How the GAPS Diet can cause health problems

We have learned that insulin resistance, type two diabetes, and metabolic syndrome are not just genetics. Numerous studies have examined the role of gut microbiota in insulin resistance and non-alcoholic fatty liver disease.

This information is fascinating to me, as I was diagnosed with insulin resistance in addition to non-alcoholic liver disease a few years back, despite my healthy weight, healthy body mass index, and healthy diet (plus, I was teetotal). Today I am going to write an article on how the GAPS diet can affect your health.

My GAPS honeymoon

I was diagnosed with Irritable Bowel Syndrome in my 20s. For many years, I was a vegetarian. Over time, I experienced severe stomach pain. I was constantly awake due to the pain and bloating.

After years of suffering from abdominal pain and many poorly-informed natural health practitioners, I decided to take a deeper look at gastrointestinal health to find the answers I was seeking.

My appendix was removed. This meant I had to endure 4 months of stabbing pains at night and 4 (!) months of sleepless nights. I was fed up with waiting for emergency appendicitis to be diagnosed. I became a Weston A Price foundation member and changed from a wholefood diet into a WAPF-approved diet. I began to soak all grains and legumes and made bone broth every week. My husband even learned how to make sauerkraut.

Despite this being a very nourishing diet, my gut symptoms have worsened.

GAPS was the best option for me. It provided immediate relief. After just one month, my gut felt its best in years.

I am a GAPS Nutrition Consultant and an absolute GAPS fanatic.

GAPS was, in my opinion, the solution to all digestive problems. I didn’t know it would be a bumpy ride. The negative effects have continued to affect my health for years.

GAPS’ dark side

After 6 months on GAPS, I began to experience severe night sweats. My mid-30s meant that there was no possibility of peri-menopause. My doctor was confused. My total and LDL cholesterol were higher, but this didn’t concern me. I was convinced that high saturated fat, provided it was 100% grass-fed, was the best way to go.

I was a good sleeper, but suddenly, my nights became restless. There were many trips to the bathroom to pee and strange sensations. My neck and scalp felt stiff and painful.

GAPS-mania was all I could see.

After being told by my GAPS mentor, that it is not uncommon to experience a second, more severe healing crisis within months of starting GAPS, I began to restrict my carb intake. He also said that I was most likely salicylate, amine, and oxalate intolerant and that GAPS had only uncovered these issues.

GAPS made me more sensitive to food chemicals the longer I was on it. After switching to a Failsafe diet (low salt and amines, gluten-free and dairy-free), I could function again. However, my insomnia was still severe, with up to 20 wakes per night. Temazepam was my only option, as other natural remedies failed to work.

To cut a long story short, the GAPS diet had ruined my gut microbiota and switched on my genetic predisposition for poor ammonia detoxification. It also severely affected my methylation ability (I have the MTHFR variant gene).

Hence, why does GAPS work for some people?

People often ask me about GAPS. GAPS Nutrition Consultant for many years. I do not treat spectrum disorders, so my opinions about GAPS are solely based on my experience as a gastrointestinal specialist.

Gluten removal

Many people have improved with GAPS, while others have experienced severe side effects. I suspect that those who improved were gluten-intolerant or undiagnosed celiacs, so a strict elimination of gluten for a prolonged period would have made a huge difference in their symptoms.


GAPS is a popular diet for people with IBS. GAPS is a low FODMAP diet that will provide relief for IBS sufferers. However, this doesn’t necessarily mean that it is their best diet. I believe that strict low FODMAP and strict GAPS combined are a recipe for creating dysbiosis.

Fresh food

This is a simple one. Going from a processed diet to a home-cooked one will make a huge difference in your health.

Complex carbohydrates can be removed.

People who follow the GAPS diet often suffer from dysbiosis, SIBO, or coeliac disease that is not diagnosed. These conditions will cause their intestinal tract to become so inflamed that they cannot produce enough digestive enzymes and brush border enzymes to begin breaking down complex carbs. They also lack the diversity of gut bacteria that can ferment them. Although it will make people feel better, it won’t solve the problem.

GAPS: Why GAPS is bad for digestion long-term

This diet is high in animal protein and saturated fat.

Research has shown that a high-saturated fat diet can lead to shifts in gut bacteria. E Coli and Bacteroides thrive on high levels of fat and protein. Both bacteria can become pathobionts which means they can cause inflammation, leaky stomach, and ammonia.

This is not a low-fat diet. However, moderate fat intake from a variety of sources is recommended.

Although it may not have been the intention of GAPS to encourage a high-protein diet, the truth is that GAPS users gorge on protein, especially in the first months.

It raises the colonic pH.

High protein and high-fat diets increase colonic ammonia levels by favoring gram-negative, ammonia-producing bacteria. My colonic pH changed from acidic (healthy) to alkaline (unhealthy). A high colon pH can cause colon cancer.

My liver was affected by high ammonia levels – my liver enzymes were elevated. High levels of ammonia cause severe brain fog and night wakings. Even though I drank 2.5L of water daily, my urine turned cloudy and smelly.

It causes dysbiosis

GAPS diet encourages the growth and production of gram-negative bacteria in the gut. These bacteria, along with the high levels of ammonia, are absorbed into your bloodstream and affect your liver health.

It lowers the levels of beneficial bacteria.

The GAPS diet should be restricted to gut bacteria associated with good health and healthy microbial diversity, such as Akkermansia muciniphila or Fecalibacterium Prausnitzii. These bacteria require large amounts of prebiotic fibers, especially legumes.

GAPS advocates can say that garlic and onions are high in prebiotics. I can answer that because 1) most people with digestive problems cannot tolerate garlic and onions, and 2) to keep the bacteria happy, you need to consume large amounts of both.

It creates the false impression that removing carbohydrates will kill ‘bad’ bacteria.

Bacteria can also ferment fats and proteins, not just carbohydrates. As mentioned above, most bacteria with this ability are pathobionts and gram-negative.

Where am I now?

Insulin resistance

After my GAPS stint, I developed insulin resistance. It’s surprising to many that insulin resistance can occur even if you are thin and eat low carbs. The solution? The GAPS diet is high in fat. Research has shown that a high-fat diet can cause insulin resistance. This is due to changes in the microbiota and increased inflammation. In a future blog, I’ll write more about this.

The only thing that has helped me with my insulin resistance is a total overhaul of my diet. I now eat a lot more plant-based foods, but I eat very little meat and fish. I also consume a lot of FOS (a prebiotic fiber – up to 15g per day) and lactulose (10g per day). Metformin is a biguanide drug. It increases the levels of Akkermansia Muciniphila, and I do high-intensity training twice weekly.

Non-alcoholic fatty liver disease

This has been resolved. The GAPS diet causes no more liver hemangiomas.


This is a constant problem for me. Some genetic variants in my DNA make me susceptible to low ammonia detoxification, such as CBS or NOS. The GAPS diet influences these genes. Thanks to a high-fiber diet, high levels of prebiotic lactulose and a probiotic Lactobacillus griseus GG, I don’t suffer from ammonia overload. Also, an ammonia amino acids formula that supports the urea cycle has helped me.

Salicylate or amine intolerances

It was all gone when I began to alter my diet, reduce inflammation, and address methylation problems.

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