Leaky Gut Diet – My Experience with GAPS & SCD

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Wellness Mama » Blog » Health » Leaky Gut Diet – My Experience with GAPS & SCD

Ever since I wrote a review of the book Gut and Psychology Syndrome and mentioned that we used it to help reverse our son’s dairy allergy and behavior issues, I’ve gotten a lot of questions about what protocol we used and the specifics of how we did it.

Our son made drastic improvements through using a specialized diet called the GAPS protocol to help reverse leaky gut. After his initial intensive period on the GAPS diet, we have now moved to a more relaxed version of the GAPS diet that also uses parts of the SCD protocol.

When I found out that I had Hashimotos Thyroiditis, I went on an autoimmune protocol (my 30-Day Reset Protocol) that is a combination of GAPS, SCD and the Leaky Gut Diet. My symptoms improved dramatically and blood tests even showed that I was able to tolerate certain foods after taking time to intensively heal my gut.

Since our family has now had 3+ years experience with a leaky gut diet of some kind, I wanted to share our experience and what worked for us. I’m not a doctor and I definitely can’t give any specific advice for your individual situation, but my hope is that sharing our story will help you find answers on your own health journey.

What is Leaky Gut?

According to the practitioners at SCD Lifestyle:

The term Leaky Gut Syndrome is used to describe the condition of “Hyperpermeable Intestines,” a fancy medical term that means the intestinal lining has became more porous, with more holes developing that are larger in size and the screening out process is no longer functioning properly. The fallout results in larger, undigested food molecules and other “bad stuff” (yeast, toxins, and all other forms of waste) that your body normally doesn’t allow through, to flow freely into your bloodstream.

So now that we have the general essentially meaningless definition out of the way let’s find out what is really going on…

The intestinal lining is the first mechanism of defense for our immune system. The outer layers of intestinal cells (epithelial) are connected by structures called tight junctions. At the tips of these cells are the microvilli, which absorb properly digested nutrients and transport them through the epithelial cell and into the bloodstream. During the normal digestion process the tight junctions stay closed forcing all molecules to effectively be screened and only pass into the blood stream through the mucosa cells (think of them like bouncers at the front of a classy bar). For reasons we will discuss later, these tight junctions can become “open” or permeable allowing un-screened molecules to flow directly into the bloodstream (think of it like a fish net with very small holes).

I knew the research but I was absolutely amazed at the changes our whole family saw from supporting gut health and working to reduce inflammation and leaky gut.

It makes perfect sense that gut health would have such a dramatic impact on all aspects of health, since the body has more bacterial cells in the gut than it does human cells in the entire body. As Chris Kresser explains:

Our gut is home to approximately 100,000,000,000,000 (100 trillion) microorganisms. That’s such a big number our human brains can’t really comprehend it. One trillion dollar bills laid end-to-end would stretch from the earth to the sun – and back – with a lot of miles to spare. Do that 100 times and you start to get at least a vague idea of how much 100 trillion is.

The human gut contains 10 times more bacteria than all the human cells in the entire body, with over 400 known diverse bacterial species. In fact, you could say that we’re more bacterial than we are human. Think about that one for a minute.

We’ve only recently begun to understand the extent of the gut flora’s role in human health and disease. Among other things, the gut flora promotes normal gastrointestinal function, provides protection from infection, regulates metabolism and comprises more than 75% of our immune system. Dysregulated gut flora has been linked to diseases ranging from autism and depression to autoimmune conditions like Hashimoto’s, inflammatory bowel disease and type 1 diabetes.

This is the reason that you find so many stories of people who saw improvements in their children’s autism, their own anxiety or depression or their autoimmune symptoms from going on a specific leaky gut diet to support the gut.

It is also the reason that I felt better on our son’s GAPS diet (even though I didn’t know about my autoimmune condition at the time) and why consciously supporting my gut helps me mitigate the symptoms of my thyroid disease. Even though I’ve been focused on a high-quality diet for a long time, I still struggled with leaky gut and needed to address it directly. I found that I had created many of the risk factors for leaky gut at various times in my life before adjusting my diet, including:

  • Overuse of antibiotics: I had taken countless rounds of antibiotics before I even entered kindergarten and eventually had my tonsils and adenoids removed. There is evidence that repeated antibiotic use can change gut bacteria and make leaky gut more likely.
  • Chronic Stress (check)
  • Chronic inflammation and illness (check- I was taking all the antibiotics to fight recurring cases of strep)
  • Eating too many processed and refined foods, especially carbohydrates  (check- school lunches)
  • Consumption of gut irritating foods like grains and vegetable oils (check and check before I changed my diet)

How to Know if You Have Leaky Gut?

The symptoms of leaky gut can vary drastically from person to person and some people can have gut problems for a long time without symptoms. I found that this online quiz was really helpful in determining some of my personal risk factors.

GAPS vs SCD vs Leaky Gut Diet:

I’ve mentioned multiple diets that we used (we now use a hybrid of all of them) but I think it is important to understand the individual protocols and what they are used for:

  • The Gut and Psychology Syndrome Diet (or GAPS diet) is really a three part program that includes diet, detoxification and supplements and which has several stages (including a very intense intro stage. It is often done for 1-2 years and can significantly help allergies and mental conditions in some people. It is based on some of the same principles as the SCD diet but really emphasizes specific nourishing foods like bone broth and homemade fermented vegetables. The GAPS diet is a 6-part intensive protocol and it is a lot of work, but in our experience, the results are well worth it. The book Gut and Psychology Syndrome is a great primer for starting with the GAPS diet.
  • The Specific Carbohydrate Diet (SCD program) is specifically geared toward gut health and has been used to help people mitigate the symptoms of Crohn’s disease, Ulcerative Colitis and other digestive problems. This is the best resource I’ve found on SCD and gut health.
  • Leaky Gut Diet is a term often used for either of these healing protocols or for an autoimmune protocol such as my:
  • 30-Day Reset Autoimmune Program – A combination of principles from GAPS and SCD that focuses on reducing inflammation and reversing leaky gut. It has been the most effective thing I’ve tried personally and it helps address the various problems I was having and greatly helped with the symptoms of autoimmune disease. For gut/brain problems or really severe cases, the GAPS intro diet can be helpful as well. Here is a recipe list with modifications for the autoimmune reset.

Our Leaky Gut Diet Protocol

We started initially with the GAPS intro diet, which is a highly restrictive program designed for intensive healing. It is outlined it detail here.

We then transitioned into Full GAPS which is less restrictive and which helps transition back to a wider variety of foods. It is outlined in detail here along with a food list.

We are now following our own leaky gut diet protocol of the 30-Day Reset Diet Autoimmune Protocol which focuses on the following foods:

Foods to Avoid:

  • Grains
  • Legumes
  • Eggs
  • Dairy
  • Seeds
  • Nightshades
  • Nuts
  • Alcohol
30 Day Autoimmune Reset

I also take specific supplements to help support the gut, and working with a qualified functional medicine practitioner is a great way to help find what supplements are helpful for a specific case.

The Bottom Line:

Gut health intricately affects so many aspects of the body. I think that we will see a rise in research on leaky gut and gut problems in the next few years, but in the meantime, I’ve found that a specialized diet (like GAPS, SCD, Leaky Gut Diet or Autoimmune) can help individuals determine their own reactive foods and nourish their bodies more effectively. Learn more about How to Know When a Diet Is No Longer Right for You: Understanding Intuitive Eating & Your Body’s Needs.

Have you ever struggled with leaky gut? Did dietary interventions work for you?

Katie Wells Avatar

About Katie Wells

Katie Wells, CTNC, MCHC, Founder of Wellness Mama and Co-founder of Wellnesse, has a background in research, journalism, and nutrition. As a mom of six, she turned to research and took health into her own hands to find answers to her health problems. WellnessMama.com is the culmination of her thousands of hours of research and all posts are medically reviewed and verified by the Wellness Mama research team. Katie is also the author of the bestselling books The Wellness Mama Cookbook and The Wellness Mama 5-Step Lifestyle Detox.


63 responses to “Leaky Gut Diet – My Experience with GAPS & SCD”

  1. Maria Avatar

    Hi Katie

    One more question, what’s the reason behind excluding eggs and nuts in the 30 day reset diet if they are allowed in the Gaps diet? Is the 30 day autoimmune diet meant to be more restrictive?


  2. Debbie Avatar

    How do you work in Low Histamine ?
    I’m trying to make a spreadsheet of the leaky gut/auto immune/SIBO/GAPS/low histamine and it’s so hard to find common foods ! I’m going bonkers, but my skin is inflamed & im itching & hives -scratching all night long…..I’m sleepless but determined and welcome any advise ! Thanks

  3. Brooke Avatar

    How do you manage the GAPS diet for a toddler? Our poor kiddos have eczema but our youngest is having severe breakouts and it seems like the more I remove what he’s reacting to he starts reacting to the foods he CAN have (according to allergy testing). I’m at my wits end and can not find a GAPS certified practitioner near me to help guide us along the way. I feel completely helpless and lost. Any suggestions?

  4. Karla Avatar

    i seem to remember you d had article on what foods you ate and then how you reintroduced foods. I’ve done 11 weeks and want to know should i add one per week?

  5. Miller Avatar

    Really interesting article Wellness Mama. I’m not sure if you’re familiar with Banting at all? It’s an eating approach that’s really taken off in South Africa, where I live. Essentially a high fat, no carb approach. Those on it have reported great success in overcoming a multitude of different physical ailments, that includes leaky gut and IBS etc. As well as marked improvement in cholesterol and sugar levels, and lowering of blood pressure.

    It’s not really a “diet” per se, but rather a different way of looking at how certain foodstuffs can affect our body (both positively and negatively) and then cutting out the stuff that’s detrimental and focusing on the stuff that’s good for our systems.

    I think it’s something that you might be interested in looking a bit deeper into – if so, check it out here:

  6. Elisa Avatar

    My Lyme doc put me on The Microbiome Diet (book by same name) and after 3 weeks, I feel great! It’s basically no sugar, dairy (except butter), eggs, grains, potatoes, sugars (& friends = honey, maple, etc.), dried fruit. At week 4, you can add sweet potatoes and eggs back in. Anyways, I feel so great! I don’t think enough people know about the Microbiome Diet – it’s the gut healing diet. https://www.amazon.com/Microbiome-Diet-Scientifically-Restore-Permanent/dp/0738218111/ref=as_li_ss_tl?ie=UTF8&linkCode=ll1&tag=wellnessmama-20&linkId=bec826c269bd3ee2b576b0d55d795b2c&language=en_US

  7. michele Avatar

    I have been searching and searching for answers for my situation. I am a type 1 diabetic and have hypothyroidism. I also have severe seasonal allergies which causes breathing problems, severe cough, congestion, severe sinus issues, and itchy and watery eyes. Obviously I need to be eating foods that will sustain my blood sugar as well as foods that will help to regulate my allergy problems. I definitely am interested in trying this to see how it works. Are there any stories of those with severe allergies that they have overcame through this change in their eating. Any with type 1 diabetes?

  8. Jennifer Avatar

    Wellness mama Katie, we are now two years from the beginning of this thread. How are you and your family now and what diet are you on? We are debating between a rotational diet and the 30 day reset diet.

    1. Wellness Mama Avatar

      This was tremendously helpful to me and to one of our children who struggled with eczema and after a few months we were able to eat a more varied diet. My husband had c.diff years ago and was on a lot of antibiotics, so he had to do a more intensive program (this one) to finally get his gut straightened out, but we are all much better now!

  9. Rainah Avatar

    I have been leaning towards a somewhat less drastic approach to managing my leaky gut, Hashimoto’s, lupus, etc. issues. I mean, I admire those who manage the GAPS diet and/or etc. However, in the past, rotational dieting (just rotating the starches in the meals we ate) was sufficient to help me feel great for a good number of years. But rotating grains is also a lot of work – so I’m looking for a way to modify that approach. My solution thus far?, I’ve been gradually accumulating entrees that fit these objectives: 1) in line with AIP objectives, 2) my husband likes them, 3) they are easy enough for my husband to prepare if I’m not in the kitchen (he’s happy enough to cook when needed, and he’s good at it, but he needs meals that are not a big burden to prepare). My *initial* hope is to put together 30 such menus. Thus far, I have about 15. I also have another 15 or so paleo meals that he likes, most of which are also simple enough for him to comfortably prep. My husband is loathe to give up some of the meals we’ve typically made that combine the entree with starches. I’m okay with that on a limited basis *when I am not experiencing inflammation*. — My thought here is that I can add rotated starches into those AIP/Paleo type meals with greater ease than what I was able to do when I was rotating starches before (the starches were built in to specific entrees all too often before – and sometimes life got in the way, and we’d have to change entrees or eat out or etc., and we eat out really, really inexpensively, making rotational dieting difficult when those days hit……). /// Anyway, with that plan above, I don’t commit to staying completely off of things that are hard to avoid on our budget when life sends us reeling towards a restaurant with few rotational/aip, etc. choices. Also, with this plan, I can avoid starches entirely when I feel I need to be that drastic (I’m not doing that yet, but I’m trying to set up for that). In the meantime, my plan is to enjoy various starches when inflammation is not causing trouble). I figure that, with a set of AIP/hubby-pleasing/easy-to-prep meals, even if I am in an accident, or life hits and I don’t manage things well enough, so that I become ill, that with the above plan, my husband and I can work together on meals we can both agree on. —- It is my hope that this will work, but I’d love to hear any cautions you might have. — One additional problem I face is simply this: 1) my husband will not invest in organic, because he often has access to low cost meats and etc. through his work (which doesn’t feel like a plague to me…..). 2) but he often stocks up on these items, 3) they come in bulk packages. 4) While I am changing everything about cooking and ‘reclaiming my home’, I do not yet have the energy to stock my freezer on a regular basis (I need to utterly reorganize the freezer before I move to that on a regular basis, but that’s another story…., and I don’t intend to try to stock my freezer until my husband and I have worked out our issues with the freezer……, hopefully that happens soon). BECAUSE OF THOSE ISSUES ON PURCHASING/THAWING MEATS IN BULK: I often have one to three types of meat to work with for a number of days/weeks, which increases the number of meals I need from each type of meat to come up with my ‘monthly 30’ (or perhaps, closer to my ‘monthly 60 or more?’). So, those 15 AIP meals are still well short of my long term goal…… Any comments? I’d love feedback if you happen to have any….

  10. Liz B. Avatar

    Wellness Mama,

    You mentioned that you battled with strep as a child and had to be on a number of rounds of antibiotics. My 18 month old has now had strep w/ scarlet fever twice in his little life (antibiotics 3 times, once for an issue with his circumcision and the other two times for the strep). I definitely plan to address his gut health through what you mention in your article but how can I avoid antibiotics in the future if/when he gets strep again? I can’t imagine giving him more rounds! What do you suggest?

    1. Wellness Mama Avatar

      Poor thing! From personal experience, the only way I’ve found is to address the underlying issues when they aren’t ill and build the gut and immune system as much as possible to help avoid the infection again. Strep can be a serious infection, as you know, so I’d work on avoiding it, rather than not taking the antibiotics unless you are working with a naturopath or specialist who can help fight the strep in other ways…

  11. Derrek Hooyman Avatar
    Derrek Hooyman

    Anyone find a diet that works? i don’t eat meat and dairy and am wondering if I should avoid grains or legumes? I can’t live on veggies and fruits. Other than that, I’m looking for starchy veggies higher in calories. Sweet potatoes and squash I’ve thought about,

  12. Simone Avatar

    Hi there, I have just done 45 days of the AIP diet and am now introducing food. I am doing this to prevent autoimmune disease which I have in my family history but also to help with endometriosis. I used to get eczema as a child and have noticed I get itchy after re-introducing certain foods e.g. dairy and chocolate. Just wondered if I can do the IgE blood tests for all foods and spices and will this just tell me what foods I should avoid to help with gut healing? Is the Ige test the same as the RAST testing? Is this useful for us trying to heal leaky gut and prevent autoimmune disease?

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