The Autoimmune Protocol vs. Other Healing Diets

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aipvsothers

One of the most common questions I get about the Autoimmune Protocol is “Why should I do AIP instead of a ketogenic diet, GAPS, SCD, low-FODMAP, or the Candida Diet?” or “Should I do AIP with SCD/low-FODMAPs etc.?” With this article, I am going to share with you the differences between these approaches, and why you should or shouldn’t layer them (or use them instead of!) the AIP.

Low-Carb or Ketogenic Diet

A low-carb diet has a few variations, but the biggest distinction is whether or not the amount of carbs one eats is enough to put one into ketosis or not. This is a state where the body relies on ketones as well as glucose to produce energy, and is achieved by eating less than 30-50 grams of carbohydrate per day. This threshold is individual—some people are able to achieve ketosis with a higher level of carbs, others need to eat less. Most people consider a diet that is between ketosis and 100 grams of carbohydrate per day a low carb diet (depending who you talk to—I’m certainly not an expert here!). Some practitioners say to try low-carb or ketogenic diets because they have been shown to be effective against neurological disorders as well as some types of cancer. Others have better success with weight loss or regaining insulin sensitivity with this approach.

There has been much heated debate in the Paleo community about what carb intake is optimal for good health, and if we even need carbs at all. Some believe that a ketogenic diet is optimal for everyone, while others believe that it is necessary to eat carbohydrates, and that ketogenic diets need only be used in specific circumstances. Dr. Sarah Ballantyne writes in The Paleo Approach that studies of those using ketogenic diets and autoimmunity show a worsening of symptoms. I’ve both had a negative personal experience layering a ketogenic approach with AIP, as well as worked with many autoimmune clients and haven’t found anyone who seems to thrive eating this way, especially with Hashimoto’s (this isn’t to say there isn’t anyone out there — I just haven’t come across them yet!).

So why do we need carbs, and why do some people feel bad on a low-carb approach? Well, first off, vegetables containing carbohydrate are our main source of fiber, which is necessary to feed a wide range of bacteria in our gut (here is a fantastic series about fiber from The Paleo Mom). This is why I think a lot of people fail on low-carb diets long term—they are not nourishing their gut flora! Secondly, insulin is needed to make the conversion of thyroid hormones, and low-carb diets can actually cause hypothyroidism symptoms in some people, even after the “carb flu” period is over. I personally experienced a worsening of my hypothyroid symptoms when I tried a ketogenic diet for six weeks in 2013, and finally gave up because I was so incredibly fatigued. My recommendation is not to layer a low-carb approach with the autoimmune protocol unless a person is dealing with a specific situation that would warrant it, like neurological disease or certain types of cancer.

The SCD Diet and Candida Diet

The SCD and Candida diets have different protocols, but they both share a pathogen-specific approach. This means their purpose is to eliminate the foods that feed pathogenic overgrowths in the gut, like all starches (including those that would be included on AIP like sweet potato, squash, and tapioca), fruit, sweeteners, fruit juice, milk, and grains, among other foods.

These approaches can be very effective at eliminating symptoms for those that have overgrowths, but neither of these diets are very effective at eliminating pathogens on their own. If someone is experiencing symptoms when eating these foods, instead of blindly going on one of these variations of a pathogen-specific diet I would encourage them to test, don’t guess! Most who are successful at recovering from these overgrowths do so knowing specifically what pathogen they are fighting. Some need to be dealt with from more than one angle—prescription or herbal antibiotics, anti-fungals, and probiotics can be helpful here (and it is important to work with a practitioner who is experienced in this area!).

Another issue I have with these approaches is that they don’t eliminate a lot of allergens shown to be a problem for some people with autoimmunity—most notably eggs, dairy, and nightshades. In addition, these approaches end up being a low-carb diet, which is not advisable because of the reasons in the section above.

A lot of people ask me if I recommend layering the Autoimmune Protocol with SCD or the Candida diet “just in case”. I don’t think this is a good idea. If you suspect you have a pathogenic overgrowth going on, I recommend comprehensive gut testing and a skilled practitioner to help you navigate this issue. Many people waste their time on a restricted diet (you can read my story about this here) when really, they need medical treatment—I don’t want you to be one of them!

The GAPS Diet

The GAPS Diet is similar to the SCD and Candida diets in that it also incorporates a pathogen-specific approach, but emphasizes the pinpointing of allergens as well as gut-healing nutrients. The GAPS intro diet consists of well-cooked meat, vegetables and broth for a period of time until additional foods are added in one by one to assess tolerance. The first foods that are added in are fermented vegetables, probiotics, egg yolks, fermented dairy, ghee, and nuts. The diet was developed for use with autism and other neurological conditions, and since has been used by people with a variety of chronic health conditions.

What I like about the GAPS diet is that like AIP, it is also an elimination diet, and emphasizes gut-healing foods at the same time as removing triggers. That being said, I don’t believe the protocol is ideal for those with autoimmunity — many of the first foods reintroduced can be problematic for people, and I believe these reintroductions come too soon in the process. The intro is also too low-carb for most folks, and they usually don’t feel well if they try to apply the diet long-term (over a couple of months).

The Autoimmune Protocol, if done in a nutrient-dense was as Sarah Ballantyne suggests in The Paleo Approach (fermented foods, bone broth, organ meats, etc.) is very similar to GAPS, except the protocol is much more refined and tailored to those with autoimmunity. Some people, especially those with acute digestive symptoms, can benefit from a GAPS intro-like start to the Autoimmune Protocol. If this is what you want to do, I just recommend that you follow Sarah’s recommendations for reintroducing foods outlined in The Paleo Approach.

The low-FODMAP Diet

The Low-FODMAP diet eliminates short-chain fermentable carbohydrates that can feed an overgrowth in the gut. Many with digestive symptoms like IBS, constipation, diarrhea, bloating, gas, and cramps turn to this protocol in order to get their digestive issues under control. All of these “high-FODMAP” foods are eliminated for a couple of weeks and then reintroduced to assess tolerance. There are a few different categories of FODMAPs, and some people react badly to one category while sparing another.

The low-FODMAP diet has been used for those with fructose malabsorption, SIBO, Candida, and other gut imbalances. While it can help with the symptoms of digestive overgrowth, it is not an autoimmune-specific diet, and includes some potential allergens like eggs, nuts, and nightshade vegetables. For those who suffer from digestive issues that are not relieved by AIP, layering a low-FODMAP approach on top for a couple weeks can be helpful. (To learn how to do so safely and effectively, Christina Feindel’s amazing eBook, 28 Days of Low-FODMAP AIP is a must-have!)

While a low-FODMAP diet can be effective at managing the symptoms of an overgrowth, it is not usually effective on its own to treat an overgrowth. The same advice above applies here — if a person discovers they are sensitive to these foods, this is a clue to get tested for the underlying cause of sensitivity. Most often, those who are sensitive to FODMAPs are suffering from Small Intestine Bacterial Overgrowth (more info on SIBO, testing, and treatment here!), fructose malabsorption, Candida, or another type of overgrowth. While not everyone with autoimmunity suffers from SIBO, it seems to be quite common and a low-FODMAP approach can help clue a person in to if that is something they are suffering from.

That being said, I think the low-FODMAP diet would be the best pathogen-specific diet for those to layer with the Autoimmune Protocol (not instead of) in order to start getting to the bottom of their digestive issues. Aglaee Jacob, author of Digestive Health with Real Food has a great list of FODMAP foods that you can print out here! And definitely check out 28 Days of Low-FODMAP AIP.

Why AIP is the best starting place

The Autoimmune Protocol is a science-based protocol designed to simultaneously remove triggers as well as nourish the body to heal from chronic illness. The elimination diet must be done 100% because the immune system needs time to heal from potential food triggers. This makes the protocol quite difficult (but not impossible!) to adhere to. Because of this difficulty, I do not recommend that people layer pathogen-specific or low-carb modifications with AIP to start out with. The only caveat here is if someone is working with a practitioner who has tested, diagnosed, and treated a gut infection and has recommended a specific dietary protocol (like the low-FODMAP diet).

If a person has done AIP for a month or two and is still having digestive issues, it may be time to do some further testing, while considering a trial of a pathogen specific approach. I believe getting tested for SIBO, a comprehensive stool test, and the low-FODMAP diet is a great starting place — in addition to finding someone to work with that is experienced in this area.

I get contacted by a lot of people who want to start the Autoimmune Protocol by layering two or more of these approaches “just in case,” or because they think that it will save them time in the long run. I don’t think this is wise, and I believe more people who take this approach end up not being able to complete the elimination diet because their variation of the protocol is too restricted. My motto is always set yourself up for success. Although there is a wealth of information out there about AIP, someone else’s journey is not your journey. Take things one step at a time, and remember that in time, you will make discoveries about your health that will enable you to make progress, but it may not happen all at once!

REFERENCES

http://chriskresser.com/do-carbs-kill-your-brain http://www.thepaleomom.com/2012/07/optimizing-carbohydrate-intake-for-your.html http://chriskresser.com/top-4-mistakes-people-make-when-treating-candida-overgrowth http://radicatamedicine.com/2014/05/13/fodmaps-could-they-be-causing-your-bloating-diarrhea-constipation-and-other-ibs-like-digestive-issues/

About Mickey Trescott

Mickey Trescott is a cook and one of the bloggers behind Autoimmune Paleo. After recovering from her own struggle with both Celiac and Hashimoto’s disease, adrenal fatigue, and multiple vitamin deficiencies, Mickey started to write about her experience to share with others and help them realize they are not alone in their struggles. She is a certified Nutritional Therapy Practitioner by the Nutritional Therapy Association, and is the author of The Autoimmune Paleo Cookbook, a guide and recipe book for the autoimmune protocol, and AIP Batch Cook, a video-based batch cooking program. You also can find her on Instagram.

39 comments

  • Tiffany says

    Thank you for this. I was contemplating adding more rules to AIP, by taking a page from SCD or low FODMAP, and I was getting confused. My real problem is keeping this diets focus on the high nutrition foods, by incorporating more liver, fish, and green veg, and having fewer AIP treats. It definitely works for me when I am careful, but my RA symptoms come back a little after a few treats containing honey or maple syrup. I think I should space the treats out to at least once a week or less. Hard to face the truth sometimes.

    • Mickey Trescott says

      Hi Tiffany,
      Thanks for sharing your experience–I’m sorry you experience regression when you have treats, that is definitely discouraging. Here is the good news though-you know what makes you feel good, so if you make a slip you know how to get back there!

  • Barbara Garner says

    Please stop referring to Paleo-AIP as unspecified “The Autoimmune Protocol” or “AIP.”…. While Paleo-AIP might be the only autoimmune protocol (AIP) that you know of, it is not the only autoimmune protocol (AIP) in the world.

    • Mickey Trescott says

      Hi Barbara! I am sorry you are offended by the terminology, but I think the Paleo community has latched on to the term “Autoimmune Protocol” to refer to the autoimmune modifications to Paleo and it shows no signs of changing. Sarah Ballantyne tried to rename it “The Paleo Approach” in her book but it just didn’t stick.

  • Jane says

    FYI. The link to Metametrics GI Effect testing does not work.
    I found it in your story (linked in this new blog essay) about wasting time on the wrong restrictive diets.

  • Gisele says

    I had been on the GAPS diet for two years and until last November I thought that I was doing well. But then all the symptoms of my dermatomyositis came back worse than before. I started the AIP on January 1st and I seem to be doing a little better. I have lost even more weight (not good) but it is hard for me to find things to eat. How long should I wait to add some things back into my diet? P.S. We live way out in the country and have very limited access to specialty stores.

  • Inge says

    Dear Mickey,
    Thank you for this much needed information. I’m wondering what your thoughts are about layering AIP with a low histamine diet, since I’m quite sensitive to histamines and can’t eat liver, for exemple, without getting reactions. Being a Hashi I worry about getting enough nutrient dense foods inside my system

    • Mickey Trescott says

      Hi Inge,
      If you know which histamine foods trigger symptoms, by all means layer that with AIP. I do a version of this since I am very sensitive to the histamine in canned and leftover fish and some cured meats, but not other high histamine foods. I would only avoid all histamine foods layered with AIP for a short trial to see if there is any benefit (1-2 weeks). Hope it helps!

  • Samantha` says

    Thank you so much for this article. Perfect timing for me as I’ve been considering an elimination diet and had no idea which on to do, or to do all of them. Thank you!

  • Rikki Tea says

    Thanks for this article. I have been trying to figure out how to layer, so this just made my life so much simpler. I am wondering what’s next after SIBO testing, how do you recognize if you need to follow foodmap or gaps diet?

    • Mickey Trescott says

      Hi Rikki,
      If you test positive for SIBO, you will need to work with your practitioner on testing and diet protocol. I would suggest a low-FODMAP diet over GAPS during recovery, as it is specific to the foods that fuel SIBO.

  • Claire says

    Thanks for this. it’s so confusing. I’m doing AIP and low FODMAPs and thought if I had to GAPS as wellI would kill myself. I’m so thin, and desparate for carbs in the form of taro, plantain or tapioca but none of them seem to agree with me. Still a little confused but can only do so much at once. I’ll stick with AIP and FODMAPS. I have a problem though, I’ve just ordered and received the FODMAPS tests and I have to drink something with lactose in it.

    • Mickey Trescott says

      Hi Claire,
      Are you sure the test isn’t lactulose? Its different from lactose. That is the most accurate test for SIBO. I’d also say that if you find you are reacting to starches, it might be wise to have your doctor order a comprehensive gut test to rule out some pathogenic overgrowth in your gut. Hope it helps!

  • Christina says

    Hello Mickey, I notice throughout your article, you say that low carb and ketogenic diets may be good for “certain cancers.” It is my understanding that a ketogenic diet is good for all cancers. Can you be a little more specific about your information re cancer and diet? Thanks.

    • Mickey Trescott says

      Hi Christina,
      While I am not an expert in nutrition for cancer, it is my understanding that some cancers have been shown to grow rapidly when exposed to ketone bodies, making a ketogenic diet a poor choice for them. While generally a ketogenic diet has been shown to be helpful with cancer, I did not want to make a blanket statement. Hope it helps!

  • […] out there that help with eliminating foods. Since one diet does not fit all I thought I would share this post that describes the different diets out there, how they work and what is […]

  • […] The Autoimmune Protocol vs Other Healing Diets – Autoimmune Paleo […]

  • Nicole says

    Hi! I’ve just stumbled upon this site and am shocked I am just now hearing of AIP. I went gluten free and dairy free after developing GERD and interstitial cystitis a year ago. After many tests I discovered I have Sjogrens Syndrome, Hypothyroid and I am currently being watched closely for beginning signs of Lupus (joint pain + skin issues). I’ve adhered strictly to the gluten free and dairy free diet and TRY to do low sugar—and have seen an amazing difference in my body with just these changes but feel I’m at 70% most days and still flare. Is expecting to be feeling 90%-100% like my old self someday through diet alone asking too much of my body? I didn’t know about nightshades, nuts or legumes being inflammatory—have you seen a big difference in eliminating these lesser known inflammants vs. just the major gluten/dairy/sugar? I’m so inspired by your blog and community, thank you so much for uplifting my day!

    • Mickey Trescott says

      Nicole! So happy you are here. Yes, many people feel great after going through an elimination diet. If you click the “articles” tab up top you can find many resources and a wealth of information. Good luck!

  • […] the concise decision to eat gluten free options, I definitely did not follow my AIP guidelines! (learn more about AIP vs other anti inflammatory diets here)  I wish I didn’t eat those dam […]

  • Heather says

    Mickey, thank you for this helpful article and for your great site. I did see that someone else asked you about combining AIP with a low-histamine protocol. Thank you for your answer to her – that was helpful. My further question is: do you have a good resource to recommend for a low-histamine food list? And also, recommendations on how to manage nutritional integrity while trying to heal on these two particularly limiting food lists? Even a nutritional coach who can work with a vast array of restrictions? Thank you so much.

    • Mickey Trescott says

      Hi Heather! Happy you are here.
      I don’t have a good histamine food list, but I’ve been writing a post on the topic for a long time. It is quite tricky, because histamine issues are very individual and don’t line up easily to lists. It shouldn’t be too difficult to eat AIP as well as avoid any histamine foods you are reactive too, as long as you can cook most of your meals fresh. If you have severe histamine intolerance, I recommend being evaluated and treated for SIBO if that is an underlying factor. Good luck!

  • Guillaume says

    Hello,

    What I like about the SCD diet and GAPS diet is that they both have this intro diet where you eat very low fiber which helps to calm the raging inflammation in the gut. I’m afraid that if I jump in the AIP diet I would not heal because I would still get all those harsh fiber from all the vegetables. Is this something that any AIP protocole take into account? I know I have a FODMAP intolerance (at least to fructans) hence a low FODMAP AIP protocole is what I would aim for and probably would go with the Ebook you linked in your article. Will that book start off with smoother low fiber food?

    Thank you for this great article and all the ressources you put forward through your site.

    • Mickey Trescott says

      Hi Guillame,
      Sounds like you may need to make some additional modifications to AIP if you have sensitivities to certain fibers, this is not uncommon. Also I might suggest working with a functional medicine practitioner to order and interpret a comprehensive stool test that might help get to the root of your intolerance of certain vegetables. Usually these pathogens do not resolve with diet and need treatment (especially SIBO). Wishing you luck!

  • Lily says

    I have Hashimoto’s, Celiac, and Sjögren’s syndrome, and I feel much better when I’m in ketosis than when I’m eating a moderate to high amount of carbs! It’s anecdotal, of course, but I’m just putting myself out there as someone with Hashimoto’s and several other autoimmune conditions who does thrive on a very low carb/high fat diet. My energy level and mood are markedly improved when I’m eating fewer than 40 net carbs per day.

    • Mickey Trescott says

      Hey Lily!
      Thanks for sharing your experience! Of course we are all individuals, which is why I don’t recommend a one size fits all approach for anyone 🙂

    • I have Hashimoto’s as well. I had previously done an elimination diet and modified my keto diet to exclude those foods that bother me (dairy, soy, gluten). Being cold and having no desire to eat were the bigger issues for me -but going Keto was life altering too!!

  • Rona says

    Hi, I have type 2 D I don’t take any meds and have been low carb for about 10 years and managed well with that, I don’t eat grains or potatoes but I do eat peppers and tomatoes I don’t take milk but have cream and butter grass fed, also eat a fair amount of nuts. I the last six months or maybe a bit longer I have very bad pain in my legs arms shoulders jaw and blader. My doc blames the way I eat and puts it down to my D but I feel there is something else my pain is muscular and joint I have not changed the way I eat in years so I cant think what has caused this other than old age, I am nearly 64 I fast most days till 12am then eat till 6pm. I would like to try API do you think it will help I am already making broth and I feel my pain has lessend I am having 3 cups a day. I think you girls are great helping everyone well done.

    • Mickey Trescott says

      Hey Rona! Welcome, hoping you find some helpful info here. We do think the elimination diet is a great place to start for people experiencing things like increasing fatigue and joint pain–this could be early warning signs of autoimmune disease. Its always important to continue the discussion with your doctor, but ruling out any food sensitivities as well as upping the nutrient density of your diet can’t hurt! Wishing you the best.

  • kristan says

    I have been helped already so very much by your website. I just bought Mickey’s cookbook & am excited for it to arrive. But your articles, videos, blog posts, “starter” kit pdfs….these invaluable tools that are free….amazing. You have no idea what hope your online site has given me. Thank you for sharing your tons of experience.

    • Mickey Trescott says

      Kristan,
      So happy to hear! Best of luck to you on your healing journey!

  • Lynne says

    Hi I am reading conflicting information on whether can have onions and mushrooms on AIP can you clarify please. Thanks

    • Angie Alt says

      Lynne-
      Onions & mushrooms are both AIP. They are, however, high-FODMAP foods (foods w/ very fermentable sugars). Folks w/ dysbiosis in the small intestine (like Small Intestine Bacteria Overgrowth) often have trouble digesting high-FODMAP foods & that leads to uncomfortable symptoms. However, you do not need to eliminate these foods on AIP.

  • Allison says

    Would you suggest the AIP for someone with cancer? You mention in your first section that the Keto diet might work for people with certain types of cancer, but I wondered what you would recommend.

    • Mickey Trescott says

      Hi Allison! The Autoimmune Protocol has been developed to help those with chronic illness get to the root of their food sensitivities. Cancer can have very unique and specific needs depending on the type, and I would suggest finding a qualified practitioner to help guide you there. Good luck!

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