“It is not an exaggeration to say that gut health is everything. The health of your gut has a profound effect on your overall health.” —SARAH BALLANTYNE, PH D, THE PALEO APPROACH
Using dietary modifications to manage autoimmune disease is far from a conventional approach. However, as research continues to clarify the link between what transpires in our guts and how that relates to our immune systems, it is becoming more widely accepted in the medical community. When inquiring with your doctor about the role diet plays in better managing your condition, you may have been told that it has no influence. This could not be further from the truth! We are here to tell you that what you eat does matter, and it can have a profound impact on your healing journey. The foods you choose to eat every day provide your body with the raw materials it needs to perform optimally. Whether your diet is a source of nourishment or strain depends on the particular foods you choose to put on your plate.
After informing yourself about your condition and getting your health-care team solidly in place, it is time for you to assess your diet. The cornerstone of living well with autoimmune disease is eating a diet that best supports your long-term health and well-being. This way of eating is going to be unique to you (no one-size-fits-all approach here!). Avoiding foods that you may be allergic or sensitive to, adding more nutrition where you need it, and preventing or controlling imbalances in gut flora can profoundly accelerate and strengthen the healing process. In the same vein, an improper diet can have a hand in causing inflammation and an exacerbation of symptoms. Figuring out what to eat can be one of the most transformative moments in your healing journey, and not one to take lightly!
Let’s go over the four key reasons why diet is a powerful component of healing.
● INTESTINAL PERMEABILITY/LEAKY GUT —Research has shown that the common thread linking all autoimmune diseases is indeed in the gut, and is known by the terms leaky gut or intestinal permeability. Simply put, this happens when the lining of your small intestine (the organ responsible for selectively choosing to let nutrients in and keep pathogens out) becomes more permeable (leaky), thereby letting some of the contents pass into your bloodstream or lymphatic system. Your immune system is then left to deal with these undigested proteins, viruses, bacteria, and toxins that shouldn’t be there in the first place, causing more inflammation and potentially setting off an immune response. What causes leaky gut in the first place? Food allergies and sensitivities (especially to gluten, a protein found in some grains), dysbiosis (the imbalance of gut flora), medications, and even stress and overexercise can cause the lining of the small intestine to become more permeable. By removing or reducing these triggers, you lower the burden on your immune system, leading to less inflammation and fewer symptoms.
● NUTRIENT DEFICIENCIES —Our modern diet is nutrient poor, lacking many essential vitamins, minerals, and other nutrients needed for well-being. Rapidly declining nutrient levels in our soils (making fewer nutrients available in the fruits and vegetables that we eat) as well as widespread digestive dysfunction compound this problem. Nutrient deficiencies are thought to contribute to the development of autoimmune diseases, with deficiencies in some nutrients (like vitamin D) scientifically linked to their development. Deficiencies can also exacerbate the symptoms of autoimmune diseases and worsen the inflammatory process. Those who suffer from autoimmune disease have a greater need for nutrients, especially those that are involved in tissue repair and modulating the immune system. In order to have the best chance at managing your condition, you need to make sure digestion is functioning optimally and that you are getting all nutrients needed to heal your body and decrease inflammation.
● FOOD ALLERGIES, INTOLERANCES, AND SENSITIVITIES —Eating foods you are allergic, intolerant, or sensitive to can hinder the healing process. While there are differences in the mechanism and severity of how allergies, intolerances, and sensitivities work, getting to the root of which dietary triggers are affecting you can help you get on the road to recovery.
● DYSBIOSIS —Our digestive tract is lined with living microorganisms like bacteria and yeasts, with many playing an essential and supportive role (such as digesting food, producing B vitamins and vitamin K, modulating the immune system, and absorbing nutrients). Dysbiosis is a term used to indicate an imbalance in these populations of microorganisms in the gut, whether it is from pathogens (such as a parasite or bacteria that causes disease) or overgrowths of otherwise helpful inhabitants of the gut (such as small intestine bacterial overgrowth, where beneficial bacteria usually found in the large intestine migrate up into the small intestine). Restoring this balance of gut flora can go a long way in helping promote overall health.
In an effort to make this information more manageable, we won’t be delving more deeply into the above topics. For further research, we recommend the fantastic resource The Paleo Approach by Sarah Ballantyne, PhD. She presents a thorough scientific analysis of each of these dietary factors that contribute to autoimmune disease.
Although making dietary changes can have a major impact on your health and recovery, there is no standard formula to eating for those with autoimmune disease. This can be frustrating! It is important to know that what works for someone else’s current state of health may not work for your seemingly similar issues. There are crucial foundations that we can all apply to our diets for best success, but not everyone needs to be on an excessively restricted diet for life. Instead, we encourage you to do some experimenting to find the least-restricted diet that is most likely to produce long-term health.
In the following section, we will present you with a range of healing diets, from what we would consider the least extreme of the dietary approaches (and for healing purposes, the bare minimum intervention) moving along to the most extreme. You can use this list to modify your diet from the top down, gradually working on finding the least-restricted approach that produces results. Alternatively, you can jump right into an elimination diet like the Autoimmune Protocol.
Gluten-Free Diet
Dr. Ballantyne says it best—“Although the exact role that gluten plays in most autoimmune diseases is elusive, the link between gluten sensitivity is so compelling that many experts in the field believe that gluten sensitivity may contribute to all autoimmune diseases.” Because of this, we recommend a strict gluten-free diet as the minimum dietary intervention for anyone suffering from an autoimmune or autoimmune-related condition. Although this sounds harsh, the research is clear. Gluten is not something you want to be consuming if you are committed to long-term healing!
A gluten-free diet is one that avoids all foods that contain gluten, a protein found in grains such as wheat, barley, rye, and triticale. According to conventional medicine, a gluten-free diet is only necessary for those with celiac disease; however, there is a growing body of evidence showing that it is possible for nonceliacs to experience a sensitivity to gluten-containing foods (called nonceliac gluten sensitivity). While celiac disease is characterized by a reaction to two parts of the gluten compound (transglutaminase and alpha-gliadin), many other components of wheat and gluten have been identified as potential triggers for those with nonceliac gluten sensitivity.
Remember leaky gut, the common thread linking all autoimmune diseases? Well, it turns out that gluten is exceptionally irritating to the lining of the small intestine, and it has been shown to exacerbate leaky gut and activate the immune system. There is anecdotal evidence that some autoimmune conditions have been put into remission simply by avoiding gluten (and we are not just talking about celiac disease! * ). If you are feeling overwhelmed at where to start with dietary intervention, going on a gluten-free diet is a great start.
A dairy-free diet is one that avoids all forms of milk products, including but not limited to butter, cheese, milk, yogurt, and all prepared or processed foods containing or made from these ingredients. Although dairy is tolerated by some people, the vast majority, especially those with leaky gut and autoimmune disease, have trouble with it for one reason or another. Depending on your ethnicity, you have a 25 to 97 percent chance of not being able to digest lactose, a sugar found in dairy products. Dairy proteins, in general, are hard to digest and a common food allergy. Even in healthy individuals, dairy products can cause mucous production that worsens symptoms and irritates the gut. Those with a sensitivity to gluten tend to be more sensitive to dairy, as dairy proteins have been shown to cross-react with (mimic) those of gluten. If you are intolerant to gluten, your body may treat dairy proteins similarly.
Not all dairy is created equal—Some people tolerate some forms and types of dairy better than others (for instance, some may tolerate ghee, butter, and hard cheese but not milk, while others do well with goat but not cow dairy). Because dairy is likely to be a problem for many, we recommend removing it from the diet strictly and then considering reintroducing high-quality dairy slowly once a recovery is made. Some people find their tolerance to dairy changes as they heal their guts, and they may be able to reintroduce high-quality dairy later on in the process, even if they had trouble with it earlier.
Excess sugar consumption is a serious issue presented by our modern diet. The low-fat craze has led to the reformulation of processed foods, with the fat being replaced by refined sugar and contributing to the epidemics of obesity and diabetes. Many are becoming mindful of the amount of sugar they consume and seeing results by drastically reducing or cutting it entirely out of their diets.
While sugar specifically does not pose a problem for those with autoimmune disease, excess sugar consumption leads to blood-sugar imbalances, which you may experience as “highs” immediately following consumption and “lows” once your blood sugar drops. Over time, this develops into insulin resistance, which means that inflammation has rendered the hormones your body uses to control your blood-sugar levels useless. It is impossible to control inflammation and manage your autoimmune condition unless your blood sugar is under control! Furthermore, excess sugar in the diet can be responsible for feeding pathogenic overgrowths in the gut, exacerbating leaky gut and dysbiosis. Last, sugar weakens the immune system and is a source of empty calories that potentially replace more nutrient-rich foods.
A sugar-free diet can have many variations but, at its simplest, a person avoids all refined sugar and the foods that contain it. While natural sweeteners like honey and maple syrup are considered healthier alternatives by some, their effect on blood sugar is the same—don’t be fooled into thinking that there is such a thing as healthy sugar! Sugar substitutes are equally problematic, with many of them being marketed as healthy alternatives despite having a detrimental effect on blood-sugar control, appetite, or containing substances that are known to be toxic.
What about fruit? Although some fruit can have a lot of sugar, in general, fresh, whole fruit is a different story because it contains fiber, vitamins, and minerals in a complete package. While dried fruit should be avoided on a sugar-free diet because of how concentrated and easy to overeat it is, fresh fruit is usually fine to include (and we’d argue, healthy, because of all of the great nutrients it provides!).
In general, if you aren’t already mindful of your sugar consumption, we recommend trying a sugar-free approach for a period of time to better control your blood sugar. Once you cut out sugar, you will become (sometimes painfully!) aware of how dependent your body is on this substance. It is important to take it easy, not cut out too many foods at the same time (like fresh fruit), and make sure you always have healthy protein and fat-rich snacks on hand to navigate those harder moments. Over time, your body will become more dependent on its own stores of energy and your blood sugar will become more stable.
Where do treats fit in? For those who are not experiencing blood-sugar issues, naturally sweetened treats (those with honey, maple syrup, etc.) should be fine occasionally. Fruit should be consumed according to tolerance and preference and not avoided (except for dried varieties, especially in those with more of a sensitivity to sugar). While some forms of sugar, as well as the processed foods in which it lurks, can be incredibly problematic and should be avoided, you should be able to reach a place of balance with sugar consumption that is enjoyable and healthy.
The Paleo diet is an approach to eating that has become popular in both the wellness as well as chronic illness communities, with many doctors, researchers, and health experts advocating for its usefulness in combating illness and disease. Paleo is a scientific approach based on the pre-agricultural diet of our ancestors, bypassing all of our modern processed, convenience, and nutrient-poor foods.
Following a Paleo approach, you would avoid grains, beans, legumes, dairy, refined sugar, refined oils, and food chemicals. Ideally, you would also be eating pasture-raised and grass-fed meat and eggs, wild-caught fish, as well as making use of the “odd bits” like bones and organ meats. Paleo also emphasizes fermented foods in order to promote healthy gut flora.
We advocate for adopting a Paleo diet for long-term healing, whether you land there by gradually eliminating foods or by working backward from an elimination diet. Although Paleo can incorporate foods some people are still sensitive to (eggs, nuts, seeds, and the nightshade family of plants), it is generally a nutrient-dense and healthy way of eating because it avoids processed foods and grains that can be problematic for those with autoimmune disease.
An elimination diet is a short-term approach where foods are eliminated for a set period of time and then reintroduced, individually, to gauge a reaction. This approach can be useful at pinpointing your food allergies and sensitivities and is still considered the gold standard for determining which foods you may be sensitive to, even taking into account all of the advanced laboratory testing that is now available.
Elimination diets vary by approach, with some only avoiding the top eight most common food allergens—milk, eggs, fish, shellfish, tree nuts, peanuts, gluten, and soy—while other approaches are more comprehensive (such as the Autoimmune Protocol, discussed below). Some elimination diets call for avoiding a set of foods for a couple weeks before reintroduction; others go for trials that are a month or longer. The idea is that once your immune system has time off from a food, you are better able to gauge a reaction when you start eating it again.
We believe an elimination diet to be the ultimate tool to determine a set of foods that best support personal long-term healing. While, in theory, nutrient-dense diets such as Paleo are quite healthy to eat longterm, you may still find that you are sensitive to some of the included foods and getting to the root of those sensitivities can take healing to a whole new level.
The Autoimmune Protocol is an elimination and reintroduction protocol that has been specifically designed to help those with autoimmune disease determine their food allergies and sensitivities, reverse nutrient deficiencies, balance gut flora, and heal their bodies. The protocol has been developed and refined by Dr. Ballantyne and is outlined in detail in her book, The Paleo Approach . We believe this is the best and most specific elimination and reintroduction protocol for those with autoimmune disease, and following it gives you the opportunity to come up with your personalized healing diet.
In a nutshell, the Autoimmune Protocol calls for removing foods that are most likely to be problematic for people with autoimmune disease—grains, beans, legumes, dairy, eggs, nuts, seeds, and nightshades, as well as food chemicals and additives. In addition, nutrient-dense foods are added to restore nutrient status, such as bone broth, high-quality meat, and wild-caught fish, as well as organ meats, fermented foods, and a wide variety of fruits and vegetables. Over the course of the elimination phase (which can last from a month to a year), you take note of the changes you experience in your health. When it comes time to slowly and systematically reintroduce foods, you will be able to tell exactly which foods are holding you back and be prepared to use this information to construct a diet that will best support your healing needs.
In the last section, we gave you the Autoimmune Protocol in a nutshell, but in this section, we want to dive into the detail. The first thing to understand is that the Autoimmune Protocol is meant to serve as a template. Templates are preset formats that can easily be duplicated but, also importantly , can be adapted to individual uses. The Autoimmune Protocol is an elimination and reintroduction diet, but “diet” only in the sense that it refers to food intake. It is not a diet in the prescriptive, follow-the-rules sense. Diets of that nature are rigid and force people into molds that may not fit their needs. That one-size-fits-all approach to food is doomed to failure, since it leaves no room for the individual. On the other hand, a template promotes self-discovery through the use of an adaptable format. Depending on your genetics, your current level of health, your resources, and your goals, you can individualize this template to heal. By using the Autoimmune Protocol as your guide, you begin with a foundation that everyone can apply and from there, with careful self-experimentation, you discover the least-restricted diet that produces your best long-term health. The Autoimmune Protocol is not a set of commandments you desperately follow, hoping for a cookie-cutter result. It is a deliberate journey of healing wherein you blaze a unique trail.
The Autoimmune Protocol has two phases, an elimination phase and a reintroduction phase. During the elimination phase, remove the following from your diet (see the charts ).
● Grains and pseudo-grains
● Beans and legumes
● Dairy
● Refined/processed seed and vegetable oils
● Alcohol
● Food chemicals
● Refined and alternative sweeteners
● Nuts and seeds
● Nightshade-family foods
Health can be boosted with the addition of the following nutrient-dense foods.
● Bone broth
● Grass-fed organ meats
● Grass-fed gelatin or collagen
● Oily, cold-water, wild-caught fish and shellfish
● Fermented foods or probiotic beverages
● A colorful array of fruits and vegetables
There are very specific reasons why these foods are intentionally excluded or included in the protocol, but we will not be going into that discussion here. For those who would like to do more research, we recommend reading The Paleo Approach by Dr. Ballantyne.
After good health is firmly reestablished, a four-part process of reintroducing foods can be attempted. (The details about reintroductions can be found in Reintroductions ). Everyone will need a minimum of 30 days in the elimination phase, many will need a few months, and some will need up to a year. The elimination phase is highly variable because individual healing timelines are unique to each person. For example, the degree of severity of your autoimmune disease at the time you begin the protocol, how long your autoimmune disease went undiagnosed (as this may have contributed to the development of additional autoimmune diseases or organ damage), how nutrient deficient you are when you begin, and your personal commitment level to the process all affect the healing timeline.
You may be wondering: Why is the Autoimmune Protocol such a good starting point for increased wellness when, in fact, there are so many other approaches out there?
1. IT REMOVES FOODS THAT MAY TRIGGER AN IMMUNE RESPONSE, ARE HARMFUL TO THE GUT, AND LEAD TO HORMONAL DYSREGULATION. As you know from Chapter 1 , autoimmune disease is all about an immune system that has gone awry. One of the common responses of our immune systems to perceived triggers is increased inflammation. With inflammation comes all sorts of aches, pains, and uncomfortable symptoms. These same potentially immune-provoking foods also damage our intestinal linings and lead to hormonal imbalance. By removing these foods, you essentially give your system a break. As it calms, inflammation subsides, damage heals, and hormones balance, and with those changes, all your discomfort diminishes. The Autoimmune Protocol gives us a clean slate.
2. IT RESTORES NUTRIENTS AND FLORA THAT PROMOTE A HEALTHY GUT AND WELL-REGULATED IMMUNE FUNCTION. Micronutrient deficiencies are common in autoimmune disease. Many of us are deficient in fat-soluble vitamins (A, D, E, and K); minerals like zinc, iron, or magnesium; B vitamins, vitamin C, antioxidants, non-vitamin nutrients, and certain amino acids. In addition, a healthy balance of gut microorganisms is often severely disrupted. The foods we focus on in the Autoimmune Protocol are very nutrient dense, fueling healing and balancing our gut flora. Over time, this replenishment from foods rich in nutrients and probiotics greatly strengthens our systems. The Autoimmune Protocol restores us.
3. IT PROVIDES A FRAMEWORK FOR BUILDING A LIFELONG DIET EXACTLY SUITED TO YOU. We’ve said it so many times already in this chapter, but it bears repeating: There is no one-size-fits-all diet. Fortunately, the Autoimmune Protocol provides a clean slate and restoration that allow us to move forward with an experimentation process that is clear. With all the “noise” of a damaged system silenced and proper functioning reestablished, you are able to take a structured approach to food that helps you discover what works best. The Autoimmune Protocol empowers us.
The list of foods to avoid may be disheartening when you begin. The list of foods to include can also be very intimidating, because many of these foods are unfamiliar and don’t often make a regular appearance in the modern diet. We want you to know that these feelings are quite normal. If after evaluating your current health and future wellness goals, you realize the Autoimmune Protocol is right for you, we encourage you to take the plunge. If you commit to this process of self-discovery, allowing for adequate healing time during the elimination phase, intentionally adding nutrient-packed foods, and committing to significant lifestyle improvements, the results usually make the process well worth the initial trepidation.
The Autoimmune Protocol also emphasizes high-quality food sources, abundant food variety, and a great deal of food preparation, but it is important to just get started with the transition (see Dietary Transition for guidance). Over time, you can tweak your approach to maximize your time and financial resources to best undertake the process. Don’t let perfection paralyze you. The Autoimmune Protocol provides a fantastic starting point for greatly increased wellness. If you put in the effort and work patiently to understand what your body needs, you will soon have a template that is personalized and promotes your best health.
Beef
Bison
Elk
Goat
Lamb
Pork
Rabbit
Venison
Chicken
Duck
Goose
Turkey
Anchovy
Arctic char
Bass
Carp
Catfish
Cod
Haddock
Halibut
Herring
Mackerel
Mahi-mahi
Monkfish
Salmon
Sardine
Snapper
Sole
Swordfish
Tilapia
Trout
Tuna
Clams
Crab
Crawfish
Lobster
Mussels
Octopus
Oysters
Scallops
Shrimp
Snails
Squid
Bacon fat (if the ingredients are compliant)
Lard (rendered pork back or kidney fat)
Poultry fat (like duck or goose)
Schmaltz (rendered chicken or goose fat)
Strutto (clarified pork fat)
Tallow (rendered fat from beef or lamb)
Avocado oil
Coconut oil
Olive oil
Palm oil
Palm shortening
Red palm oil
Avocados
Cucumbers
Okra
Olives
Plantains
Pumpkin
Summer squash (zucchini)
Winter squash (like butternut, delicata, and acorn)
Arugula
Beet greens
Bok choy
Brussels sprouts
Cabbage
Celery
Collard greens
Dandelion greens
Endive
Kale
Lettuce
Mizuna
Mustard greens
Radicchio
Spinach
Swiss chard
Turnip greens
Watercress
Arrowroot
Beets
Carrots
Cassava
Celeriac
Daikon
Garlic
Ginger
Horseradish
Jerusalem artichoke
Jicama
Parsnips
Radishes
Rutabagas
Sweet potatoes
Taro
Tigernut
Turmeric
Turnips
Wasabi
Water chestnuts
Yams
Artichokes
Asparagus
Broccoli
Cauliflower
Chives
Fennel
Leeks
Onions
Rhubarb
Seaweed (like arame, nori, wakame)
Shallots
Apples
Apricots
Blackberries
Blueberries
Cantaloupe
Cherimoya
Cherries
Clementines
Coconut
Cranberries
Currants
Dates
Durian
Figs
Grapefruit
Grapes
Guava
Honeydew
Huckleberries
Kiwifruit
Lemons
Limes
Mangoes
Mulberries
Nectarines
Oranges
Papaya
Passionfruit
Peaches
Persimmons
Pineapple
Plantains
Plums
Pomegranate
Quince
Raspberries
Strawberries
Tamarind
Tangerines
Watermelon
Fermented meat or fish
Kombucha
Kvass
Lacto-fermented fruits and vegetables
Nondairy kefir (made with fruit)
Sauerkraut
Chanterelle
Cremini
Morel
Oyster
Porcini
Portobello
Shiitake
Truffle
Asafetida
Basil
Bay leaf
Chamomile
Chervil
Chive
Cilantro (coriander leaf)
Cinnamon
Clove
Curry leaf
Dillweed
Fennel leaf
Garlic
Ginger
Horseradish
Kaffir lime leaf
Lavender
Lemon balm
Lemongrass
Mace
Marjoram
Oregano
Parsley
Peppermint
Rosemary
Saffron
Sage
Savory leaf
Spearmint
Tarragon
Tea (both green and black; check herbal teas for nightshades and seeds)
Thyme
Turmeric
Vanilla (whole)
Apple cider vinegar
Balsamic vinegar
Capers
Carob powder
Coconut aminos
Coconut concentrate (otherwise known as butter, manna, or cream)
Coconut milk
Coconut vinegar
Fish sauce
Olives
Red wine vinegar
Sea salt
White wine vinegar
Coconut sugar
Coconut syrup
Honey
Maple sugar
Maple syrup
Molasses
Amaranth
Barley
Buckwheat
Corn
Kamut
Millet
Oats
Quinoa
Rice
Rye
Sorghum
Spelt
Teff
Triticale
Wheat
Adzuki beans
Black beans
Black-eyed peas
Cannellini beans
Chickpeas
Fava beans
Green beans
Kidney beans
Lentils
Lima beans
Mung beans
Navy beans
Peanuts
Peas
Pinto beans
Soybeans (including soy products like tofu)
Butter
Buttermilk
Cottage cheese
Cream
Ghee
Ice cream
Kefir
Milk
Sour cream
Whey
Whipping cream
Yogurt
Canola oil
Corn oil
Cottonseed oil
Palm kernel oil
Peanut oil
Safflower oil
Soybean oil
Sunflower oil
Chicken eggs
Duck eggs
Other species
Acesulfame potassium
Aspartame
Erythritol
Mannitol
Neotame
Saccharin
Sorbitol
Stevia
Sucralose
Xylitol
All alcohol
Artificial and natural flavors
Artificial coloring
Carrageenan
Guar gum
Lecithin
Monosodium glutamate (MSG)
Nitrites or nitrates (naturally occurring are okay)
Phosphoric acid
Propylene glycol
Textured vegetable protein
Trans fats
Xanthan gum
Yeast extract
Any ingredient names you don’t recognize
Almonds
Brazil nuts
Cashews
Chestnuts
Hazelnuts
Macadamia nuts
Pecans
Pine nuts
Pistachios
Walnuts
Anise
Caraway
Celery seed
Chia
Cocoa
Coffee
Coriander
Cumin
Dill seed
Fennel seed
Fenugreek
Flax
Hemp
Mustard seed
Nutmeg
Poppy
Pumpkin
Sesame
Sunflower
Ashwagandha
Bell peppers
Cayenne pepper
Eggplant
Goji berries
Hot peppers
Paprika
Potatoes
Tomatillos
Tomatoes
Allspice
Anise
Caraway
Cardamom
Juniper
Pepper (black, green, pink, or white)
The biggest mistake you can make in adopting the Autoimmune Protocol is overlooking the concept of nutrient density. It’s easy to get lost in eliminations, but of equal importance is replacing the removed foods with those that have the nutrients needed to reverse deficiencies and heal the body.
Common nutrient deficiencies in the modern diet include the B vitamins (especially B12 ); the fat-soluble vitamins A, D, E, and K; minerals like magnesium, calcium, and iron; antioxidants like vitamin C; essential fatty acids EPA and DHA; fiber that feeds our gut flora; and the amino acids that make up our structure and perform functions throughout our bodies. Luckily, the Autoimmune Protocol focuses on including nutritional powerhouse foods, like organ meats (especially liver—check out our recipes—Bacon–Beef Liver Pâté with Rosemary and Thyme and Hidden Liver Chili ), bone broth , fermented vegetables , oily, cold-water fish and shellfish, and a wide variety of colorful fruits and vegetables. You might be surprised to find your healing accelerated and your energy dramatically increased after eating these powerful foods.
On the next page, we have provided a chart to help you to compare the nutrient density of some key foods so you can choose which ones to prioritize in your diet. You will find the most nutrient-packed foods at the top of the list. Making sure to include them as often as you are able gives you the best opportunity to heal.
It may be tempting to seek out supplements instead of focusing on eating these nutritional powerhouse foods, but our experience is that getting nutrition from food is always ideal. Nature has packaged these nutrients in the easiest way for your body to assimilate them—containing the necessary cofactors and macronutrients required for proper digestion and absorption. If you are working with a practitioner, you may find that some smart supplementation speeds the process early on, but be sure to review your diet as well.
I believe incorporating nutrient density when I embarked on the Autoimmune Protocol was one of the early keys to my success in healing my body. Prior to this way of eating, I had followed a vegan diet (no animal products) for more than a decade and was suffering from severe nutritional deficiencies that were not responding to supplementation. When I embarked on the elimination diet, I was sure to include lots of nutrient-dense foods like bone broth, beef liver, salmon, and fermented vegetables, and I believe these foods helped me to make quick progress. In fact, including beef liver pâté (see my recipe Bacon–Beef Liver Pâté with Rosemary and Thyme !) weekly for a month helped to reverse my anemia so quickly that my doctor believed my prior bloodwork to be in error!
Vitamin A
Vitamin B1
Vitamin B2
Vitamin B3
Vitamin B6
Vitamin B12
Vitamin D
Vitamin K
Folate
Pantothenic acid
Choline
Iron
Selenium
Zinc
Copper
Calcium
Magnesium
Phosphorus
Gelatin
Collagen
Vitamin D
Vitamin B12
EPA and DHA
Phosphorus
Selenium
Iron
Zinc
Copper
Selenium
Phosphorus
Iodine
Probiotics
Vitamin K
Vitamin K
Folate
Manganese
Magnesium
Insoluble fiber
Antioxidants
Calcium
Vitamin E
Vitamin C
Antioxidants
Fiber
Transition Styles
Making a big change in any area of our lives is difficult. Everyone knows it is hard to learn new ways of doing things and even harder to drop old habits. Deciding on the best method for transitioning can be just as tough, especially when it comes to a shift in something as fundamental as the way we eat. There are plenty of expert opinions about the best way to handle dietary transition, but there isn’t a ton of solid research that tells us for sure what the absolute best way is for long-term success. It comes down to knowing yourself well. Understanding your personality and realistically evaluating your lifestyle are the most important factors in choosing a transition method.
Once you’ve decided to change your diet, you have two options.
1. COLD TURKEY —If you know you thrive with a rip-off-the-Band-Aid approach, cold turkey might be best for you. Maybe you are great at envisioning your goals and steadfastly taking on a challenge. Cold turkey requires a great deal of self-motivation.
2. SLOW AND STEADY —Many people immediately rebel at the thought of such a drastic change to their familiar patterns. Maybe an all-or-nothing approach feels scary or makes you certain you’ll fail. Baby steps can be an effective method for dietary transition. Slow and steady requires a high level of endurance.
Do you feel like there are times when you are both cold turkey and slow and steady? Most of us feel that way. Next, you’ll find a self-test designed to help you pinpoint your transition style. Once you know the best method, you can start implementing some healing dietary changes.
If you’ve determined that a fast transition is best suited to you, we recommend a 3-day jump-start process. You’ll start with a weekend of planning and preparation. The focus will be to do as much as possible to get prepared for a Monday morning transition to the full-elimination phase of the Autoimmune Protocol.
● FRIDAY— Plan a menu and shopping list for the week ahead with all the foods to avoid eliminated and nutrient-dense foods included, using the meal plan , if needed. Clear out your pantry using the exercise in Pantry Guide .
● SATURDAY— Shop for foods necessary for your menu (you may find the shopping list helpful here). Be sure to focus on bringing in as many Autoimmune Protocol–compliant ingredients as possible, so that you feel fully capable of maintaining the diet once you begin.
● SUNDAY— Batch-cook to prepare for the week ahead. This means cooking multiple dishes to eat as leftovers or use as components of quick meals throughout the week. Great batch-cooking recipes include broths, soups, stews, roasted meats, and some vegetable sides. You might also consider using Sunday to reach out to a few key family members or friends and ask for support for your upcoming transition.
Here are a few questions to ask yourself when considering which transition approach is best for you.
◻ Am I willing to make substantial changes to my schedule in order to prioritize healing?
◻ Am I child-free or do I have older children who won’t be strongly impacted by this process?
◻ Do I feel ready to commit immediately?
◻ Do I have strong planning and preparation skills?
◻ Do I know my way around the kitchen?
◻ Am I at a point with my disease where I need relief as quickly as possible?
◻ Do I have a partner or a family member who will support me through a rapid transition?
◻ Do I have a history of successfully diving into big changes?
◻ Am I willing and able to prioritize my budget to focus on food immediately?
◻ Do I have an extremely busy schedule with little flexibility?
◻ Do I have young children or other family members who may not be adopting this diet?
◻ Is full commitment something I normally need to take time to consider?
◻ Do I prefer to take on planning and preparation tasks in phases?
◻ Will I need time to learn my way around the kitchen?
◻ Does the stress of a rapid transition seem more uncomfortable than my disease symptoms?
◻ Will the process be difficult for my partner and require more time for him/her as I make adjustments?
◻ Do I find myself repeatedly trying to make all-or-nothing changes and failing?
◻ Do I have a very tight budget without much room to reallocate funds to groceries quickly?
If you’ve determined that a slow-and-steady transition is best suited to you, we recommend a 6-week process. You’ll start with a weeklong planning and preparation phase, which includes seeking support, and then use the next 5 weeks to tackle 2 food group eliminations per week, while also adding 1 new nutritional powerhouse. The eliminations with the greatest impact on your health are up first, and the eliminations with the least impact are last; this gives you some bang for your buck early in the process and hopefully adds to your motivation. The end result will be compliance with the full-elimination phase of the Autoimmune Protocol.
● Ask a few family members or friends to offer you encouragement as you transition your diet.
● Plan a menu and shopping list for next week eliminating all GRAINS and ALCOHOL and including HEALTHY FATS , like olive oil, coconut oil, and solid cooking fat (see Rendered Animal Fat ).
● Shop for the foods necessary according to your menu.
● At the end of the week, remove all GRAINS and ALCOHOL from your house in preparation for next week.
● Do one batch-cooking session to prepare your meals for next week.
● This week, start avoiding GRAINS and ALCOHOL in your diet, and start adding HEALTHY FATS , following the menu you prepared last week.
● Plan a menu and shopping list for next week eliminating all LEGUMES and NIGHTSHADES and including BONE BROTH .
● Shop for the foods necessary according to your menu.
● At the end of the week, remove all LEGUMES and NIGHTSHADES from your house in preparation for next week.
● Do one batch-cooking session to prepare your meals for next week.
● This week, start avoiding LEGUMES and NIGHTSHADES in your diet, and start adding BONE BROTH , following the menu you prepared last week.
● Plan a menu and shopping list for next week eliminating all DAIRY and COFFEE and including PROBIOTIC DRINKS (see Resources ).
● Shop for the foods necessary according to your menu.
● At the end of the week, remove all DAIRY and COFFEE from your house in preparation for next week.
● Do one batch-cooking session to prepare your meals for next week.
● This week, start avoiding DAIRY and COFFEE in your diet, and start adding PROBIOTIC DRINKS , following the menu you prepared last week.
● Plan a menu and shopping list for next week eliminating all FOOD ADDITIVES , REFINED/PROCESSED SUGARS , EGGS , and REFINED/PROCESSED OILS and including FERMENTED FOODS .
● Shop for the foods necessary according to your menu.
● At the end of the week, remove all FOOD ADDITIVES , REFINED/PROCESSED SUGARS , EGGS , and REFINED/PROCESSED OILS from your house in preparation for next week.
● Do one batch-cooking session to prepare your meals for next week.
● This week, start avoiding EGGS , REFINED/PROCESSED SUGARS , REFINED/PROCESSED OILS , and FOOD ADDITIVES in your diet, and start adding FERMENTED FOODS , following the menu you prepared last week.
● Plan a menu and shopping list for next week eliminating all NUTS , SEEDS , and FRUIT- AND BERRY-BASED SPICES and including ORGAN MEATS (see Bacon–Beef Liver Pâté with Rosemary and Thyme recipe).
● Shop for the foods necessary according to your menu.
● At the end of the week, remove all NUTS , SEEDS , and FRUIT- AND BERRY-BASED SPICES from your house in preparation for next week.
● Do one batch-cooking session to prepare your meals for next week.
● This week, start avoiding NUTS , SEEDS , and FRUIT- AND BERRY-BASED SPICES in your diet, and start adding ORGAN MEATS following the menu you prepared last week.
● As of this week, you are compliant with the full-elimination phase of the Autoimmune Protocol!
● Continue to use meal planning and batch-cooking as you maintain your elimination phase.
Reintroducing Foods
The elimination phase of the Autoimmune Protocol is not meant to be followed long-term—the next, and equally important, phase is called reintroduction . Through a slow and systematic process of putting foods on trial that you avoided on the elimination diet, you will find out if any food allergies or sensitivities are potentially contributing to your symptoms. This is a delicate but informative process that requires you to learn how to access your own inner wisdom about the cause and effect of what you put into your body. The end product is the least-restricted diet that is most supportive of your long-term healing, one that gives you the best chance of success without driving you crazy.
Before you decide to reintroduce foods, you need to assess whether you have done the elimination phase long enough, with 100 percent compliance. Initially, you may want to give yourself a goal of 30 days, and then make a reassessment if you’d like to continue on longer at that point—it is hard to gauge at the beginning of the process how it will go for your unique situation. Sometimes, people feel initial improvements (such as better digestion, energy, and clearer skin) in 30 days but wish to proceed for 60 to 90 days to see if they continue to progress upward. Others may see a dramatic reversal of symptoms in that 30-day period, making them great candidates for reintroduction sooner rather than later. Your experience on the elimination diet is going to depend on a lot of factors—your state of health going in, autoimmune conditions, degree of tissue damage, and starting nutritional status. How long to stay on the elimination diet varies from person to person, and advice from your key player might also be useful here.
You are ready to reintroduce foods when you have seen measurable improvements during the elimination phase. This can be general health improvements, like better sleep, less pain, or mental clarity, or specific improvements, like a lessening of your autoimmune symptoms. Which improvements you see aren’t as important as the fact that they are there, and that they are clear—if you don’t have an improved baseline to compare with when you start to reintroduce foods, you won’t learn much. If you are not experiencing any changes after 30 to 90 days on the Autoimmune Protocol, you will want to check out our troubleshooting section or enlist the help of your key player to look for underlying root causes that are acting as roadblocks to your success.
It is common to see a lot of improvements and sometimes a full reversal of symptoms while on the elimination diet. When this is the case for you, it may be tempting to think “well, maybe I will continue to eat this way forever!” While some people find that they are not able to successfully reintroduce many foods, it is more common to be able to tolerate some of the foods in the first stages of reintroduction (which we will cover in the following section). Especially when you are experiencing success, reintroduction is an essential part of the Autoimmune Protocol. Successful reintroductions expand the list of foods you can eat, making your diet less restrictive and easier to integrate into your life over the long-term. While it is not advised to reintroduce foods when you haven’t experienced success (see the troubleshooting guide ), you can and should start reintroducing foods when you start to feel better!
We know it’s tempting to start eating all of the foods you have eliminated right away after experiencing success, but embarking on the reintroduction process carefully ensures that you don’t have to start over! This is a very delicate process and not to be rushed. The more systematic you are about reintroductions, the easier it is going to be to make an assessment about whether or not a food is in or out. Familiarize yourself with the reintroduction protocol as well as the stages of reintroduction before you get there, so that you know what to expect.
The protocol for reintroductions, as outlined by Dr. Sarah Ballantyne in The Paleo Approach, is the following:
1. Pick a food to challenge and get ready to eat it a couple of times in 1 day.
2. Eat the food for the first time, only having a nibble. Wait 15 minutes, and if you don’t have any symptoms, take a small bite, a little larger than the last.
3. Wait another 15 minutes, and if you still don’t have any symptoms, take another bite, again slightly larger.
4. Wait 2 to 3 hours, watching to see if symptoms appear.
5. Next, eat an average quantity of the food, either by itself or as part of a meal.
6. Watch your symptoms for 3 to 7 days afterward, being sure to avoid the food you reintroduced as well as not reintroducing any other foods.
7. You may incorporate that food into your diet if you have no symptoms during this whole process.
This protocol may seem overly cautious, but it is the safest way to reintroduce foods after a long period of elimination. During the time you have avoided potential triggers, your body becomes less inflamed and your immune system gets a break from the constant attack. Sometimes, even when you reintroduce a food you used to eat all the time, you may be surprised to feel an obvious reaction. Many of us have been here before! To avoid unnecessary setbacks, it is important to take this reintroduction process slowly and methodically, even if you suspect that a food is not a problem going into the process.
Journaling is an invaluable tool when going through the reintroductions. It helps you recognize symptoms and patterns that might indicate the source of a food reaction that would be otherwise hard to gauge.
Reintroductions can be such a confusing process! When I first began attempting them, I wasn’t really sure what signs or symptoms I should be looking for that might indicate I was sensitive to a food, or more happily, that I could begin including it in my diet again. Dr. Sarah Ballantyne’s guidance on the topic wasn’t yet published, but to my surprise, as I undertook the process, I was able to discern my body’s communication. It was like all the “noise” I’d previously been hearing was silenced and signs of sensitivity were so much easier to spot. One example was when I first attempted to reintroduce white potatoes, a nightshade vegetable. The next morning, I woke with searing pain in my hip joints. This had been something I lived with all the time prior to the elimination diet and it made it clear to me that I was still sensitive. The good news is that with several more months of healing, I no longer got the joint pain. I can eat homemade French fries without fear these days!
When deciding which foods to reintroduce and when, it may be tempting to try the foods you are craving the most first—perhaps grains, tomatoes, wine, or cheese. However, it is important to choose the order of reintroduction carefully to avoid a flare or setback. Not all foods avoided during the elimination phase of the Autoimmune Protocol carry an equal potential to be problematic, so it is best to start with foods that are least likely to cause a problem before working into the category of most likely to cause a problem.
Dr. Ballantyne has categorized the foods in reintroduction stages, starting with those that are least likely to cause a problem. We recommend starting with the foods in stage I and only moving on to the next stage after you have a few successful reintroductions under your belt. While you may find some foods you are sensitive to in the early stages, they are less likely to produce strong reactions that can cause a major setback. The foods in the later stages, III and IV, are most difficult to reintroduce.
| STAGE I | egg yolks, legumes with edible pods, fruit- and berry-based spices, seed-based spices, seed and nut oils, ghee from grass-fed dairy |
| STAGE II | seeds, nuts (except cashews and pistachios), cocoa or chocolate, egg whites, grass-fed butter, alcohol (in small quantities) |
| STAGE III | cashews and pistachios, eggplant, sweet peppers, paprika, coffee, grass-fed raw cream, fermented grass-fed raw dairy (yogurt and kefir) |
| STAGE IV | other dairy products (grass-fed whole milk and cheese), chile peppers, tomatoes, potatoes, other nightshades and nightshade spices, alcohol (in larger quantities), white rice, traditionally prepared legumes (soaked and fermented), traditionally prepared gluten-free grains (soaked and fermented) |
When reintroducing foods, you want to be aware of all of the potential reactions you could have and ready to take note of them in your journal . Reactions can range from severe and obvious to subtle and unclear. After going through the process of elimination, it is possible to react to foods you may have been eating on a regular basis before you started your elimination. Because of this, you need to be aware of the potential reactions you could have—some of them may surprise you!
● RETURN OR WORSENING OF AUTOIMMUNE SYMPTOMS —If you experienced relief from your autoimmune symptoms while in the elimination phase, look for signs that they could be coming back (for instance, joint pain for rheumatoid arthritis, or a rash for psoriasis).
● DIGESTIVE CHANGES —Subtle or obvious changes, depending on how your digestion functioned before the elimination phase, can be a bad sign. You want to be on the lookout for things like heartburn, constipation, diarrhea, stomach pain, gas, bloating, or burping when reintroducing foods.
● HEADACHES, RACING PULSE, OR DIZZINESS —These can be common warning signs of food sensitivities.
● FATIGUE —Check in with your energy levels when going through the reintroduction process. Although this can be a tricky one to pinpoint, some people feel a return of exhaustion when reintroducing certain foods.
● SLEEP DISTURBANCES —Trouble falling asleep, staying asleep, or waking up throughout the night can be a sign that a food is problematic.
● JOINT OR MUSCLE PAIN —Increased joint or muscle pain, especially with certain foods like those in the nightshade family, can be common with food sensitivities.
● SKIN CHANGES —Anything from flushing to rashes, hives, itchiness, or acne indicates an issue. Pay attention to your skin and if there are any changes to it as you reintroduce foods.
● MOOD CHANGES —Although many are surprised when they encounter this reaction, some can feel anxiety, depression, or other mood changes (like anger, tearfulness, or rage) when they are sensitive to a food.
If you have done the elimination diet with 100 percent compliance, seen measurable improvement, and are having a hard time telling if your food reintroductions are successful or not, it is sometimes helpful to take a slower approach to reintroduction. Instead of taking 3 to 7 days between reintroductions, give yourself 1 to 2 weeks to see if anything crops up over the long term. Having added fewer variables into the mix, it will be easier to note reactions.
Hopefully, if you reintroduce foods in the order we advise (see the stages in Reintroduction Stages ) and start with the foods you are least likely to react to, you won’t have a severe response. However, this can happen, and if you find yourself in this situation, you need to go back to the full-elimination phase to recover. Once you have returned to the level of health you were at when you started reintroducing foods, you can try again with a different food. If you encounter a reaction that is particularly severe, this may be a good indicator that this food will not work for your body long-term.
You may find that you react to many foods early on in the process, but as your gut health, nutrient status, and general wellbeing improve, you may tolerate more foods over time. This is why it is important to continue to reintroduce foods over the longterm and not operate on the assumption that nothing will change. Reacting to a lot of early-stage foods may mean that you need some more time in the elimination phase, letting your body do some healing before trying them again.
That being said, there may be some reintroductions that may not be possible for you, at least if you want to continue to see the benefits of being on the Autoimmune Protocol. Later-stage foods like dairy, nightshades, and grains can be a lifelong problem for some, but it is up to the individual to see where he or she lies on the spectrum of tolerance and if those foods are supporting healing.
It is important to keep a journal when reintroducing foods so that you don’t have to rely on memory alone to evaluate your trials and successes. The more information you are able to track here, the better.
Finding Balance
It is no surprise that many of us have had long, difficult, potentially even traumatic experiences with our autoimmune diseases. We may have tried numerous approaches to healing or symptom management, from medications to fad diets. The journey can be fraught with mental and emotional struggles and balance, especially in terms of diet, often seems unattainable.
When we speak about balance here, we mean finding the sweet spot where you are no more food restricted than is absolutely necessary for your personal best health and you are enjoying a healthy relationship with food. You may find yourself vulnerable to losing perspective and spiraling into uncompromising, even harmful, food relationships when adopting food-elimination protocols. In the beginning, this process may go unnoticed. In your attempt to heal, you may find that certain food eliminations help alleviate symptoms and perhaps even have added benefits like a more slender physique or clearer skin. Your thoughts move in the direction of “more is better,” and before the pattern is even recognized, unnecessary levels of restriction may have led to intense anxiety around food and disordered eating.
We absolutely believe in the healing power of food. We know the Autoimmune Protocol can have an enormous impact on the foundations of good health and is not “disordered eating,” but the line between food as medicine versus food as fear can be difficult to discern for some. Our hope is that with mindfulness and self-awareness, we can all approach healing with diet and lifestyle with a spirit of enjoyment and transformation. This journey is about restoring our best selves, not developing burdened hearts and minds. In the following pages, you’ll find more detailed explorations on maintaining balance.
You might confront food-related fears on your path with the Autoimmune Protocol. Food fear can be a temporary issue you learn to quickly overcome or a severe clinical disorder that significantly impacts or even threatens your life. Fears might have a legitimate basis in a life-threatening allergy on one end of the spectrum but range to harmful impaired thinking on the other. If you think your patterns are verging on severe and not as easily addressed as less-complex fears, there are ways to get help.
Clinically recognized eating disorders have a variety of signs and symptoms. There are also eating disturbances that are not classified, but have much in common with the recognized disorders. If you notice yourself edging toward an unhealthy place or if you have struggled with disordered eating in the past and recognize yourself being triggered into old, harmful patterns, please seek help. There are many trained professionals who can assist you in addressing these serious issues. You can start by contacting the National Eating Disorders Association, The Alliance for Eating Disorders Awareness, or using Eating Disorder Hope’s directory to find many other organizations that are ready to help.
We’ve said it several times already in this chapter, but a few more repetitions won’t hurt—you are not meant to eat according to the elimination phase of the Autoimmune Protocol long-term. A strict elimination phase allows your system to calm and a “wellness baseline” to be established. Depending on many factors, your elimination phase may be longer or shorter than others’ before you attempt reintroductions . The key words here are phase and reintroductions . The goal is the least-restricted diet that supports wellness and allows you to live a full life (without crazy-making food rules to follow forever!).
Now for some generalizations, because having some basic guidance helps.
● Everyone does a minimum of 30 days in the elimination phase.
● Many reach best results with a bit longer time frame, usually 60 to 90 days.
● For some, improvements are not quite enough after 90 days. For this set, some troubleshooting and help from their key player can uncover underlying issues that require treatment beyond dietary and lifestyle changes (see next column). Remaining in elimination phase while working on these root issues can be helpful, since it removes variables.
● The vast majority do not need to remain in elimination phase beyond a year, even if they are continuing to explore root issues.
The important takeaway here is that once you’ve experienced successful healing, you can and should start expanding your diet. We all agree that chocolate is worth it!
Your health is a precious gift. That is such a cliché statement, but those of us who have experienced the depths of autoimmune disease have had this dramatically demonstrated in our own lives. Enjoying robust health in a fully functioning body is unfortunately something very easily taken for granted, until you no longer have it. Having perfect hair, flawless skin, and a model’s shape pales in comparison to an intestine that can absorb nutrients, a heart that can maintain rhythm, or lungs that can expand with life-giving oxygen.
Everyone wants to be seen as attractive, but if you make achieving wellness the primary motivator of this process, not a certain number on the scale or reflection in the mirror, you will benefit greatly from the balance that comes with that focus. In time, the work you have done to restore health and the deep appreciation you have for it will shine in unexpected ways. That kind of vitality is something everyone notices!
Sometimes, despite your best efforts, there may be something holding you back from experiencing the benefits of the elimination phase. In this section, we have outlined some areas you may want to explore should you find yourself not improving 30 to 90 days post transition. Support from your key player can be useful here, as testing, treatment, and expert guidance can help you navigate these complex situations.
When the beneficial bacteria that should reside in the large intestine (colon) migrate up into parts of the small intestine, a condition called SMALL INTESTINE BACTERIAL OVERGROWTH (SIBO) occurs. These bacteria wreak havoc on the digestive process by consuming food that should be absorbed into your body and produce hydrogen and methane gas as an end product. You end up with burping, gas, bloating, diarrhea, and constipation.
The bacteria that are involved in SIBO consume foods rich in short-chain fermentable carbohydrates, oligosaccharides, disaccharides, monosaccharides, and polyols (otherwise known as FODMAPs). Many commonly eaten foods contain these FODMAPs—onions, garlic, apples, and avocados to name a few. While healthy individuals are likely to feel no difference eating some of these foods, those suffering from SIBO may feel an exacerbation of their symptoms like bloating, abdominal pain, or stool changes.
SIBO is a common condition for those suffering from complex health issues like autoimmune disease, and successful treatment can provide benefit in many areas. While avoiding FODMAPs can be helpful in managing some of the symptoms caused by SIBO, you will need treatment (prescription or herbal antimicrobials) to eradicate it for good. We don’t recommend attempting to self-manage or treat suspected SIBO without a practitioner. That being said, trying an elimination of FODMAPs for a couple of weeks can help you assess if your continuing digestive symptoms may be caused by this issue. If so, you can take this information to your key player and request to be tested for SIBO.
For more information about testing, treatment, and recovery from SIBO, we recommend the book Digestive Health with Real Food by Aglaée Jacob.
The High-FODMAP Foods List includes high- and moderate-risk foods that also overlap with foods included during the elimination phase of the Autoimmune Protocol. If you have been diagnosed with or suspect SIBO, you may want to experiment with eliminating these foods and reintroducing according to a schedule defined by your practitioner’s suggestions, as it can vary with treatment. You will find the foods on this list to be in two categories, denoting how potentially problematic they are for someone with SIBO. The word in parentheses next to the food is the fermentable sugar contained within.
A couple important notes: Not everyone with SIBO reacts to all foods in every category, so while you may tolerate avocados, another person with SIBO may not. Another thing to keep in mind is quantity: Sometimes you can get away with eating a small quantity of a certain food before experiencing symptoms. This is another place where diligent journaling can be a helpful practice.
HISTAMINE is a chemical produced by the body or contained in food that is a neurotransmitter (hormonal messenger), as well as a part of the body’s inflammatory response. Under normal conditions, it is broken down and detoxified in the gut. Some people have HISTAMINE INTOLERANCE , a condition where their bodies cannot handle the excess histamine. This can cause symptoms such as headaches and migraines, flushing, rashes, hives, congestion, racing heart, anxiety, nausea, and vomiting. Histamine intolerance can be caused by genetic predisposition (like a mutation in the enzymes that degrade histamine or methylation), or more commonly, an overgrowth of bacteria in the gut (like SIBO ). Sometimes, histamine intolerance can be improved by treating the underlying root cause. Talk to your key player about testing and treatment.
Histamine content in food is a direct product of how it has been handled and processed. Meat, fish, and shellfish naturally produce histamine as soon as they are butchered or harvested, and this histamine level increases as time goes on. Cured or aged meats, as well as foods that have been improperly handled or stored, will have a higher histamine content than fresh. During the fermentation process, histamine is created by the multiplying bacteria.
If you find that you are reacting to foods high in histamine, following a low-histamine diet can help manage symptoms. Histamine intolerance is not like an allergy, where a very small amount of a substance can cause a problem, but more like a threshold that is passed before symptoms appear. You may find that you react to some high-histamine foods but not others, or you may get comfortable with serving sizes and combinations that allow you to stay below your personal threshold. In addition, it is important to work with your key player on pinpointing the root cause of your histamine intolerance, as it can sometimes be resolved.
Artichokes (fructose)
Asparagus (fructose)
Cabbage (fructan)
Garlic (fructan)
Jerusalem artichokes (fructan)
Leeks (fructan)
Okra (fructan)
Onions (fructan)
Raddichio (fructan)
Shallots (fructan)
Apples (fructose and polyol)
Apricots (polyol)
Blackberries (polyol)
Cherries (fructose and polyol)
Dried fruit (fructose)
Fruit juice (fructose)
Grapes (fructose)
Mangos (fructose)
Nectarines (polyol)
Peaches (polyol)
Pears (polyol)
Persimmons (polyol)
Plums (polyol)
Watermelon (polyol)
Honey
Avocados (polyol)
Beets (fructan)
Broccoli (fructan)
Brussels sprouts (fructan)
Butternut squash (fructan)
Cauliflower (polyol)
Celery (polyol)
Fennel bulb (fructan)
Mushrooms (polyol)
Sauerkraut (fructan)
Sweet potatoes (polyol)
Yams (polyol)
Bananas, unripe
Longan (polyol)
Lychee (polyol)
Rambutan (polyol)
Coconut flour
Coconut milk
Coconut sugar
Dried coconut
Maple syrup
Foods on the Autoimmune Protocol and common reintroductions that are also high in histamine include:
Alcohol (even when
cooked off)
Canned fish
Canned meat
Cheese
Coconut aminos
Cured meat (bacon, sausage, lunchmeat)
Dried fruit
Fermented vegetables (including sauerkraut)
Fish
Fish sauce
Fruit (bananas, grapes, citrus, pineapple, strawberries)
Kefir (including coconut)
Mushrooms
Pork
Shellfish
Smoked fish
Smoked meat
Spinach
Vinegar
Yogurt (including coconut milk varieties)
It is common for those with autoimmune disease to suffer from an imbalance of gut microflora, otherwise known as dysbiosis. This can present itself in a multitude of ways—maybe you simply have too few of the beneficial bacteria that are necessary for regulating the immune system, making essential vitamins, and keeping your colon healthy. Others may have bacterial infections, overgrowths, or issues with yeast and parasites. Many imbalances in gut flora lead to other imbalances, and you can be left with a complex web of gut problems that is difficult to unravel.
A big red flag that you may be suffering from dysbiosis is an intolerance to carbohydrates, even when contained in a “real food” package like fruit or tubers such as sweet potatoes. Often, these foods contain the “food” that these organisms thrive on, causing symptoms to worsen. Although avoidance of carbohydrates can be helpful for managing symptoms, it is not a great long-term approach because you end up also starving your beneficial flora, which can have negative consequences. If you notice you don’t tolerate certain carbohydrates or continue to have digestive symptoms after 30 to 90 days in the elimination phase, it would be wise to ask your key player for a comprehensive stool test, one that can help diagnose your issue.
Treatment of dysbiosis can be multiphase and generally takes time. First, it may be necessary to kill off the worst offenders with conventional or natural antimicrobial agents. Next, beneficial strains of flora must be slowly reintroduced, and dietary modifications may be necessary to starve out certain species or feed others. The treatment for some types of dysbiosis may be exactly what exacerbates another type, so it is important to work with a practitioner who is using testing to determine the type of treatment required.
This is a checklist that will help you determine if you should talk to your key player about being evaluated for dysbiosis.
◻ I have a history of excessive antibiotic use.
◻ I have a history of eating a high-carb diet.
◻ I suffer from constipation or diarrhea.
◻ I suffer from brain fog.
◻ I suffer from abdominal pain, bloating, or gas.
◻ I have foul-smelling stools and/or gas.
◻ I notice my symptoms worsen when I eat sweet foods.
◻ I notice my symptoms worsen when I eat starchy foods.
◻ I crave sweet or starchy foods.
◻ I continue to have skin problems like acne or rashes.
◻ I feel worse in damp or musty environments.
◻ I suffer from frequent headaches.
Optimal digestion is necessary to see the benefits of a great diet. Unfortunately, digestive issues can be a common roadblock to success during the elimination phase, as just changing which foods you eat may not be enough to restore optimal gut health. While many of these issues can be remedied by supplements and rarely warrant medical intervention, it may be helpful to have a practitioner guide you to ensure that you are only supplementing in areas where there is a clear need.
● LOW STOMACH ACID (HYPOCHLORHYDRIA)— We need adequate stomach acid to fully break down and digest proteins and prepare our bodies for further digestion. If you are experiencing acid reflux, indigestion, or noticing large pieces of food in your stool, ask your key player to determine if you have enough stomach acid.
● BILE INSUFFICIENCY— Bile is necessary to emulsify and digest the healthy fats that we eat. Not having enough bile can lead to symptoms like nausea, pain, diarrhea, and greasy or fatty stools. Those experiencing these issues, as well as those without gallbladders, should ask their key player for support in this area.
● ENZYME DEFICIENCY— Your pancreas makes enzymes that are essential for the complete breakdown of proteins, fats, and carbohydrates in your diet. Lacking enzymes can lead to incomplete digestion and gastrointestinal distress.
● LACK OF BENEFICIAL GUT FLORA— Beneficial flora, otherwise known as probiotics, are an essential and necessary component of healthy gut function. If you have a history of antibiotic use (which can wipe out the bad and the good) or are experiencing digestive issues, you may not have enough beneficial bacteria in your gut. Three common types of probiotics are Lactobacillus species, Bifidobacterium species, and soil-based probiotics (various species found in the soil).
Additional Food Allergies
Although the Autoimmune Protocol removes most foods likely to be problematic for you from an autoimmune standpoint, it can be common for you to have additional food allergies and/or sensitivities to foods on the “include” list. If you notice that you are getting new or worsening symptoms after introducing a food you typically did not eat before, or now are eating much more frequently, it is important to remove that food as a potential allergen. This often happens with foods like coconut, which is pretty uncommon in the modern diet but can be heavily relied upon as a dairy replacement in the elimination phase. It is important to also exclude any food you have a known allergy, sensitivity, or intolerance to while on the Autoimmune Protocol.
If you find yourself unusually tired while on the elimination phase, you may have inad vertently started eating a low-carbohydrate diet. While the Autoimmune Protocol is not by definition low-carb, you can end up here especially if you don’t go out of your way to eat compliant starchy carbs. If you are having issues, the fix is simple—try to include some starchy carbs in your diet on a daily basis. Everyone has a unique individual tolerance to the amount of carbohydrate in his or her diet so we don’t have a specific recommendation, but it is worth trying to up your intake if you find yourself feeling run down and fatigued.
● Arrowroot
● Cassava
● Parsnips
● Plantains
● Sweet potatoes
● Tapioca
● Taro
● Turnips
● Winter squash (like pumpkin or butternut squash)
● Yams
This chapter is extensive and dense with information. It’s with good reason though; nourishing yourself is the basis of living well with autoimmune disease. The foundation for success is laid by how you choose to fuel your body. Pouring the wrong kind of fuel into the gas tank of a car destroys it, ruining each part of its carefully assembled machinery. This is a very apt metaphor for your body; exactly the same principles apply.
We’ve worked to show you that taking the time to learn about sound nutritional choices and then putting them into practice with planning, preparation, and balance will pay huge dividends. After you’ve decided on the right dietary transition for yourself, dive in and give your body time to receive the benefits of increased nourishment. If you find yourself with lingering issues even after making major dietary change, don’t be discouraged. Simply troubleshoot, with the help of your health-care team, to get to the root causes of your symptoms.
This point on the journey is likely to be one of the, if not the most, transformative experiences. Learning to nourish your unique system is a delicate and demanding process, but the wisdom gained is likely to change your life.
* If you or anyone on your health-care team suspects that you may have celiac disease, you will want to request antibody testing before you begin a gluten-free diet, as your results may be inaccurate after adopting this way of eating.
