So, you’ve healed your leaky gut… Now What?


By completing the leaky gut protocol, you have taken an important step in optimizing your health. Chances are you have seen significant improvements in the past month and are eager to find out what’s next? 

If you want to experience more improvement, consider the following:

Personalized Nutrition Consult

Many of our patients benefit further from a personalized nutrition consult with our clinical nutritionist or health coach. They both realize that change is a process that occurs over time. They work with you each step of the way to create a personalized, sustainable plan that facilitates healing and promotes optimal health. We always encourage you to bring in your significant other, particularly if they do most of the cooking, to maximize the experience. In this way, a custom, personalized nutrition plan can be created. This takes into account your individual goals, needs, and dietary preferences.


Additional Treatment Considerations

Depending upon your response to the first month of the protocol and the degree to which you were sick previously, some people need more time to heal their leaky gut and will elect to continue the protocol for up to three months or more. Alternatively, some of our patients will elect to do the protocol once every two or three days as a meal replacement. Note-the lining of the small intestine under normal circumstances is replaced every three days as the small intestinal lining cells are the fastest growing cells in the body. The amount of time it takes to heal a leaky gut varies with each individual. Sometimes just taking a quality probiotic supplement or eating fermented foods is all you need to do if you are really doing well. Many patients have done so much better just by cleaning up their diet and when they do cheat now they will often suffer adverse symptoms.

Here is a sampling of a few things we would consider for our patients after they have gone through the initial phase of the leaky gut protocol.


Digestive Enzymes and/or Hydrochloric Acid Replacement

If you are still experiencing excessive gas, bloating or difficulty with digestion (especially protein), you may have a deficiency of various digestive enzymes and/or hydrochloric acid. Simply replacing with one of these supplements can have a dramatic positive impact.

Iodine Deficiency

Iodine is an important constituent of the thyroid hormone molecule and deficiency can produce all the symptoms associated with an underactive thyroid such as fatigue, difficulty losing weight, constipation, dry skin and brittle hair. Iodine is also important for the prevention of fibrocystic breasts, cysts on the ovaries, and thick sinus secretions.

A simple iodine supplement replacement can help significantly with these problems.


Additional Diagnostic Considerations 

Whereas many functional medicine practices will do extensive, cutting-edge functional medicine testing upfront, our practice is to wait and see clinically how you are doing after the initial four weeks of the protocol. At the end of the day, we are more concerned about how you are feeling than any abnormalities noted on a particular test. Additionally, most these tests are not covered by insurance and can be expensive. We would rather see our patients spend their hard-earned dollars on treatment rather than a bunch of tests.

We will often recommend more what I would consider routine blood testing (electrolytes, liver functions, lipids) that may be part of an annual exam. There are a handful of tests that we consider important that may or may not be covered by your insurance such as hemoglobin A-1 C, CRP, homocysteine and B12 levels. We may also consider ordering blood tests to evaluate your adrenal glands or more in-depth analysis of the thyroid such as anti-thyroid antibodies. Having said that, here are some tests that we routinely consider for patients who are still having some symptoms. 

BioTek IgG Food Allergy Tests

This blood test looks at specific IgG antibodies produced by white blood cells in the lining of the intestine the so-called GALT (gut associated lymphoid tissue) to identify which foods should be eliminated to avoid an immune reaction. It is important to realize that this test is looking at one subset of immune mediated reactions to certain foods and if you don’t react on this test it doesn’t mean you might be reacting to a particular food through a different mechanism. For example, this is not a test for IGE antibodies, which is often performed in the allergist office and may produce a different set of symptoms.

On the other hand, if you do react to a particular food you need to pay attention and consider decreasing or eliminating that particular food from your diet depending on the level of your reaction. We often find patients reacting to some “quirky” foods such as bananas, almonds are even garlic. It’s just nice to know what might be causing an unsuspected reaction.

Although mainstream medicine considers this test controversial, we have performed the test on hundreds of patients and find it to be “spot on” in helping to identify specific individual food reactions.


Cyrex Labs

Cyrex labs has several helpful tests for looking at markers of leaky gut, foods which cross-react with gluten in gluten sensitive patients, and various autoimmune disorders.


Metamextrix Stool Analysis

This test, which requires you to send in a stool specimen, uses a variety of technologies to look for both friendly and pathogenic microorganisms (bacteria, yeast, and parasites). It also will determine if you have a preponderance of a strain of obesity causing bacteria referred to as firmicutes, which if present can make weight loss very difficult.

Did you know that the bacteria H. pylori has been associated with stomach ulcers and inflammation of the stomach or gastritis? This bacteria has also been associated with chronic hives, asthma, and even atrial fibrillation of the heart. This is one of the many disease causing bacteria that this test will help identify.

We have discovered this organism in patients with chronic hives who had no digestive complaints. We eliminated the microorganism and the hives resolved. This is just one of many examples I could give regarding the notion, as Hippocrates said that “all disease begins in the gut”.


Neurotransmitter Test

Our emotions are controlled by various chemical messengers in the brain that we refer to as neurotransmitters. Often, nutritional deficiencies arising from a leaky gut can result in various neurotransmitter imbalances leading to various mood disorders such as insomnia, anxiety, and depression. This very helpful urine test will identify any potential neurotransmitter imbalances or deficiencies in patients with mood disorders. These imbalances can often be improved by taking appropriate supplements to support neurotransmitter balancing.

For example, we often see patients who have an iron deficiency, which leads to deficiency of the neurotransmitter dopamine, as iron is a cofactor for the conversion of the amino acids tyrosine to dopamine. Dopamine deficiency can cause problems with anxiety, depression, apathy, fatigue and even restless leg syndrome. Iron deficiency is on the rise for a variety of reasons and the overuse of acid blocking medications (example Prilosec) is one of the leading causes of iron deficiency.

I know this all may seem a little bit complicated, however you should begin to see how one of the basic tenets of functional medicine is to remove anything that might be making you sick and replace anything you may be deficient in.

ZRT Iodine Test

We mentioned replacing with iodine earlier. There is a simple test available to check for deficiency of this vital nutrient. A deficiency in iodine can result in a variety of symptoms including fatigue, weight loss resistance, cold hands and feet, and mental fogginess. Our body cannot make iodine so it is imperative that we obtain it through our diet or supplementation.


SIBO Testing

Small intestinal bacterial overgrowth (SIBO) has been getting a lot of attention recently as a cause for various digestive symptoms. The main symptoms are excessive gas, bloating, diarrhea, constipation and abdominal pain, which occurs because of excessive amounts of certain strains of bacteria in the gut. Often these bacteria are felt to be of the “good” variety.


We have found that many of our SIBO patients find significant relief after doing the protocol. However, if you find that you experience a lot more gas or bloating when you eat fermented foods or take a probiotic then you might have SIBO. Also, if you have noted temporary improvement in your digestive symptoms when you have taken an antibiotic for another reason than that might be another clue for SIBO. IF SIBO is suspected there is a special breath test we occasionally recommend, which will help determine this.



This is by no means a comprehensive discussion of all the diagnostic or therapeutic options available. We wanted to give you a sampling of the things we most frequently consider for our patients on follow-up visits. Our goal is to always partner with you on your journey to achieving optimal wellness.

Additional Leaky Gut Resources:

What is Leaky Gut?
Leaky Gut Protocol
Leaky Gut Diet
Causes and Treatment
Elimination Diet