changes.


4. Detoxification

As the bacteria, yeast and viral balance in our gut shifts, organisms that die release mycotoxins. Detoxification and Drainage help ensure that these toxins and leave our bodies instead of building up. If they do build up, symptoms will often arise. This is called a ‘Herxheimer reaction” or “Herx”. A few of the common symptoms of Herx are autism, brain fog, fatigue, inflammation, and skin issues. Our oldest child started exhibiting severe autism symptoms when we changed her diet, only taking out the last portion of rice and fruit. Luckily I knew enough to realize that this was a die-off reaction, and that it was actually to be expected.


Detoxification refers to treatments and supplements that help pull circulating toxins out of our bodies. Detoxification doesn’t necessarily mean that our bodies will effectively excrete, we also need drainage pathways open. Both are necessary. Detoxification supports the above steps to healing leaky gut.


How do we make sure our bodies can detoxify effectively as the bacterial balance is shifted? We use muscle testing to determine what extra support is needed at a given point in time. The detoxification help that we need can change over time. We have (again!) spent a small fortune and a long time testing various detoxification supplements and treatments. The most helpful we’ve found for GI die-off are, in rank order:


  • Activated Charcoal
  • DE – We found that animal grade from the pet store tests best on us, better than the other various forms of silica made for humans.
  • Chlorella
  • Zeolite

I don’t have an example video of how I test for GI herx or die-off reactions specifically, since our days with GI die-off are long gone. The closest I have is an instructional video showing how I debug a skin issue. This particular skin issue seems to be caused by a detox problem, which is similar to the process I would go through for a die off reaction. If unfamiliar with the general technique, check out the Overview Video first.





If none of the above supplements are testing well, or solving the problem, then there are more tips at Detoxification.

5. Drainage

Drainage Remedies
Most practitioners don’t understand the concept of drainage, let alone how to fix it. This is a real tragedy. Drainage refers to opening excretory pathways in the body. These pathways are at the physical and energetic levels. These may already be open for some people, but they often aren’t, especially if symptoms of die-off are present.


Typically drainage remedies are homeopathic or herbal. We’ve also had ZYTO drainage treatments and those can work as well. We’ve spent thousands of dollars trying different drainage remedies. Different brands. Different lines from those brands. Different formulations. Herbal. Homeopathic. The most effective drainage products we’ve found, in rank order from most helpful to least helpful are as follows (remember, I don’t get any $$ from referral links or product endorsements):


  1. TerrainMax Terrain Remedies – The problem with these is that there are a lot of different ones to test. The one needed will often change every 2-4 weeks. We have tested them all over many years both at home and with ZYTO. If I were to only buy a few of them, our most frequented for healing the gut are: Colon, Kidney, Liver, Skin, Neural, Brain, Stomach, and Lymph. Although these are our most frequented, when we really need Pancreas or Gallbladder, for example, then we really need them. Honestly, I highly recommend buying the whole line. The bottles will last for a long time. Dosage is 5-10 drops 2x/day either rubbed into the arm or taken orally. If just starting on Terrain Remedies, I would ramp up the number of drops starting with one. You can get these from You need to call them and mention that your practitioner is out-of-town in order to purchase the products directly.
  2. Energetix Remedies – Again, there are a lot of these to choose from. Our most frequented for healing the gut are Bacteria Chord, Core Echina B, Lymph Tone I, Lymph Tone II, Lymph Tone III. Dosage is the same as the terrain remedies.
  3. ZYTO Drainage Treatment – These biocommunication devices and energetic treatments can really help with drainage pathways. Really. We may not fully understand them, but they can work. We also use ZYTO to determine which of all of the other drainage remedies to take. We have them all in our database, and ZYTO will rank them for us. This ranking is consistent with our home testing, and yields great results. After a biocommunication session, I usually spend about 45 minutes per person ‘digesting’ the information. This includes updating drainage remedies. Typically we take the top three drainage remedies recommended by ZYTO at all times.
  4. Futureplex Line – Similar instructions to #1 and #2, Lmph-Max and Kdn-Max. Note they are cheaper at acuatlanta but you will need to setup an account and call and say your practitioner is out-of-town.

We are typically each on 2-4 drainage remedies at all times while working on healing the gut. The ones testing the best are the ones we take. Without symptoms, we re-test and change these about once per month. At the first hint of symptoms, we immediately re-test and change remedies.


We either muscle test at home or use ZYTO for testing. Here is a list of videos that demonstrate how we test at home. Check out the Intro Video first if these debugging techniques are new.


Note that we typically get the fastest reduction in symptoms by putting the drainage or detox remedies that test the best into an enema:

Is figuring out drainage really essential to healing leaky gut? Yes – open drainage pathways are supportive of the other steps in the how-to-heal-leaky-gut protocol. Leaky gut symptoms or other symptoms may worsen if drainage pathways are closed.


6. Clearing the Stool Test

Our next step to healing leaky gut was ‘clearing’ the Doctor’s Data Microbiology + Yeast Stool test. Last I checked, the test was $89 and it must be ordered through a practitioner. Doctors Data cultures any dysbiotic bacteria found in the stool against several natural and prescription antimicrobials and/or antifungals. An example of our initial stool test results can be found here
Luschas, Soraya – Microbiology – 08-30-11.


‘Clearing’ the stool test means that we got rid of all items in the dysbiotic column, and had at least some level of everything in the beneficial column. Note the NG=No Growth of Lactobacillus under the beneficial column. I’ve learned that Lactobacillus is a big deal for proper digestion.


We took supplement suggestions from the natural antimicrobials on the stool test. I figured if they didn’t work we could always try the pharmaceuticals. We never had to use pharmaceuticals. The most useful and commonly used for us were Grapefruit Seed Extract (we usually a whopping 2g/day at mid-day, away from probiotics), Caprylic Acid, and Berberine. As our GI tract shifted, we experienced stool changes.
Sometimes we had herxheimer or die-off reactions. The Detoxification and Drainage sections above offer ideas for eliminating these symptoms. I interpreted these symptoms as a positive sign – a sign that the balance in the gut was shifting. Here are some tips I learned while clearing the stool test:

  • Supplement Dosing – This can be difficult because the Doctors Data stool test doesn’t give a suggested dosing of supplements. It also doesn’t tell how long the supplements should be taken. Back then, I experimented for months to find the correct dosing, by repeating stool tests and increasing dosing. . If I could do it over again, I would use energy testing to determine dosing and how long to take the supplement. Here is an instructional video showing how I dosed my husband on probiotics:

    In general, the dosing of natural supplements had to be high – about 2g/day of Grapefruit Seed Extract taken mid-day away from probiotics, about 2-4 caps of Berberine, and about 2 caps of Caprylic Acid. I liked the Nutrabiotics Grapefruit seed extract because it came in 250mg so we only had to take 8 pills. The brands of the other supplements didn’t seem to matter much.

  • E. coli – The hardest to clear for us was hemolytic E.Coli. The only thing I could find that worked was a beneficial E.Coli. I ordered Mutaflor from Canada. My theory is that the good E. Coli was able to keep the bad E. Coli under control.
  • Strep / PANDAS – A quote from Dr. Klinghardt MD: “Chronic Strep is the single most overlooked issues in 95% of children with autism.” Our blood tests have confirmed the finding of strep in our stool test. Many doctors call this PANDAS, or PANS, especially in children. Strep is one thing we haven’t been able to kick in our family. The homeopathic Pleo Strep works for us (see FAQ below), but as soon as we go off of it the strep slowly comes back. After $3k and about 3 years of working on strep, I have given up trying to treat Strep directly. I am now of the opinion that Strep is a normal part of our flora and the only way to solve a strep overgrowth is to change the ‘terrain’. (Agreeing with me on this opinion this is Simon Yu, MD). A bad ‘terrain’ can make our gut and body prime for various viral and bacterial infections. Primary terrain issues for Strep would be going after toxins, chemicals, heavy metals, and parasites. I am now of the opinion that the only way to work on strep is healing leaky gut, chelate and work on parasites.
  • Candida / Yeast – Our family never had a major Yeast or Candida problem, likely because we never ate much sugar. We do see it flaring up sometimes on ZYTO testing or clinically, especially if we are chelating or working on parasites. Tightening up our diet seems to take care of it. I feel the same way about Candida that I do about Strep (see previous point). It’s a normal part of our flora and we’ll never win the battle to eradicate it. I’ve never seen Nystatin or anything else work long-term for yeast. We’ve never directly used Nystatin but friends have. The only way I’ve seen work to keep yeast under control is through diet and healing leaky gut – permanently. I’m hopeful that I can report back later that after more chelation we are less prone to yeast flare ups. Stay tuned.


7. Probiotics

It might seem weird that probiotics are the last (i.e. least important) on this list for healing leaky gut. It is often the first thing suggested by practitioners, but I found it the least helpful. We learned that unless we were probiotics with 20 billion+ CFUs then forget it – we weren’t getting enough to effect change in the bacteria balance.


We spent years of trial and error and thousands of dollars on probiotics. More details on the results of our probiotic experiments can be found in the article “Which Probiotic is Best?” The ones I thought were most supportive for healing leaky gut, in rank order:

Probiotics that we tried that were not helpful include:

  • Biokult
  • Ohira
  • Florastor (awesome for the stomach flu, but not helpful for chronic dysbiotic bacteria)
  • Energetix’s Flora 12+ (also helpful for stomach flu recovery)
  • BioGaia
  • Klaire Labs
  • Primadophilus Reuteri
  • Custom 11 (expensive)

I have come to the conclusion that probiotics with FOS or inulin are not helpful when there are dysbiotic levels of bacteria. These ‘prebiotics’ feed dysbiotic bacteria just as well as they feed beneficial bacteria. Since the dysbiotic bacteria are already established, the prebiotics make them flourish. This is consistent with my dietary findings – that we needed to stay away from sugars and starches to reduce/eradicate the dysbiotic bacteria. It didn’t make sense to be on a strict diet and then eat a sugar/starch from a probiotic. Clinical findings confirmed this theory – our stool tests didn’t budge and our children’s moods and GI symptoms didn’t improve when they were on probiotics with FOS and inulin. In this example educational video I found out that my youngest child was not doing well on a probiotic with FOS. The summary and probiotic part starts around minute 10:02. I tried this probiotic many years after her symptoms had resolved, mostly because ZYTO recommended it.


I have found that the best probiotic for us changed over time, depending on what our bodies were experiencing. We re-tested and switched our probiotic about once a month. This instructional video shows how we figure out which probiotic to take.


Now that our leaky gut symptoms are resolved and our guts are healed, we don’t test well on any probiotics. So, we no longer take any. Healing leaky gut might actually be cheaper than taking probiotics for the rest of your life… I haven’t done the math.


We do eat fermented foods at almost every meal, but I don’t think that the levels of probiotics in fermented foods are high enough to recolonize or majorly shift the bacterial balance in the GI tract. I do think that they can help with transient digestion of food. They are also supportive in maintaining a healthy bacterial balance.

We are still working on some health issues, specifically chelating heavy metals and toxins. I am always watchful to make sure our gut is functioning properly as we chelate. Now that I have this how-to-heal-leaky-gut list, I can usually get the gut back to a healed and well-functioning state pretty quickly – a month or so.

8. Parasites Make it Hard to Keep the Gut Healthy

Parasites can eat and attach to the lining of the intestine for parts of their lifecycle. My experience is that probiotics can feed parasites. When they die, they can release dysbiotic bacteria and viruses directly into the intestine!
It is possible to heal leaky gut even with a parasitic infection. My family has done it. However, it will be hard to keep the gut in a healthy, healed state if parasites are still present.
If one has had leaky gut, I would at least consider the possibility that there may be a parasite infestation. If leaky gut issues keep coming back even though good diet and lifestyle is maintained, then I would really consider parasites. More details on diagnosing and treating parasites are in the parasites in humans section.

Keeping the Gut Healed

Now that the gut is healed, how does one keep it that way? Here’s what kept our guts healed and our health radiant:

  • Diet – Maintain the best diet for health. This had to become the way we eat. Permanently. Not a ‘diet’ or passing fad. Physically, mentally, and emotionally we feel the best when we eat this way. Still, maintaining a ‘different’ diet is really, really hard in today’s society. Check out the social and emotional aspects of healing for more support.

  • Eat Fermented Foods with Every Meal – We have gotten so used to sauerkraut in our salads and pickles on our burgers, that we can’t do without them anymore. We make our own ferments and eat them at pretty much every meal. Fermented foods are supportive of digestion and a healthy bacterial balance.

  • Stay off Antibiotics – There’s nothing better at ruining a healthy gut than antibiotics. Unfortunately many dysbiotic bacteria these days are antibiotic-resistant. Lactobacillus is generally not resistant, and it tends to die down with antibiotics. Without Lactobacillus, chances for a healthy gut are slim. Mold and fungal issues also tend to arise with antibiotic use. If for some reason antibiotics are absolutely needed, then here’s my protocol: VERY strict diet eliminating all grains, sugars, processed foods, and even sweet veggies like carrots, squashes and root vegetables. Think beef and broccoli. Proactively take 2-4g Grapefruit Seed Extract & 2-4 caps Berberine / day taken mid-day. Take 20+ billion probiotics without FOS/inulin in the morning & evening. Continue this during antibiotics and for 3 months after antibiotics are stopped.

  • Check in on Stomach Acid, Hernias, Stool Tests – For the first few years after healing leaky gut, we checked in every 6 months on stomach acid, hernias, and stool tests. Occasional cases of not being hungry or tummy aches caused us to check in too (although these were usually the stomach flu). Our main finding was that the hernia sometimes would pop up again. The child with the worst hernia needed several follow up treatments. The low stomach acid problem typically did not return. Stool tests generally stayed clear. Remember, though, we were following all of the above list items!


Things that didn’t work

We also tried a whole slew of supplements, diets and therapies that were supposed to be good for healing leaky gut. None of these were obviously helpful in our case:

  • Local honey, local pollen (from our backyard!)
  • Lack of hand sanitizer, playing in the dirt
  • Gluten Free, Dairy Free diet
  • GAPS diet, SCD diet
  • ZYTO – This is one instance where ZYTO wasn’t so helpful. It often recommended probiotics with FOS/inulin which we found fed the dysbiotic bacteria and prevented progress. ZYTO was helpful with die-off and herx reactions as our GI bacterial balance shifted. ZYTO drainage treatments were also supportive, and the ranking of detox supplements was helpful. Now, however, I know which supplements are useful for die-off reactions, and I can test them at home (See Clearing the Stool Test).
  • Arabinogalactan
  • Aloe Vera
  • Apple Cider Vinegar
  • Digest Gold
  • DGL
  • Beta Glucans
  • Tummy Tamer by Gentle Warriors
  • Grow and Thrive by Gentle Warriors
  • GI Microb-X
  • Bio-HPF (Used this later with Gastromend for an acute H.Pylori infection. It took about 3 months, but it worked)
  • Gastromend (Used this later with Bio-HPF for an H.Pylori infection. It took about 3 months, but it worked)
  • L Glutamine
  • NAC
  • Bromelain
  • Vitamin A
  • Cod Liver Oil
  • Collagen
  • Zinc
  • Vitamin D – didn’t help with leaky gut, but we take 10kIU/day in winter for immune support
  • Vitamin C – didn’t help with leaky gut, but we take 2g/day for immune support

We didn’t have significant clinical improvement with any of these alone. In some cases, we saw some improvements, but they went away when we went off the supplements. These supplements didn’t seem to get at the fundamental leaky gut problems.

Practitioner Team

We spent thousands of dollars on Pediatricians, gastroenterologists, naturopaths, MDs, NDs, acupuncture, Bioset and ZYTO. The most helpful practitioner was the chiropractor, who helped us with hiatal hernia and digestive valve issues. More details above.


Well, that’s it. Our recommended practitioner team – a chiropractor who can diagnose and treat hernias and digestive valve issues. The above steps will hopefully help too, and don’t forget the best assets of all – our own brains, debugging skills, and determination to achieve health.


Q: Can you suggest a reference for understanding the gastrointestinal tract and how it works?

A: Honestly, there’s a lot that we don’t know yet about our own digestive tract. We are in the infancy of our understanding. The best book I’ve found is commonly called the GAPS book. It was written by a British doctor, Dr. Natasha Campbell–McBride MD.


Q: What about reflux? What is your opinion about babies diagnosed with acid reflux?

A: For adults with reflux, I would follow the same steps outlined above under ‘How to Heal Leaky Gut.’ I am generally against the prescriptions of Zantac because I think most people with acid reflux are not digesting properly, possibly have hernias, and probably have too little stomach acid, not too much. For babies with acid reflux, I am also against Zantac prescriptions. The stomach acid test is hard to do on babies, so I would tend to skip this step. My sense is that babies will quickly start producing enough stomach acid if they dysbiotic bacteria are cleared up. If I really had a hunch that the baby needed stomach acid supplementation, I would energy test for necessity and dosing at home using a surrogate on Betaine HCL & Pepsin. Then I would skip to steps #2-7 on the list under ‘How-to-Heal-Leaky-Gut.’


Q: You said Strep always came back, but how did you clear Strep short-term?
A: Here’s the Pleo San Strep homeopathic remedy that we used to clear the Gamma hemolytic strep. You need to ramp slowly on this. The instruction sheet is here: Pleo-Strep Instructions. It’s a very strong homeopathic and apparently a lot of people react to it. It will take at least 3 weeks to clear. Along with the Pleo Strep, we found Bacteria-Chord supportive for draining the Strep.

Q: What about food allergies – will they go away after healing leaky gut?

A: Yes, in my experience. Our food and environmental allergies have disappeared since our leaky gut is gone and our digestive tract is functioning properly. We did use ZYTO to help us clear up allergies, but found that our ZYTO treatments kept reversing until we healed our gut. More details can be found in the Allergies section.

Q: Can you comment on Dr. Axe’s book “Eat Dirt”?

A: Honestly, I haven’t read the book. I can, however, offer some comments based on the marketing summary. First off, I can say that our family has never used hand sanitizer and has always let our kids play in the dirt (we are proud to have the dirtiest kids on the block!). We grow lots of our own vegetables. We also have backyard bees and produce our own honey, which we make by crushing the pollen into the honey. So we were eating very local honey with pollen. And we still got very, very sick and had bad, bad cases of leaky gut. It was our experience that breaking the sugar addiction was essential to healing leaky gut. (Yes, honey is sugar.) I don’t agree with a one-size-fits-all supplement plan. The bacteria that are overgrown varies from person to person. As for eating dirt, this sounds great if you have some good dirt around. We don’t. We have rats, raccoons, possums and all kinds of critters that live in the sewers and drains. They poo all over our yard. The poo caries parasites and diseases. Parasites rely on animals ingesting eggs found in poop to propagate. In theory, eating dirt sounds great, but I wish we had a good source of dirt! A safer option would be to try the soil-based probiotic Prescript Assist. In summary, Dr. Axe’s program sounds fine for people who want some healthier lifestyle tips. However, for those of us with dysbiotic bacteria and really leaky gut, I’m afraid his protocols will come up short.
Q: Do you believe that most cows have Lyme and that you can get Lyme from drinking raw milk? (Note: It may seem like this question doesn’t belong here, but I included it because of the answer)

A: If you are producing enough stomach acid, then no bacterial / virus that you eat in relatively small quantities should be able to get through. If the gut bacterial balance is strong, even if it does get through, it shouldn’t take hold. However, if you’re not producing enough stomach acid and have leaky gut, then it seems possible that you can get Lyme from raw milk.
Q: When did you take the HCL? With a meal or after a meal? The link you have to the stomach acid assessment test says after a meal?

A: We took the HCL all at once right before meals. This was the time we normally take the pills from our pillbox. I’m afraid that after the meal we would’ve forgotten to take the HCL! Now let’s rephrase the question as ‘What is the optimal timing to take HCL?’ HCL is produced in the stomach as the first step to digesting food. To me it makes most sense to take the HCL half at the beginning and the rest spread out evenly with the food. Maybe grind it into a powder and sprinkle it on the food? Way too much work! I would take it half before the meal and half mid-meal, ideally. I’m a fan of before because it stimulates the stomach before it is overwhelmed with food – hey wake up, this is what you should be doing. Taking all the HCL after the meal makes me wonder how much mal-digested food has already made its way into the duodenum and small intestine. Note that our family had good success with HCL and we took it all before meals.



[1] Natasha Campbell-McBride MD, Gut and Psyhology Syndrome, Medinform Publishing, 2010.



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Last Updated: Feb 8, 2018 @ 6:31 pm