Autoimmune Protocol 101

NOTE: This page was revised on 3/7/17.

If you’re reading this page, you’re likely wondering what the Autoimmune Protocol (AIP) is, or looking for guidance on how to go about it. You might wonder, what’s the difference between Paleo and AIP?

Simply put, both are focused on reducing systemic inflammation, but the AIP takes it a few steps deeper to address underlying factors that drive autoimmunity and chronic illness.

This page covers a lot of ground. If you are curious what foods are included or excluded on the AIP, you can scroll down the page, but I encourage you to read through the whole thing – it will help the food list make much more sense.

What is the autoimmune protocol?

The autoimmune protocol (AIP) is a dietary and lifestyle protocol that helps to remediate these factors common to autoimmunity, leading to remission of symptoms and the suffering they cause:

• Gut dysbiosis
• Leaky gut
• Nutrient deficiencies
• Systemic inflammation
• Hormone dysregulation
• Improper immune response

The protocol removes foods that drive the above factors, and includes nutrient-dense foods that support healing.

It also supports lifestyle habits that encourage healthy sleep, appropriate levels of exercise, stress management and more, all of which are key for recovery.

The dietary and lifestyle factors of the AIP work together to support the body in healing from a place of stability and strength.

For some people, the AIP is a temporary healing protocol that serves as a launching pad from which to explore other options. For many, it serves as a long-term lifestyle that allows reduction or removal of symptoms, and the ability live life normally.

Leaky gut, gut dysbiosis, and nutrient deficiencies

Leaky gut
A common factor in all autoimmune conditions is a hyper-permeable gut lining, commonly known as leaky gut. In leaky gut, inflammation causes damage to the lining of the digestive tract, and causes gaps between cells in the intestinal wall.

This allows particles into the bloodstream that wouldn’t normally be there, such as toxins, bacteria, and large undigested food molecules. The presence of these particles, perceived as pathogens by the body, combined with the body’s inability to discern them from body tissue, helps drive the “autoimmune fire” that causes cell damage, leading to symptoms (see the section called “Extra credit geek out” at the bottom).

Gut dysbiosis
Another common factor is gut dysbiosis – an imbalance in the number, types, and location of helpful versus harmful bacteria in the digestive tract. Gut bacteria play a critical role not only in digestive function, but other bodily systems such as immunity, mood (really! there is lots of cool new research on that), and brain function.

Nutrient deficiency
Nutrient deficiency is a third common factor in autoimmunity. Commonly seen are deficiencies in: fat soluble vitamins such as A, E, D and K; minerals such as zinc, iron, copper, magnesium, and selenium; B- and C-vitamins; omega-3 fatty acids; and certain amino acids. Ironically, even though leaky gut creates larger than normal holes in the gut lining, it can also contribute to improper nutrient absorption – and nutrient deficiencies.

Systemic inflammation, hormone dysregulation and immune response

While this section could be book-length, to keep this page from getting ridiculously long, I’ll simply say that systemic inflammation lies at the root of all autoimmunity and chronic illness. It is a huge driver of hormone dysregulation and incorrect immune responses body-wide. We must reduce or eliminate inflammation in the body if we have any hope of symptom relief, and at best, remission.

These factors – leaky gut, gut dysbiosis, nutrient deficiencies, systemic inflammation, hormone dysregulation, and incorrect immune response – lead us to the autoimmune protocol, or the AIP.

This page sticks to the dietary aspect of the AIP; the lifestyle factors are a whole other discussion. It’s really fascinating stuff to learn about, and even if you don’t have autoimmunity or chronic illness (thanks for reading this far!), some of that information may come in handy for you over the long term anyhow: inflammation affects everyone, as do lifestyle habits that either support or undermine our vitality.

Elimination and reintroduction

On the dietary end, the AIP is intended as an elimination/reintroduction protocol.

Elimination: Initially, foods that drive the inflammatory disease process are eliminated for a period time to help reduce inflammation and clear symptoms. Depending on the individual, this may take 30 days, months, or up to a year.

Reintroduction: Once the majority of symptoms have abated, items are reintroduced to determine food sensitivities and tolerances. Some items are never returned to the diet, due to how they drive the autoimmune reaction.

Once someone is through reintroduction, things do not necessarily remain static; many people find that as healing progresses, they are able to continue adding more foods over time. In addition, if lifestyle and stress factors increase systemic inflammation (more below), some foods may have to be eliminated again until symptoms subside.

Autoimmunity takes a winding road, so the truth is that for most folks, it’s a long term matter of adjusting to meet the body’s needs. Done right, one can find a middle ground where we live free of symptoms, or nearly so. Having this protocol (or variations of it) as a baseline sets us up for the best chance at living well.

Foods to eat and avoid on the autoimmune protocol

For the purposes of this blog, I’m not going into great detail about the science behind the ‘yes’ and ‘no’ food lists. There are great resources that explain the science behind the food limitations, linked at the bottom of this article. Don’t get your panties in a bundle if all this is new to you; it may seem like a lot, but it becomes everyday when you live it.

Now, a deep breath… the foods list…

Foods Encouraged on the Autoimmune Protocol

Most organic vegetables: Include as much variety as possible, making sure to include the full color spectrum; anise, arrugula, artichoke, asparagus, beets and their greens, bok choy, broccoli, cabbage, carrots, cauliflower, celery, chives, cucumbers, garlic, kale, kohlrabi, leeks, lettuce, mustard greens, olives, onions, parsley, radishes, rhubarb, shallots, spinach, squash, sweet potatoes and yams (not true potatoes), water chestnuts, watercress, zucchini, etc.

Quality meats: beef, chicken, bison, pork, lamb, turkey, and wild game. Select hormone-free and antibiotic-free chicken, turkey, and lamb. Select beef that is grass fed, hormone free, and antibiotic free. Avoid factory-farmed meats that contain antibiotics and hormones. Chicken has high Omega 6 (inflammatory fatty acid) content; eat in moderation, and if you consume more, also eat extra Omega 3 oils to compensate.

Organ meats and offal: An important concentrated form of nutrients including vitamins, minerals, healthy fats, and essential amino acids; heart, liver, kidney, tongue. Include glycine-rich foods containing connective tissue: organ meat, joints, skin, bone broth.

Fish and shellfish: Seek ocean-caught cold water, low mercury fish with high fat content.

Quality fats: pasture-raised, grass-fed animal fats, fatty cold water fish, olive oil, avocado oil, coconut oil, low-mercury Omega 3 supplements. If you eat palm oil, please do your research – palm oil production is quickly advancing orangutans toward extinction due to rapid habitat destruction.

A note on fatty acids: Consuming a proper ratio of Omega 3 to Omega 6 fatty acids is important for minimizing inflammation. The average “Sad American Diet” (SAD) ratio is a shocking inflammation-producing 25:1. To minimize inflammation, consume a ratio of omega-6 to omega-3 between 1:1 and 4:1.

Low glycemic organic fruits: Eat all fruits in moderation (except goji berries: nightshades). Some people have strong reactions to excess sugar, so watch your reaction. Keep intake between 10 and 20g per day – however, for big backcountry days, I go higher. In general, dietary sugar moderation is key for healthy blood sugar regulation and brain function.

Edible mushrooms: Mushrooms are fine for most individuals, however some with autoimmune conditions react to immune-stimulating fungi; monitor your response.

Probiotic and fermented foods: sauerkraut, kimchi, pickled ginger, fermented cucumbers, coconut yogurt (w/o guar-gum), kombucha, water kefir, coconut milk kefir, supplements. Search for information about anaerobic fermented foods in air-tight containers; these ferments do not produce histamines that are reactive for some people (rashes, digestive upset, inflammation) commonly found in aerobic, or open, ferments typically using mason jars.

Coconut: coconut aminos, coconut milk (no guar gum), coconut water, coconut water vinegar, coconut cream (not concentrate), and coconut oil. Whole coconut products (coconut butter, coconut cream concentrate, coconut flakes and chips, unsweetened coconut yogurt, fresh coconut) have a high amount of inulin fiber and moderately high phytic acid; this causes some individuals digestive issues – consume in moderation until you know your tolerance.

Noodles: Shirataki yam noodles; avoid the noodles that contain tofu (soy). Cassava noodles (home-made).

Herbs and Spices: basil, cilantro, cinnamon, coriander, clove, cumin, garlic, ginger, horseradish, lemongrass, mace, mint, oregano, parsley, rosemary, sage, saffron, sea salt, thyme, turmeric (black pepper is considered a reintroduction item).

Vinegars: apple cider, balsamic, champagne, coconut, red wine, sherry, ume plum, white wine. Avoid grain-based vinegars: rice and distilled white.

Teas: in moderation: black, green white, yerba mate (avoid tea if you have adrenal fatigue).

Other: herbal teas, rooibos tea, carob, DGL (licorice root extract) (but not whole licorice root), vanilla extract (but not alcohol tincture) or powder (but not whole bean).

In moderation: fructose (in fruit and starchy vegetables), pomegranate molasses, maple syrup and maple sugar, honey, dried fruit, dates and date sugar, molasses, unrefined cane sugar (sucanat, evaporated cane juice, muscovado). Each person has unique tolerance to sugars – monitor your response.

Grey areas depending on sensitivities: legumes with edible pods (green beans, snow peas). Whole bean coffee in moderation NOTE: In testing, many instant coffees show gluten contamination. Seaweeds (high in iodine): Some people with Hashimoto’s may not do well with additional iodine in the diet – it can drive TPO antibody production.

Foods to avoid on the Autoimmune Protocol

Grains: barley, bulgur, corn, couscous, kamut, millet, oats, rice, rye, spelt, wheat, wheat germ, wheat grass (contains wheat germ agglutinin), brown rice protein.

Pseudograins: amaranth, buckwheat, chia, quinoa.

Nuts: all nuts and nut butters including peanuts (actually a legume).

Seeds: chia, cocoa, flax, sesame, sunflower, instant coffee (in testing, many brands had gluten contamination).

Seed-based spices: anise, annatto, celery seed, coriander, cumin, fennel, fenugreek, mustard, nutmeg, poppy seed, sesame, allspice, star anise, caraway, cardamom, juniper, peppercorns, sumac, whole vanilla bean.

Dairy: cow, goat and sheep milk, butter, cheese, creams, frozen desserts, margarine, mayonnaise, whey, yogurt.

Eggs: For reintroduction, introduce yolks and whites separately; yolks first, then whites, then whole egg.

Beans and legumes: black beans, lentils, peanuts, peas, pinto beans, etc.; all soy products including edamame, miso, soy milk, soy protein, soy sauce, tempeh, tofu, soy lecithin, etc.

Nightshades: eggplant, goji berries, sweet and hot peppers, hot pepper sauces, tomatillos, tomatoes, and potatoes (sweet potatoes and yams are okay – not in the same family).

Nightshade-based spices: cayenne, chili powder, paprika, red pepper, curry, and spice blends that contain these.

Medicinal mushrooms: Some people with autoimmune conditions react to immune-stimulating fungi such as Maitake and mushroom-derived beta-glucan; monitor your response.

Refined and processed oils: This includes vegetable oils; stick to the approved oils in the ‘foods encouraged’ list.

Sugars: agave, candy, chocolate, corn syrup, high fructose corn syrup, sucrose, etc.

Stevia and non-nutritive sweeteners: acesulfame potassium, aspartame, neotame, and sucralose.

Emulsifiers, thickeners, and other food additives: guar gum, carrageenan, zanthan gum, cellulose gum, soy lecithin.

Alcohol: all alcohol.

Gluten-containing compounds: barbecue sauce, binders, bouillon, brewer’s yeast, chewing gum, cold cuts, condiments, nondairy creamer, emulsifiers, fillers, hot dogs, hydrolyzed plant and vegetable protein, ketchup, lunch meats, malt and malt flavoring, malt vinegar, matzo, meat glue, modified food starch, monosodium glutamate, processed salad dressings, seitan, soy sauce, some spice mixtures, stabilizers, teriyaki sauce, textured vegetable protein. Beware of non-specific ingredients like “natural flavorings” or “spices”.

Potential gluten cross-reactive foods (refer to my ‘molecular mimicry’ mention above): dairy, oats, yeast (brewer’s, baker’s, nutritional) instant coffee, milk chocolate, millet, soy, corn, rice, potato.

NSAIDS: non-steroidal anti-inflammatory drugs such as aspirin and ibuprofen. … Oh gods, you say. These items are really good at increasing leaky gut. If you must use them for an emergency in the backcountry, certainly do. Better to reduce that swelling broken ankle and repair your gut health later.

Other: canned foods, processed foods, barley grass, pea protein, hemp protein, licorice root (DGL is okay), aloe, slippery elm bark, commercial egg replacers, supplements containing ashwagandha (a nightshade) or oat seed, immune stimulants such as chlorella and spirulina.

Don’t throw your computer in the lake yet. Keep reading.

The backcountry food conundrum or, why Backcountry Paleo was created

As you can see, the AIP doesn’t allow for many any 😉 of the foods we were used to bringing into the backcountry. Don’t despair! That’s why I started this blog. I needed to create nutritious, delicious, lightweight AIP/Paleo food options for the trail, so I could fully enjoy my time in the wild. And I know there are lots of Paleo/AIP outdoorsy sorts who wonder what the heck to eat on the trail, so BCP was born.

Extra credit geek out: A wee bit of science and… molecular mimicry!

This is so cool. Well, really, its terrible, but in concept it’s really interesting: In any autoimmune condition, the body loses the ability to differentiate between self and other. Self is the proteins of the body, and other is proteins belonging to foreign invaders such as bacteria, viruses, parasites, and even food molecules.

It’s a case of mistaken identity, commonly called molecular mimicry. For example, the Hashimoto’s body (thyroid autoimmune) is primed to attack thyroid proteins; however, it mistakes foreign proteins (such as certain foods, viruses, or environmental toxins) as “self” and attacks not only those perceived pathogens, but also the body’s thyroid proteins at the same time.

The same goes for any autoimmune condition: In rheumatoid arthritis, the joints are attacked; in Type 1 Diabetes, the attack is on the insulin-producing cells in the pancreas; in scleroderma, it’s connective tissue.

In a nutshell, the presence of these perceived (or real) pathogens in the body leads to destruction of bodily tissue. This cell damage leads to symptoms of autoimmune disease; joint pain, rashes, brain fog, weight gain, hair loss, mood changes, hormone changes, extreme fatigue, etc. ad nauseam.

And worse, autoimmune diseases tend to come in clusters, which means if you have one AI disease, you are statistically highly likely to get another.

How does this play into the AIP? Many foods are included in the molecular mimicry process. Remove the food proteins your body has ‘flagged’ for destruction, and you can go a long way toward saving the organs your body is wired to destroy.

A thanks to the science geeks

Autoimmunity is still not very well understood, despite all the information we now have at our fingertips. Research abounds, and every year more amazing discoveries come to light. In this quickly changing landscape, we’re all doing our best to ride that current.

Having lived through a personal hell and come out this side feeling as good as I do, I’m forever grateful to the researchers and doctors who’ve advanced our knowledge about autoimmunity.

Some great AIP resources to check out

• For in depth info on the science behind the AIP food lists (plus fabulous recipes for at home), check out The Paleo Mom website.
• I also suggest you check out Sarah Ballantyne’s amazing books The Paleo Approach for the really geeky scoop on the science behind the autoimmune protocol. The Paleo Approach Cookbook is great too.
• For information on Hashimoto’s thyroid autoimmunity, go to Dr. Datis Kharrazian’s blog.
• If you are thinking of embarking on the autoimmune protocol and want some guidance, check out Phoenix Helix blog. She has great articles on how-to, the common speed bumps, alternate options for those who need them, and more.