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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!

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