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AIP for IBD: The Paleo Autoimmune Protocol and Inflammatory Bowel Disease


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Do you have inflammatory bowel disease? A recent study put the Paleo autoimmune protocol to the test in patients with Crohn’s disease and ulcerative colitis, and the results are quite remarkable.

AIP protocol
This dish as part of a paleo autoimmune protocol can have a significant positive effect on those with inflammatory bowel disease. istock.com/JooCalvet

I was recently contacted by Mickey Trescott of autoimmunewellness.com, who had some very exciting news to share. The Paleo autoimmune protocol (AIP) has been put to the test in a formal research study, and the results are nothing short of fantastic.

For those of you who are familiar with scientific research, you know that it’s incredibly hard to get a study like this funded. Not only is there no pharmaceutical company to profit, but it also completely overturns current paradigms in clinical research. No agency wants to fund something that is “too out there” or “doesn’t yet have any evidence.”

Sometimes, though, things just work out. In this case, a gastroenterologist at Scripps was introduced to AIP after witnessing one of her patients with ulcerative colitis make an astonishing recovery using the elimination diet. She decided to put together a study to formally investigate the diet in both ulcerative colitis and Crohn’s disease patients. It was entitled “Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Diseases,” and it was published last month in the journal Inflammatory Bowel Diseases.

In today’s article, I’ll break down the methods of the study—and the impressive results they found. First, I’ll review the two types of inflammatory bowel disease (IBD) and discuss why an elimination diet might be effective.

More evidence that the AIP diet is effective for IBD.

What Causes IBD?

Inflammatory bowel disease includes both ulcerative colitis (UC) and Crohn’s disease (CD). Like other autoimmune diseases, conventional therapies for IBD typically focus on suppressing the immune system. This has numerous unwanted side effects, including an increased risk for infection, and the efficacy of the drugs is quite variable.

As of 2015, 231 single nucleotide polymorphisms (SNPs) within 200 different genes are associated with IBD risk. Still, genetics only account for a small proportion of the variance in disease (8.2 percent for CD and 13.1 percent for UC) (1, 2). This means that environmental factors likely play a significant role. Factors implicated in IBD include gut dysbiosis, environmental toxins, and diet, among others.

The Standard American Diet has been associated with an increased risk of IBD, while anti-inflammatory diets have shown some promise for relief (3). Many patients with IBD have known food sensitivities (65 percent, 4), yet some patients may not know which foods might be harming them. I’ve discussed the limitations of food sensitivity testing previously on my podcast. This is where an elimination diet can be really helpful.

Enter the Paleo Autoimmune Protocol

The Paleo autoimmune protocol (AIP) is a Paleo-type diet, which removes grains, legumes, dairy, refined seed oils, and refined sugar, but also recommends initial removal of eggs, nightshades, coffee, alcohol, nuts, and seeds. The basic rationale is to avoid foods that might trigger intestinal inflammation or promote gut dysbiosis and immune dysregulation.

Like Paleo, AIP encourages consumption of nutrient-dense, healing foods, including bone broth, organ meats, and fermented foods. The elimination phase is typically followed by a maintenance phase until sufficient improvement in symptoms is achieved. At that point, select food groups can be carefully reintroduced. This allows patients to expand their diets, while identifying any foods that might be contributing to their symptoms.

I’ve mentioned before that the restrictions of AIP really aren’t based on any peer-reviewed evidence. While the study discussed today was not a randomized controlled trial, it certainly adds to the credibility of AIP, beyond just anecdotal support and my clinical experience with patients.

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SAD to AIP in 6 Weeks

For the study, 15 patients were enrolled that had been living with IBD for an average of 19 years. A team including a nutritional therapist and registered dietitian led the participants through a six-week phased elimination program to transition from their current diet (SAD) to AIP. They remained on the full AIP diet for five weeks. Mayo score (a measure of ulcerative colitis activity) or Harvey-Bradshaw score (a measure of Crohn’s disease activity) was determined at baseline, after the six weeks of phased elimination, and at eleven weeks after a month on full AIP. Seven of the 15 patients were actively taking medications to help manage the symptoms of their disease during the intervention. Patients who were identified as deficient in vitamin D (three patients) or iron (six patients) were also started on nutritional supplements to correct these deficiencies.

Unexpectedly Effective

So, the results? The authors write:

Clinical remission was achieved by week 6 by 11/15 (73%) of study participants, and all 11 maintained clinical remission during the maintenance phase of the study.

Wow. Seventy-three percent of participants achieving clinical remission in six weeks rivals most drug therapies for inflammatory bowel disease, without any of the side effects. Let’s look at the breakdown by disease across the three timepoints.

Average Mayo score (disease activity) in ulcerative colitis patients:

  • Baseline: 5.8
  • Week six: 1.2
  • Week eleven: 1.0

Average Harvey-Bradshaw index (disease activity) in Crohn’s disease patients:

  • Baseline: 7.0
  • Week six: 3.6
  • Week eleven: 3.4

Additionally, four participants were able to discontinue some or all of their medications.

What It Means

This study suggests that the Paleo autoimmune protocol can be used as an effective treatment in many patients with IBD and that remission occurs quite rapidly. I’ve witnessed it quite often in the clinic, but I’m thrilled to see it documented in the literature as well!

For more information on AIP, be sure to check out these resources:

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Join the conversation

  1. I personally have had mixed success over the past 5 years since reading Robb Wolf’s original book.

    Things can be going very well and then suddenly I get a colon stricture that lands me in hospital. I then need steroids to open up the blockage.

    Partly this is a compliance issue since when I feel better I then take more liberties with what I eat.

    However also I believe this is an issue of an underlying infection that has yet to clear. Uva ursi for me has worked to suppress the infection but never seemed to have cleared it (or different infections have come and gone due to a compromised gut).

    Any extra thoughts would be welcome.

  2. Hey there! I was diagnosed with Crohn’s in 2010. The few years leading to the diagnosis and the following 5 years after diagnosis where the worst years of my life. I nearly literally died on at least one occasion and was in horrible crohnic pain for many years, add in the severe depression that comes with discovering you have a major illness and I was a hot mess.

    I began researching food as a cure about 3 years ago and I slowly made permanent changes at my own pace to a Paleo lifestyle and now I’m full Paleo Auto Immune Protocol with further veggie and meat restrictions that suit my body and follow low FODMAP as well. I don’t drink bone broth it’s gross to me, but I use it to cook with instead. I don’t eat offal, it’s just not for me. I haven’t gotten into fermented foods either, I take probiotics instead. Don’t find barriers find compromise!

    This works! Don’t be overwhelmed like I was at first. First you may not even eat some of this stuff anyway! Cross those off the list and celebrate! Next just decide to focus on one thing first like grains, and just be aware of how much you eat it then try to eat one less serving a day, when that becomes easy reduce it by one more serving a day. Eventually you will be eating one serving a day, then slowly move to 5 times a week, then 3 times a week, then 1 time a week, then none. Then pick the next thing you want to remove from your diet and repeat!

    That’s how I did it, slow and steady. I didn’t beat myself up and I was patient with myself. I could tell a big difference each time I removed foods on the banned list. I knew I wanted to make a permanent change and I gave myself time to figure out what to eat instead, and how to prepare those things to keep from getting bored.

    I’ve reached my goals now and have transitioned completely to full AIP and low FODMAP now since November 2017. I’ve never felt better, my pain is nearly nonexistent and my poop is fully formed, something that hasn’t been like that in nearly a decade.

    I take vitamins and probiotics and I’m full of energy. Since I eliminated things so slowly I rarely miss any foods because some of them I eliminated years ago. Currently the only thing I’m missing is berries (the tiny seeds that can’t be removed were problematic), but that is the most recent thing I removed.

    If you decide to eat or drink something that is on banned list as a treat, don’t beat yourself up. Eat a small portion, like the actual serving size listed on containers. Or just have half! Be positive with it and it will be positive! Good luck!

    PS as bonus I’m obese mostly from steroids prescribed by doctors and I’ve lost 41 pounds and it’s coming off without exercise because my body loves what I’m eating!

  3. This is very exciting news! I have had Anxiety and IBS for over 12 years and was considering getting a colostomy bag. Long story short, since I have been on the Paleo diet I have been slowly getting better!
    I still have a few foods that set me off and I can’t work out what they are so I was thinking of trying AIP. I am a bit overwhelmed though because there are a lot of foods on the AIP diet that I can’t eat so I will have to modify it.

  4. Chris: I would like to add that this type of protocol is perfect for patients with active gum disease. Remember, the mouth is just an extension of the gut. It really is the beginning of the process of digestion. If there are irritants under the gum tissues (tartar) that are stimulating inflammation and infection, these must be removed by a dental hygienist or dentist. But, the Paleo AIP is the perfect way to enhance healing and change a damaged lifestyle. I recommend this to all my patients with active gum disease.

    • How interesting! Thanks for sharing this information on its affects on gum disease. I follow AIP for my Crohn’s but I’ve noticed an improvement in my tartar buildup between cleanings recently so maybe that’s why!

    • Nope! The SCD allows dairy, nightshades, inflammatory oils, coffee and legumes— not okay for AIP 🙂

  5. I am a type 1 diabetic. I was skeptical that diet could make that much difference since I thought I cleaned up my diet, eating lower carb, but 3 years ago I decided to try Sarah Ballantyne’s Autoimmune Protocol diet. AIP was a challenge. For three months I was on this very restricted diet in order to see the difference. Before starting the diet, I made a list of AIP foods and recipes that I liked and worked with my blood sugar issues. I faithfully followed the diet for the three months, and before reintroducing foods, I saw amazing changes!
    — 1/3 less insulin use and more even blood sugar
    — A1C of 5.6 – 5.9 without the wide swings of up and down
    — hearing loss better and dry eyes better
    — less global body aches and stiffness and quicker recovery period
    — maybe one to two migraine a year instead of 1-2 weekly at the hight of my migraine period. So far none this year.
    — cooler body temperature at night and sleeping 5-6 hours and many times more hours
    –constipation less and more regular bowel movements
    I am sold that diet can play a bigger role than we think!

  6. A good study that will lay the groundwork for further research. I started primal/paleo 9 months ago to heal a lifetime of gut issues. The results were so significant to me but my docs have curbed enthusiasm. Of note regarding AIP; the main trigger foods are eliminated just like your doc might advise, yes (coffee, chocolate, alcohol, spices, nuts and seeds, dairy, etc). Here the doctor advise usually stops. Where AIP wins is from the important addition of nutrient dense and healing foods. So instead of having porridge and granola for breakfast, sandwich for lunch and pasta for dinner (and ending up sicker, constipated, and nutrient deficient) I now delight in vegetables for each meal, good quality protien, bone broth, and liver, plus lots of fat. I still slip up with the trigger foods (chocolate – wahhh!) And suffer a relapse. The healing foods get me back on track faster than just eliminating the triggers. So this is an important distinction from the paleo diet and I really notice the difference when I sometimes get swept away in the paleo vibe. Paleo people can eat more things and I can’t. It’s simple but it’s hard to ignore the enthusiasm towards keto, bulletproof coffee, and paleo chocolate desserts.

    • I’m now 11 months into paleo and I’ve just had a painful flare up. It sends me running back into AIP. I wish I could stay there for longer. This latest was triggered either by eggs or by my attempt to make a yeasted paleo bun with almond and arrowroot. (It was delicious by the way). So I’m feeling bagged out and bummed out. The healing is happening fast though so I hope in a few days I’ll be better again.

  7. I have been sharing this research on a Facebook group for people with IBD. Of course, a few of them agree that dietary factors have an effect on IBD. They mention that the patients are taking drugs, but there is no indication on how long they have been taking them, so the patients could actually have less symptoms because of the drugs.. What do you think? I believe in changing the lifestyle to go into remission as I have done it myself, but it is so hard to convince those who don’t believe it even with a study.

  8. Great that researchers are looking, but I think that the removal of certain foods from the AIP (ie. lentils, potatoes, Nightshades, seeds, spices, nuts) was short-sighted.

    • Hey Tim

      I think the removal of those foods is necessary in the initial stage – certainly based on our experience. My wife has MS. In remission for several years now due to a Paleo style diet.

      My wife can tolerate a bunch of things now, in moderation, that at one point were totally no go

      • Doh – had not finished that comment. 🙂

        Certain foods trigger almost instant fatigue and whilst she can now enjoy some foods in moderation (eggs, nuts and spices) others just don’t work out for her even several years in (tomatoes, peppers etc).

        I guess the point is to pull these things out – see some improvements and do a reintroduction to see how you get on. Get some personalised intel on what actually works for you. Hopefully, many folks can bring a lot of these things back in moderation as they improve.

        Fortunately, she is okay with potatoes though. 🙂

        • Wow thanks for commenting! I have Crohn’s and I follow AIP modified for my needs. I’m glad to know that it works for so many others too!

    • Why? Nightshades are certainly known to be troublesome for people with autoimmune disease. I tried a standard elimination diet, but my psoriasis did not start to clear up until I removed nightshades. And when I reintroduced them, wow. My psoriasis flared up, and I had severe joint pain and earache. Lesson learned!