The Leaky Gut Protocol


The Leaky Gut Protocol:

Small intestinal bacterial overgrowth (SIBO) is a condition that is characterized by too many microorganisms in the small intestine.  These can be a combination of both good (progenic) and bad (pathogenic) microorganisms.

SIBO damages the intestinal lining and creates a state of mild-severe leaky gut syndrome and resulting food intolerances and chronic inflammatory processes.  Beat SIBO with the leaky gut protocol put together by Dr Jockers.

SIBO Symptoms and Conditions:

Individual with SIBO will often experience abdominal pain, nausea, gas, bloating, belching, flatulence, chronic constipation or diarrhea.   The sheer amount of microorganisms and the metabolic waste they produce through their life cycle can be very challenging to the body.  As the metabolic waste is released it causes the build-up of methane and sulfur based gases that produce the bloating, gas and flatulence.

Many physicians now believe that Irritable Bowel Syndrome which has always had a loose definition is now better understood as SIBO.  SIBO is also known to be associated with Celiac disease, fibromyalgia, all auto-immune conditions, rosacea, liver problems, gallstones and gastritis.

SIBO may not be the major driving factor in 100% of these conditions but it is almost always present in individuals suffering from these disorders.  The leaky gut protocol is very effective at helping individuals suffering with these health problems.


Parasites Steal Valuable Nutrients:

The pathogenic organisms steal valuable nutrients that cause dysfunction in the body.  These parasites consume massive amounts of iron and vitamin B12 which leads to differing forms of anemia.  They also affect fat absorption by deconjugating bile which leads to fatty stools and poor absorption of essential fats and fat soluble nutrients such as vitamin A, D, E & K.

The parasites also create inflammatory metabolites and excite the immune system to create an inflammatory response.  Because the dysfunctional microenvironment persists over time it creates a chronic inflammatory process that damages the gut lining creating open gap junctions and leaky gut syndrome.

Large food particles and microorganisms cross through the gaps in the gut and get into the bloodstream creating a whole body inflammatory response that can affect the joints, organs, brain, cardiovascular system, etc.

SIBO Healing Protocol:

This is a three phase protocol that includes a fasting period to regulate and minimize the amount of microbes in the gut.  Then comes a re-innoculation period to bring in healthy microbes in abundance.  Finally, comes the probiotic lifestyle that becomes the foundation for the individuals daily lifestyle.  After three to six months they may have a vacation meal or a few vacation days but it is best to stay as close to the probiotic lifestyle as possible for 350 of the 365 days out of the year.

How To Begin the Process:

The leaky gut protocol begins with a 3-7 day fasting cleanse.   During the fasting period the individual should consume organic broths with garlic and onions.   Bone broth provides a megadose of critical nutrients like gelatin and key amino acids that support the rapidly growing cells in the gut and soothe inflammation and scarring of the gut lining.  Garlic and onions are powerful anti-microbials that help regulate the microenvironment.

Fiber should be minimized as it is a fuel source for all types of microbes.  Someone with SIBO will react poorly with a lot of fiber in their diet.  They will notice more bloating and gas when they consume beans, nuts and veggies.  These individuals need to go through a fasting period to regulate the gut microbes and then they begin adding in fermented veggies and fermented chia, etc. as healthy fiber sources that are also probiotic carriers.

Fasting/De-Inflaming Period:

During the fasting period of the leaky gut protocol it is key for the individuals to consume organic acids and fluids so using apple cider vinegar and/or lemon in water is especially useful.  It is also highly adviseable to use herbal teas and coconut oil throughout the day.  These will help strengthen the body through the fast and provide good clean fats and anti-oxidants.

1)  GI Regulator:  This is a blend of natural anti-microbials that have a powerful effect on reducing bad bacteria, yeast and parasitic counts.

I typically recommend 2 caps – 2 times daily with food or broth each day for individuals with more severe SIBO.  Milder cases would be 1 caps – 2x daily.


2)  Daily Detox:  This is a blend of nutrients designed to detoxify the cells, blood, liver, kidneys and gut of endotoxic debris and environmental pollutants.

Severe cases – 4 caps of Cell Detox and 4 caps of Body Detox daily.  Mild-Moderate cases – 2 caps of Cell Detox and 2 caps of Body Detox

3)  Gut Repair:  This is a blend of nutrients designed to heal and seal the gut membrane and replenish the mucosal membrane.

Moderate-Severe Cases – 3-4 spoonfulls daily     Mild-Mod Cases:  1-3 spoonfulls daily


4)  Gut Defense:This is a high quality IgG supplement that improves sIgA levels which is the immune component of the gut membrane.  This is very important for preventing future parasitic and/or yeast or bacterial infections.

Severe:  2 caps of 500 mg – 2x daily       Mild-Moderate – 1-2 caps of 500mg -1x daily


5.  Nrf2 Power:  These have a very powerful effect at reducing inflammation in the gut and improving healing.



Re-Inoculation and ReBuilding Period: 

After the fasting period you move into the re-innoculation period where you consume lots of good fats and fermented and steamed veggies.  This period lasts for ten to fourteen days while you slowly add in new foods and see how the body tolerates them and what is going to support your microbiota and body the best.  Be sure to watch out for how your body responds to the various FODMAP foods listed here

The only foods consumed on this part of the plan are small amounts of steamed cruciferous veggies like broccoli, cauliflower, cabbage, brussell sprouts, etc.  Small amounts of steamed carrots can be nice too.  You want to find the veggies your body is able to tolerate.  If you notice gas, bloating, cramps, heartburn, etc. after consuming something be sure to journal that and try it again the next day.  If you notice 2 days in a row of this sort of reaction eating the same thing than stay off that particular food for a while (a month) before retrying.

Fermented veggies and beverages such as sauerkraut, kimchii, beet kvaas, kombucha and coconut water and coconut milk kefir are good foods to try in small quantities and see how your body tolerates these as well.  Using small quantities of chia and/or flax seed is really good for fiber and essential fats.  Coconut oil, coconut butter, coconut flakes and coconut milk in small quantities are good during this stage and make sure you apply all the rules above to see if they are disturbing your gut.

Continue to use the supplements recommended above.

During the second week begin adding in small amounts of avocado, raw veggies, olive oil, pasture-raised meat and eggs.  See how your body tolerates these foods by eating them alone or with a food you know you are already tolerating well.  Be sure you are eating small quantities and observe if you feel like you have good or bad energy after eating them and whether they give you digestive discomfort at all.

Probiotic Lifestyle and Recoding Phase:   

Intermittent fasting strategies should be used to where the individual restricts themselves to a 4-8 hour eating window.  This would mean eating all the food for the day between the hours of 3-7pm (4 hour window) or 11am – 7pm (8 hour window) as an example.

Example Meal Plan:

Begin your day with lots of fresh, clean water – 32-48 oz the first hour or 2 you awaken to super hydrate and flush out toxins and stimulate bowel movements.  You can add in lemon and/or apple cider vinegar too.  If you enjoy coffee you can add in an organic black coffee with some coconut milk (full-fat organic or Toasted coconut milk).  You can also have a super-greens shake if you like.

First Meal – Sometime in later morning if possible like 11am – Protein shake with coconut milk (I like Toasted coconut milk – almond milk + coconut cream are the only ingredients), good protein powder (vegan protein powder or non-denatured whey protein from grass-fed cows.

Second Meal –3pm:  Big salad with avocado, olive oil, chia seeds, vinegar & lemon/herbs or flax crackers and guacomole.

Third Meal – 6pm – Grass-fed beef, sauerkraut, big salad or steamed/sautéed veggies.  EV Olive oil or grass-fed butter/ghee, fresh squeezed lemon and herbs all over everything.

Or you could do 2 meals in a 4 hour window for a more advanced version of a cleansing lifestyle.   Be sure to use high quality digestive enzyme with any larger meal and specifically a meal with meat.  One of my favorite enzymes is Super Digest-Zyme here


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4 Responses to The Leaky Gut Protocol

  1. Liz May 27, 2013 at 7:03 pm #

    Good information! My dad, 79 yrs of age, has been battling the above for two years now. He has lost a considerable amount of weight, has watery, uncontrollable diarrhea and has had so many expensive tests run. He took 4 rounds of Remicade – each round making his condition worse.

    When he was up at Johns Hopkins, they found an intestinal parasite. This didn’t surprise any of us as my parents have been serving overseas as missionaries in West Africa for 30 plus years. They gave him a round of antibiotics and basically said, “There ya go!” (Still fighting this just as strongly as before.)

    It is my understanding that parasites don’t leave that quickly – and if there’s one, there are others. Reading the above diet, I can’t see my dad, at his age, able to go on such a severe diet. Is there another option to restore his gut flora and provide him relief?

  2. Ella October 31, 2014 at 6:37 pm #

    I started reading this article, and was impressed by the information, but then was introduced to one product, and then another, and another… I’ve just mentally dismissed this article as one big clever advertisement.

    • Dr. Jockers November 1, 2014 at 5:51 am #

      Sorry you feel that way Ella. This article used to contain no product info but I got tons of questions about what products to take so I included that. Just trying to make it as user friendly as possible. Blessings!

  3. Bobbie Dallas Lee December 28, 2014 at 6:56 pm #

    I am a hepatocellular carcinoma survivor! Diagnosed 12-2006. I am alive today bc God sent me a Angel on Earth who had cured herself of terminal lung cancer! I am alive after chemo & being given maybe 30 days in Oct. of 2009. I am still here with my liver & appear to be cancer free, will no after next b/ Jan. but I do believe I have the leaky gut syndrome atleast it sounds like it! I have such a problem digesting food & be constipated all the time I take a lot of turkey ruhbarb & diet is all organic, no meats!! I do take Bl walnut wormwood & cloves daily along with other supplements but this is really sounding like my digestive problem. Can u give me any advice I follow u on fb! Love ur recipes!!!!

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