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7 Keys To Any Autoimmune Diet Protocol

April 23, 2018


It is estimated that approximately 50 million Americans suffer with an autoimmune disease (according to the American Autoimmune Related Diseases Association). Learn about the 7 keys to any autoimmune diet protocol.  

If you have recently been diagnosed with an autoimmune disease, you are anything but alone. With approximately 50 million Americans who suffer from an autoimmune condition, it is incredibly common to receive this diagnosis. According to recent projections, the prevalence of autoimmune conditions is rising. This comes as no surprise, as there are no current nutritional or lifestyle recommendations that are endorsed by doctors. If you are one of the millions suffering from any of the 80-100 autoimmune diseases that exist, treatment options can seem unsatisfying at best.

7 Keys To Any Autoimmune Diet Protocol

Because conventional medicine does not address diet, many individuals are unaware that changes to diet and lifestyle can have a profound impact on autoimmune symptoms. The root cause of autoimmune disease flare-ups is inflammation. Therefore, when you manage inflammation within your body, you will also manage your autoimmune flare-ups.

The best diet & lifestyle for autoimmune disease can make a remarkable difference in the frequency and severity of autoimmune flare-ups. If you are considering the use of an autoimmune diet protocol to best manage your symptoms, explore my seven recommended keys to success.

Key #1 - Regular Fasting

Fasting, without question, needs to be a regular part of any autoimmune diet.

When done properly and regularly, fasting carries with it numerous benefits. Whether you choose a bone broth fast or a 24 hour fast, this practice is an incredibly important part of an effective autoimmune diet. In addition to replenishing and restoring the body, fasts have several benefits that specifically impact autoimmune symptoms.

Fasting helps change gut bacteria, and encourages fat burning. When the body uses fat as its main source for energy, 50 times fewer free radicals are produced. These two key benefits are essential in reducing autoimmune flare-ups.

Unfamiliar with how to fast? You can begin by using one of the following methods:

  • Block water fasting of 1-4 days
  • Bone broth fasts of 1-4 days (read more about specific benefits of bone broth fasting)
  • Intermittent fasting - This kind of fasting is effective in regenerating the immune system, increasing cell repair, and increasing a cell’s defenses.

Key #2 - Regulate Blood Sugar

Blood sugar levels and autoimmune conditions are more related than you may have previously believed. As mentioned already, inflammation is a major factor in autoimmune disease flare-ups. Consuming too much sugar can lead to chronic inflammation, which can make your condition worse.

Additionally, research has linked insulin resistance to autoimmune thyroid issues. Therefore, managing your symptoms through an autoimmune diet requires careful monitoring of sugar consumption and blood sugar levels.

In order to keep blood sugar levels within a healthy range, it isn’t enough to simply eliminate the obvious high-sugar foods (e.g. candy, soda). Foods that are converted to sugar within the body, as well as many fruits and high carboydrate foods, must either be avoided or enjoyed in moderation. These hidden sources of carbs can have just as much of an impact on your blood sugar levels as junk food. 

regulate blood sugar

Carbs & Blood Sugar

How can you keep your blood sugar stable using an autoimmune diet? First, avoid most fruits and sources of high carbohydrates and sugar. If you do want to consume fruit, stick with berries, green apples, avocados, green bananas, green mango, and green papaya.

Why eat so many green fruits? When fruits are at this stage, they are considered resistance starches and feed good gut bacteria. Research has identified significant differences in the gut bacteria of those with type 2 diabetes and those without the condition. Keeping a healthy population of gut bacteria is crucial in managing autoimmune conditions.

When you first start down your journey with an autoimmune diet, try to avoid fruit, high glycemic carbs and sugar as much as possible. Keep your carb intake under 5-10% of the total calories you consume in a day to get started. 


Key #3 - Support Gut Bacteria & Don’t Damage the Gut

Did you know: Approximately 70%-80% of your immune system resides in the gut!

As hinted at in key #2, supporting a population of healthy gut bacteria is another essential component of your autoimmune diet protocol. Why? About 70%-80% of your immune system is located in the gut. Gut bacteria serves many core functions, especially as it relates to autoimmunity. Not only does normal bacteria strengthen the gut lining, but the gut microbiome also plays a big role in controlling inflammation.

Because your diet can influence gut bacteria and autoimmunity, there are numerous things you can do to directly influence the health of your gut microbiome.

To support healthy gut bacteria, take the following steps:

  • Be sure to fast regularly
  • Eat prebiotic rich foods (including sweet potatoes, carrots, Brussels sprouts, asparagus, and avocados)
  • Consume grass-fed ghee (grass-fed ghee is high in butyrate, which is a short-chain fatty acid that is good for the gut)
  • After the gut has been restored to health, greens should comprise the majority of your carbohydrates

In addition to building healthy gut bacteria, there are foods, beverages, ingredients, and medications that should be avoided to prevent damage of gut bacteria:

  • Alternative sweeteners
  • Alcohol
  • Antibiotics
  • Dairy
  • Pain medications
  • Conventional meat and chicken (they contain high levels of antibiotic residue, GMO corn, and GMO soy) 
  • Excess stress can also affect gut health
  diet variation

Key #4 - Diet Variation

One common misconception about diets in general is that you should eat the same foods to promote health. In order to prevent autoimmunity, the exact opposite is true. Although there are general guidelines to follow (as listed in each of the 7 keys), it is crucial that you rotate your nutritional plan.

Unsure of where to start? Here are some tips to ensure that you are implementing diet variation in your autoimmune diet:

  • Start adding variety slowly. Although it may sound easy, it is likely to be a more significant change in your diet than anticipated.
  • Eat seasonally.
  • Avoid all fruit (with the exception of avocados) during the winter months. Over the last couple thousand years, the body was not used to being exposed to fruit year-round. As a result, your gut bacteria has not developed to accommodate this relatively recent change.
  • During the winter months, practice more fasting strategies and intermittent fasting to resemble the season. As a result, your nutritional plan will be lower in carbs, and higher in fats and proteins. 
  • Once spring and summer arrive, start eating more vegetables, and add fruits back into your autoimmune diet in moderation. Also, limit protein intake and consume only 4-6 ounces of meat per day a couple of times each week. 

Diet Variation Autoimmune Protocol 

Here is another example of how to implement diet variation: For five days of the week, consume a low-carbohydrate, ketogenic diet with plenty of high fiber vegetables, healthy fats, and clean organic protein. One day per week, complete a full 24-hour bone broth fast or water fast. If you choose a bone broth fast, you can add some MCT oil/coconut oil and sea salt to your broth for a boost of energy.

For the final day of the week, do a carbohydrate or protein “load day,” in which you dramatically increase carbs or protein. This practice reminds the body it’s not starving. Depending on your autoimmune condition, your protocol could change. The key is in the variation. Variation is a dietary stress that focuses the body on adapting and changing for the better. 

7 Keys To Any Autoimmune Diet Protocol Infographic

Key #5 - Proper Autoimmune Supplements

If you have autoimmune problems of any kind, it is likely that your gut is leaky. As a result, you won’t absorb all of the nutrients you are eating. Supplements serve the purpose of both supporting a healthy lifestyle and fixing deficiencies. When you identify your individual deficiencies, it is easy to simplify your supplement regimen. 

While the lists below do not cover every supplement that is beneficial for autoimmunity, this is a great place to start. Understanding the fundamentals of autoimmune supplements for an autoimmune diet can help you make the best possible choices.

Supplements that support balanced stomach acid:

  • Betaine HCL
  • Digestive enzymes before meals - Your body naturally produces enzymes that help break down food so that you can absorb its nutrients. The enzymes often stop working in the face of leaky gut. Removing enzyme inhibitors like grains and legumes, and using a high-quality digestive supplement, can improve overall digestion and vitamin absorption.
  • Apple cider vinegar - When taken before meals, this supplement helps with digestion. Apple cider vinegar also keeps candida and yeast away. 

Herbs For Autoimmune & Inflammation

Additionally, the following supplements are exceptional in reducing inflammation:

  • Turmeric
  • Krill oil - This type of oil is high in omega-3s, and has low toxicity compared to fish oil. When taking krill oil, you don’t have to be concerned about heavy metals. It is also full of antioxidants that reduce inflammation. 

Autoimmune diet herbs:

  • Ashwagandha - Ashwagandha and thyroid play a large role in autoimmunity. This herb can help balance Th1 and Th2 immunity, and is one of the best herbs for hypothyroidism.  Th1 and Th2 act as the two “arms” of the immune system. Ashwagandha has been shown to not only support lowering cortisol levels, but it has also been successful in reducing autoimmunity by balancing the immune system.  When starting to take this herb, begin slowly. It is also important to note that ashwagandha is part of the nightshade family.
  • Licorice root (good for energy, stress, and leaky gut).
  • Selenium - Acts as an essential nutrient to support autoimmunity and thyroid issues.
  • Collagen in the form of bone broth or in supplement form (rebuilds the gut lining).
Sunshine for immunity

Supplements for Immunity

Best supplement to support the immune system:

  • Liquid vitamin D3 w/ vitamin K2 - Most of the body’s vitamin K supply (70%) is made by gut bacteria. It is important to supplement the other 30% with vitamin D for optimum absorption. 

It is also worth noting that once you have an autoimmune condition, supporting vitamin D levels is essential to support immune function. Healthy vitamin d levels are crucial to eliminiating autoimmune symptoms.

Vitamin D is strongly associated with autoimmune disease because of its role in regulating the immune response. Sufficient levels of vitamin D not only calms the immune response, but it also decreases the severity of symptoms.

Key #6 - Avoid Trigger Foods  

Key #6 - Avoid Trigger Foods

Certain foods are consistently shown to trigger autoimmune symptoms in the majority of sufferers. In order to make the most of your autoimmune diet, the following foods should be avoided:

  • Wheat - Not only does the main protein found in wheat (gluten) cause leaky gut, but high levels of glyphosate found in most wheat crops create added autoimmunity.
  • Rye & barley (shown to increase gut permeability)
  • Peas 
  • Soy
  • Beans
  • Nightshade vegetables (such as eggplant, potatoes, tomatoes, and peppers)
  • Seed, vegetable, and canola oil
  • Dairy
  • Corn
  • Oats
  • Grains and legumes can inhibit enzymes, which affects digestion and absorption of nutrients. 

The following list is comprised of foods that I recommend limiting (depending on your sensitivity). However, it is good to reintroduce these foods over time:

  • Nuts (such as walnuts, pecans, macadamia nuts, and coconut)
  • Seeds (such as hemp and flax)
  • Eggs - Limit to no more than two per day. Also, only consume organic, pastured eggs. 
  • Reduce high lectin foods - For individuals with autoimmune issues, lectin sensitivity is common (learn more in Are Lectins Bad for You?).

Key #7 - Fix Your Fats to Lower Inflammation

Good fats and bad fats are often categorized together. A good example of this happening on a large scale was the low-fat movement that began in the 1960s and 1970s. It was proven to be one of the biggest mistakes, since good fats are essential in supporting overall health and wellness!

Even with what is now known, the differences in these types of fats are not often communicated.

When grain-fed meat, butter, cheese, and damaged omega-6 oils are consumed (bad fats), an extreme spike in inflammation occurs. Consistent, extreme spikes in inflammation greatly increases your risk of developing a chronic sickness or disease (including autoimmune disease).

Good fats, however, yield a much different result. Eating the right fats in your autoimmune diet will help you look and feel incredible. Counterintuitively, these fats actually help you to burn fat, speed up your metabolism, lose weight, stabilize your blood sugar, and lower your insulin levels.  Healthy fat transports vitamins and minerals throughout the body, sends signals to your glands to produce good hormones, regulates healthy brain function, and boosts immunity.

  healthy fats

Healthy Fats Guide 101

Where can you find sources of good fats? The following are some of the top foods that contain healthy fat:

  • Avocados
  • Walnuts
  • Macadamia nuts
  • Marine algae oil
  • Coconuts
  • Raw unrefined coconut oil
  • Cold-pressed extra virgin olive oil and olives
  • Grass-fed meats (up to 6oz, 1-2 time per week) are actually good for your heart, digestion and overall health
  • Cold water fish (salmon, sardines, mackerel, herring, and halibut)
  • Plant sources (flax seeds, green-leafy vegetables, seaweed, Brussels sprouts, pumpkin, hemp seeds, and walnuts)
  • Omega-3 oil (acts as an anti-inflammatory)

Bad fats can be found in the following products: canola oil, sunflower oil, safflower oil, vegetable oil, margarine, cottonseed oil, and soy oil. These oils are found in all processed foods, and in foods at most restaurants (unless it’s stated otherwise).

Omega fats are essential for any diet (especially as part of your autoimmune diet). Since you need to consume these fats in your diet to survive, it is crucial to balance your omega-6 and omega-3 intake. Increasing your consumption of healthy fats is necessary for your immune response to work properly.

Work on getting your body between a 1:1 – 1:4 ratio of omega-3 to omega-6 for optimal health. These levels should be checked by your functional medicine practitioner yearly.

Jumpstart your autoimmune diet protocol

Starting Your Autoimmune Diet Protocol

Taking the right approach to your autoimmune diet is essential for controlling your symptoms. While you may have relied on the results of food allergy tests in the past, simply avoiding specific foods does not resolve the underlying issue. Supporting your overall nutrition, maintaining a healthy gut, reducing inflammation by fasting, and adding diet variation are some of the key components in an effective autoimmune diet protocol.

If you have struggled with multiple autoimmune diet plans like paleo, ketogenic, vegan, or even Mediterranean, you were likely eating in a way that does not fit your individual needs. As much as I am passionate about nutrition, I also recognize that only the right food is medicine when you are autoimmune. These 7 keys apply to anyone dealing with autoimmune symptoms. 

Once your immune system calms down after completing the autoimmune diet protocol, you can transition back to the nutritional plan of your preference. This is where considering genomic testing can further optimize which plans work the best for your genes and autoimmune problems. Consider talking to trained functional medicine practitioner about the best place to start. 

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