Today’s post is a guest post my very good friend and colleague, Melanie Christner NTP CGP RWP. Melanie has written on Eat Naked before about her remarkable journey healing her family’s ailments with the GAPS protocol. It’s a great read, which I highly recommend. Today, Melanie shares some strategies and next steps for what to do if you’re on GAPS and it’s not working – ways to troubleshoot and testing to consider. 

I am continually impressed with the dedication of parents (mothers especially) to do whatever is necessary to help their children when they are struggling. Many, many families and individuals have invested countless time, energy, and money into better food to heal their bodies. I work specifically with the GAPS Protocol, which folks generally commit to for 1 – 2 years, depending on their situation. That’s dedication.

For many families, food has an incredible power to give them, and their children, the healing, symptom relief, and new lease on life they are craving. But what if it doesn’t quite hit the mark, even when doing it perfectly?

This is when we GAPS Practitioners employ what Dr. Natasha Campbell-McBride calls “cherries on the top”.

I’ve Done GAPS—Why Am I Still Struggling?

Traditionally, it has been easier to see great improvement in children’s health quickly. But even children are presenting with tougher case histories in current times.

Health issues can be complex, to the point that, even after eating the best foods, and doing a healing protocol like GAPS™, some folks aren’t having success and don’t know where to go next.

If one has been living with processed foods, imbalanced blood sugar, too many drugs/vaccines, surgeries, toxins from foods and personal care products — the damage goes even deeper and takes longer to rectify.

What does one do, when their best efforts with healing foods aren’t working?

Can the answer still be food and natural remedies, but in a more targeted, individualized way?

I say, yes. Below is an approach to consider.

What to do when the GAPS diet isn't working |

Lab Tests

There are many tests that are unnecessary to do from the beginning of the GAPS™ protocol, and testing is generally not recommended until one has been on the protocol for a full year to do its strengthening, nourishing work. Again, it is amazing how many issues are resolved using the intense nutrition that comes from doing GAPS well.

In my work I make some exceptions, however, which I will explain. Let me talk about the pros and cons of lab tests, and what I recommend.

Testing Drawbacks

Testing is expensive. I’m a researcher by nature and would love to do every test available to me, just to satisfy my natural curiosity about what is happening in my body. However, this level of testing is out of financial reach for many (myself included). Testing must be targeted and interpreted well by a trained practitioner.

Testing is based on TODAY’s science, which is continually changing and never “complete”. This is why test results must always be viewed within the context of a person’s health history and physical observation, and the tests chosen must have a record of accuracy and efficacy.

Testing needs to be used in conjunction to a personal approach. Talking with a client, listening, observing, and examining is where my work as a practitioner begins. I find that an extensive amount of time listening to a client’s health history can actually initiate the healing process.

Most testing is limited to a metabolic “snapshot.” Your metabolism changes continually, so it is wise to learn to listen to your body. Only your body can navigate the many complex intricacies and calculations of what it needs from day-to-day, even hour-to-hour.

When the “interrupters” are removed — refined sugar, processed food, and toxic cravings — it’s time to listen to your body. There is always room for adaptation and variation, even in a diet like GAPS.

Here are some factors which influence what your body needs:

  • Heredity & Constitution
  • Anabolic/Catabolic Cycles (daily, seasonal, as needed)
  • Parasympathetic/Sympathetic Dominance
  • Acid/Alkaline Balance
  • Energy Production Sources Switching (glucose vs. fats)
  • Hormonal Shifts
  • Water & Electrolyte Balance

The Case for Testing

By no means does the above imply that testing is of no value. It simply means that it needs to be targeted, accurate, and usefully applied.

To quote Dr. Natasha Campbell-McBride:

_Testing is a very helpful tool, but it
Some of the reasons to consider testing are as follows:

If you want to know, from the beginning, what foods will halt your healing process. Perhaps you have unknown sensitivities to chicken and cabbage — if you go through the GAPS Introduction Diet consuming quarts of chicken stock, and adding sauerkraut juice to each bowl of soup, for example, you’re going to slow down, or even halt your healing process. The right testing can steer you towards Intro food alternatives.

If you’ve been on GAPS for 6 – 12 months and there are lingering issues that you are unsure of. Every person is unique and has their own set of circumstances and health history. Some of us have been sick longer than others and need some additional assistance. Following the GAPS Protocol for 6 – 12 months gives the body nutrients and the strength that it needs before attending to deeper issues. It also allows time for the body to go through the cycles of die-off and detox, which can bring symptoms of their own as well as worsening current symptoms for a time.

If you are not yet confident in listening to your body, and using (free) tests like the Coca Pulse Test or the Skin Sensitivity Test to determine food sensitivities is not enough.

If you have the funds and you want to monitor yourself as you follow the protocol. From a purely scientific point of view, it is very interesting to observe progress through regular testing.

Tests I Recommend

The two tests I recommend, in combination, to clients are:

  • Comprehensive GI Stool Panel
  • MRT Leap 150 Food Sensitivity Test

These two tests, used together, are extremely valuable.

For example, your stool test may reveal a need for digestive enzymes, and your food sensitivity test may reveal a sensitivity to pineapple, papaya or pork…three very common sources of digestive enzymes in supplements. So, if you took these common digestive enzymes, you would be causing yourself daily digestive distress, instead of digestive help.

Comprehensive Stool Test

A comprehensive GI Test can be used for early immuno-detection of parasites and testing of inherited food allergies/sensitivities, fungal dysbiosis, inflammatory markers, pancreatic digestive strength, pathogenic bacteria, and infectious organisms like Giardia, Cryptosporidium, C. difficile, occult blood, functional markers, etc.

The comprehensive stool test is important for determining if someone is in need of targeted digestive help in addition to GAPS foods. Although GAPS tends to balance out issues like parasites and fungus, it is helpful to have the other markers.

Some good labs for GI tests are:

  • Doctor’s Data
  • Genova Diagnostics
  • DiagnosTech

Food Sensitivity Testing

As Margaret has already laid out in her fantastic series on food sensitivity testing — Part 1, Part 2, Part 3, & Part 4 — we consider the MRT Leap 150 Food Sensitivity Mediator Release Test to be one of the best options for testing most food sensitivities.

Eating foods we are sensitive to, even “healing foods”, can cause inflammation, worsen intestinal permeability, and act as obstacles to our healing protocol.

Additional Tests To Consider

These are tests I would consider for clients when they have done some good healing work, but still need additional help.

Adrenal Saliva Test (other hormones as needed)
The adrenals are a major player in our steroid hormone pathway, responsible for much more than our “fight or flight” response. They direct and have a role in many bodily functions — energy, sex hormones, blood sugar regulation, immunity, anti-aging, inflammation, fluid balance, and daily tissue repair.

Adrenals are impacted by ALL forms of stress — physical toxins, emotions, food sensitivities, infections, acute and chronic stress. With all the roles they carry out and the stress they are susceptible to, it is important to check on their wellbeing and give them support. Genetic Testing
This is testing done with a saliva sample, and therefore non-invasive. Genetics don’t need to be our destiny, but understanding if we have certain predispositions, such as difficulty in detoxing and MTHFR genes, can help us (with the help of a knowledgeable practitioner) make adjustments to our nutrition plan and lifestyle.

Organic Acid Urine Test
This test shows indirectly what pathogenic yeasts and bacteria might be living in the gut microflora by measuring the chemicals produced by those microbes…absorbed and then excreted through the urine.

Helpful for testing:

  • Vitamin and mineral insufficiencies
  • Amino acid insufficiencies
  • Oxidative damage and antioxidant sufficiency markers
  • Detoxification sufficiency
  • Functional markers of B-complex deficiency
  • Neurotransmitter metabolites to assess central nervous system (CNS)
  • Mitochondrial energy production assessment
  • Methylation sufficiency status
  • Lipoic acid and CoQ10 sufficiency markers
  • Dysbiosis markers for bacterial and yeast overgrowth

Example of this test’s use: D-arabinitol is an organic acid that’s produced in fungal metabolism, so if you have an overgrowth of D-arabinitol in the urine, then that can indicate a yeast overgrowth in the gut.

Hair Tissue Mineral Analysis (HTMA)
HTMA is both non-invasive and inexpensive. A sample of hair is sent to a laboratory, and a qualified practitioner interprets the results to outline a mineral and nutrient balancing protocol.

Helpful for:
Showing mineral levels, including heavy metal levels and more. Testing is usually done several times with some months between each test.

When results are interpreted properly they can give an indication of:

  • Adrenal status
  • Thyroid hormone uptake at the cellular level
  • Protein use
  • Cortisol production
  • Carb tolerance
  • Kidney health
  • Diabetic tendencies
  • Heart health
  • Immune status
  • Toxic metal exposure
  • Underlying causes contributing to unexplained mental symptoms such as brain fog, anxiety, anger, and depression
  • Female and male hormone issues
  • Nervous system health
  • Liver health and overall detoxification pathway health


Hydrogen and Methane Breath Tests
This test is helpful for identifying SIBO (small intestinal bacterial overgrowth) and is similar to tests for lactose intolerance.

The person consumes a sugar solution of glucose or lactulose on an empty stomach. The sugar solution is quickly metabolized by the bacteria in the small intestine, which produce gases that are measurable in the breath by breathing into a special tube. Hydrogen and methane gases are then measured at 2–3 hours (based on the transit time in the small intestine). For more information on SIBO, click here -> SIBO and SIBO testing.

Gut Permeability Profile
This test is done by swallowing Polyethylene glycol, which contains molecules of different sizes. Over the course of 6 hours, the levels of these molecules are measured in the urine, which shows how damaged the digestive lining is. Commonly available from many laboratories.

Helpful for:
Measuring damage to the gut lining.

Kryptopyrroles Urine Test
This test is also commonly available in many laboratories.

Helpful for:
Determining if you have Pyroluria

Kryptopyrroles are metabolites of abnormal gut flora and are relatively harmless in low levels. However, if an above-average amount builds up, it can lead to a condition called Pyroluria, a familial disorder which occurs with stress. High levels of these pyrroles systemically bind with B6 and zinc, preventing the use of these essential nutrients in the brain and body. Supplementing with magnesium, zinc, B vitamins, and evening primrose helps to metabolize the pyrroles and balance the condition, and the GAPS Protocol can help to fix the root of the problem.

In Summary

The GAPS™ Protocol is the best I know for building up little bodies (and big ones!) with deep nutrition, cleansing, and natural remedies for the whole family. It can be adapted to fit many body types and needs. However, for a targeted approach it can be necessary to have carefully chosen tests done.

If you are interested in using the GAPS™ Protocol for your own family and want guided step-by-step application, and support from a Practitioner guided community of families, I invite you to check out my Academy of classes, including the most popular, the GAPS Class.

GAPS Class begins soon!


Melanie Christner, NTP CGP

Melanie delights in helping you apply healing protocols to everyday life, while eating really great food…and becoming friends with your body again.

She writes at As a mom of four children herself, she works with moms and their kiddos to help them feel their best and to have all the life and energy they were meant to have.

Melanie is an NTP, Certified GAPS Practitioner, and Healing Foods Specialist in Vermont. For fun you can either find her playing in her kitchen, or Nordic skiing, or swimming in the Green Mountain rivers with her family.

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