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Important Updates to The Autoimmune Protocol

May 25, 2013 in FAQ, Resources, The Autoimmune Protocol

I have been diligently working over the last few days to completely update The Autoimmune Protocol page to reflect all of the recommendations in my upcoming book The Paleo Approach.

When I started writing my book, I decided that I would not make a single recommendation that I couldn’t back up with solid science. I decided that I wouldn’t rely on what I’d read on other people’s blogs or in their books, but instead read the medical/scientific journal articles myself and re-evaluate every single aspect of the autoimmune protocol. After all, I am making recommendations for some very sick people. There’s some pretty intense pressure to get it right.

This page now reflects my most current understanding of the optimal diet for managing autoimmune disease. There are some important updates for those following The Autoimmune Protocol so I urge everyone to have a look.

Please note that my site is in the process of migrating to a new (and a billion times better) web host because my old host can not handle my traffic (it’s a good problem to have!). If you are having trouble viewing this page or any other post on my site, just keep trying (the migration should be happening any day now, but until then, you might see a “database connection error” during higher traffic times). If it’s really frustrating, overnight and mornings are the quietest times on the blog so are also the most likely for you to be able to “get through”.

Tags: approach, autoimmune, Diet, disease, faq, illness, info, information, Lifestyle, manage, natural, paleo, Paleolithic, primal, protocol, treatment, update
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“How Do I Know When It’s Working?” A Quick Troubleshooting Guide to Paleo

April 15, 2013 in FAQ, FAQ, How To Get Started

It’s a question that many people new to paleolithic nutrition ask either while they are going through that initial adjustment period (especially when jumping into paleo with both feet but also with gradual transitions) or as the months wear on and the difference is not as magical as anticipated. How do I know when it’s working? When will I start to lose tons of weight and have lots of energy? When will my health conditions miraculously disappear?

Well, the answer is “it depends”.

How different did you eat before committing to paleolithic nutrition? Generally, the more different you are eating now to before you discovered paleo, the harder and longer your adjustment period. This is especially true if you ate a lot of carbohydrates before. It can take up to a month for your body to switch over to a metabolism that runs better on fat and in the meantime, you may feel tired, lethargic, have headaches, and generally feel pretty terrible. But, this isn’t true for everyone. And of course, the opposite can also be true: some people are made so sick by the foods they were eating before that they notice an instant improvement to their health.

What health issues are you challenged with? In my personal experience, most gut health issues will improve dramatically the first couple of weeks on paleo and then continue to improve slowly over the next six months as your gut continues to heal (for more posts on gut health, see here and here). Issues relating to inflammation typically take longer to show significant improvement depending on how well you are sleeping and managing your stress (typically another month or two). Remember that for many health issues, you need to address all of the tenants of a paleolithic lifestyle (get good sleep, manage stress, get outside).

Are you in autoimmune denial? I was. While out-of-the-box paleo tackled most of my health issues, I still had unresolved autoimmune issues even after four months of strict paleolithic nutrition. I had to do the autoimmune protocol (I’ve written about the autoimmune protocol extensively and this is also the topic of my book), in which you also exclude all the gray area foods. If you have been eating a strict paleolithic diet for two months and are still dealing with health issues, you might have to do this too. The good news is that after a few months of no eggs, no nuts, no seeds, no nightshades, no alcohol, no NSAIDs, low caffeine and no cheating, with a concurrent focus on eating extremely nutrient-dense foods (lots of vegetables, grass-fed meat, organ meat, fish and bone broth), most people can add at least some of those things back in.

Is your gut in REALLY bad shape? It is possible that your gut was very leaky before you started paleo, so healing is just plain ol’ going to take a while. Especially, if you suspect that you have Small Intestinal Bacterial Overgrowth or extensive gut damage, you’ll need to focus on Repairing The Gut, which can take 6 months to 2 years (although you should see continuous gradual improvement). For all of the posts I’ve written on gut health, click here.

How is your digestion? You might need to add some digestive support supplements for a little while to help your body heal. These include digestive enzymes, ox bile, and stomach acid supplements (which are contraindicated for those with ulcers, blood clotting disorders, or taking NSAIDs). Digestive enzymes and ox bile, while they can be expensive, are generally very safe to take as directed on the bottle (just make sure you actually eat once you take digestive enzymes because taking them and then not eating can cause damage to your gut). If you are interested in a stomach acid supplement, check out my post on stomach acid here and this post by Steve Wright.

Do you have unknown food sensitivities? If you’ve had a leaky gut for some time, you may have food sensitivities that you are unaware of. Many alternative health care practitioners will order an IgG and/or IgA antibody screen which tests for food sensitivities. The good news is that if you leave those foods out of your diet for a while, you can usually add them back in after your gut has fully healed. If you have symptoms of Irritable Bowel Syndrome (like diarrhea, constipation, gas, bloating, acid reflux), another possibility is a FODMAP sensitivity. Other potential culprits include salicylate sensitivity and food allergies (such as latex allergies, citrus, fish and shellfish, tree nuts, eggs, and dairy).

Do you need liver detox support? If you had/have an overgrowth of bacteria or yeast in your gut that are now dying off in great numbers, your liver might be working in overdrive. B-vitamins (rich in red meat and organ meat), sulfur (rich in cruciferous vegetables and vegetables from the allium family), selenium (rich in seafood and organ meat) molybdenum (rich in organ meat) are important to support the liver. Milk thistle (extract or tea) may also be helpful. Choosing foods rich in these substances (or supplements) to help support liver detox is also useful for anyone losing weight, especially if the weight is coming off quickly. This is because the body uses the fat tissues to store some toxins and excess hormones like estrogen (which gets them safely out of the body’s circulation) and rapid weigh loss has the potential to release these putting an additional strain on the liver.

Are you sleeping enough? Yes, this has nothing to do with diet. But sleep has a profound effect on every system in your body and if you are not getting enough of it, you can’t heal properly. Aim for 8-10 hours per night in a pitch black room (see this post if you’re having trouble getting good sleep). You can read more about the importance of sleep on the immune system in this teaser excerpt from The Paleo Approach.

Are you stressed? If you are not taking adequate measures to manage your stress (like getting activity but avoiding excessively strenuous exercise, spending time outside, having fun, getting enough sleep and developing strategies to manage psychological stressors), then your stress hormones might be out of whack. If you have been under high stress for a long time and have trouble sleeping, you may have adrenal fatigue. Both www.RobbWolf.com and www.BalancedBites.com have lots of great suggestions for healing from adrenal fatigue.

Did you go too low carb? What types of carbs (fruit versus starchy vegetables versus both versus neither) and how many carbs we should eat (varying from ketogenic diets and 20g per day to plenty of “safe starches” and upwards of 300g per day) is probably the most hotly debated topic within the paleo community. One of the reasons for there being no clear answer as to what is best is that the carb intake of historically-studied and modern hunter-gatherer populations varies wildly. On one end of the extreme are the Eskimos, who consume a diet composed approximately of 50% fat, 35% protein and 15% carbohydrate. On the other end of the extreme are the Kitavans, who consume a diet composed approximately of 20% fat, 10% protein and 70% carbohydrate. And of course, everything in between. This probably reflects the fact that macronutrient ratios are not as important as food quality and nutrient density. So, if your introduction to the concept of paleo was through a resource that expounded on the benefits of low carb, it is important to understand that this view is not representative of the entire paleo community and no consensus exists. It’s also important to understand, that while blood sugar regulation is extremely important, going too low carb can be tough on your thyroid and can decrease leptin sensitivity (see this post and this post). Also, eating adequate carbohydrates and especially insoluble fiber is important for proper regulation of ghrelin levels (see this post). So, what is a good carbohydrate intake? That’s actually highly individual (you can read this series of posts about optimizing your carb intake here, here and here), but if you are not feeling very good on a standard paleo diet, adding a little fruit or starchy vegetables is a good idea to try.

Are you inappropriately IFing? There are many enthusiastic supporters of Intermittent Fasting, but it’s important to understand that this is only appropriate for very healthy people. If your sleep is not great, if your stress in not managed, if you are substantially overweight or if you have any kind of chronic disease, skipping breakfast (or breakfast and lunch) can cause dysregulated cortisol and undermine your other efforts. This is not something to experiment with early on in your paleo journey.

What are your goals and how far away from them are you? If you have a lot of weight to lose, you will probably notice a big drop in weight fairly quickly. This will be mostly water weight, but don’t worry, fat is also being burned and you should eventually settle down into some nice steady weight loss (slow and steady wins the race, so there is no reason to be frustrated with weight loss if you are “only” losing a half pound per week-that’s actually very healthy!). When your body seems resistant to weight loss, try addressing sleep quality and stress levels, but also be aware of the impact of female hormones and hunger hormones (levels and sensitivity). For more tips and tricks for losing weight, see this post.

Are you truly complying with paleolithic nutrition? There are few things worse than being “almost paleo” (depending on your health challenges and what “almost” actually means for you). While many people can successfully navigate the murky waters of cheats and occasional gluten consumption, if you are asking the question “when will I feel fabulous” while not actually following a paleo diet as strictly as you can, then you might be a person who just can’t cheat or tolerate occasional gluten exposure. And from a metabolism, hormone and taste-bud adaptation standpoint, allowing yourself the occasional slice of pizza or pie a la mode can really derail your efforts to get healthy and perpetuate cravings, food addictions, and feelings of deprivation. I advise eating very strict paleo for at least a month before you play with eating small amounts of dairy or legumes or allowing yourself cheat meals (and I recommend a lifelong avoidance of gluten for most people). If strict paleo isn’t enough to make you feel great, look at the gray area foods in your diet (eggs, nuts, seeds, nightshades, alcohol, caffeine). Maybe one of them is the culprit (nightshades are my number one suspect). But if you are truly sticking to it, my guess is you are already feeling much, much better!

Tags: acid, activity, adrenal fatigue, allergies, autoimmune, bacterial, betaine, Breakfast, carb, carbohydrate, carbs, chronic, cortisol, detox, digestion, disease, eggs, enzymes, Exercise, faq, Fat, FODMAP, FODMAPs, Fructose, ghrelin, HCl, help, hormone, How To, hunger, illness, insulin, intermittent fasting, ketogenic, ketosis, leptin, liver, lose, Loss, metabolism, nightshades, nuts, overgrowth, ox bile, paleo, plateau, problem, protocol, seeds, sensitivities, set-point, SIBO, Sleep, stomach acid, Stress, supplements, support, tomatoes, toxin, troubleshoot, troubleshooting, Weight, yeast
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Gluten Cross-Reactivity UPDATE: How your body can still think you’re eating gluten even after giving it up.

March 13, 2013 in FAQ, FAQ, Foods in Moderation, Gut Health, The Autoimmune Protocol, The WHYs of the AIP

In my research for The Paleo Approach, I feel that it is important to provide scientific references for every single statement I make. This has me doing a great deal of fact checking, scouring the medical literature to verify information often gleaned from other paleo authors and bloggers. Most of the time what I find out just helps reinforce concepts, filling in blanks, and typically making a strong case for my assertions. But, every once in a while, I find information that makes me completely reevaluate a concept and sometimes even an aspect of the autoimmune protocol.

The update for this blog post comes from my further examination into the science behind gluten cross-reactivity. While there are plenty of papers confirming how cross-reactive antibodies can be formed, I could not find any published studies confirming the results from Cyrex Labs (and my motto with the paper is if I can’t cite it, I don’t say it). I contacted the company to request further information (I was particularly interested in the reported cross-reactivity to tapioca as I was trying to decide whether or not tapioca starch and/or pearls should be included in The Paleo Approach). Cyrex labs responded quickly and informatively and my level of esteem for that company (which was high to begin with) elevated another couple of notches. While they were unwilling to share proprietary data with me, they were able to point me to a recent publication that evaluated gluten cross-reactivity and share a summary of their proprietary findings (the paper did not show up on my PubMed searches). As I devoured the paper (figuratively, not literally), I realized that an update to this post was required. This is not an excerpt from The Paleo Approach but it is a direct result of my research for the book and much of the information that follows is still presented in it.

For those 20% of us with celiac disease or gluten-intolerance/sensitivity (whether diagnosed or not), it is critical to understand the concept of gluten cross-reactivity. Essentially, when your body creates antibodies against gluten, those same antibodies also recognize proteins in other foods. When you eat those foods, even though they don’t contain gluten, your body reacts as though they do. You can do a fantastic job of remaining completely gluten-free but still suffer all of the symptoms of gluten consumption—because your body still thinks you are eating gluten. This is a very important piece of information that I was missing until recently.

Proteins are made of long chains of amino acids (small proteins may only be 50 amino acids long whereas large proteins may be 2000 amino acids long) and it is the specific sequence of these amino acids that determines what kind of protein is formed. These amino acid chains are folded, kinked and buckled in extremely complex ways, which gives a protein its ‘structure’. This folding/structure is integral to the function of the protein.

An antibody is a Y shaped protein produced by immune cells in your body. Each tip of the Y contains the region of the antibody (called the paratope) that can bind to a specific sequence of amino acids (called the epitope) that are a part of the protein that the antibody recognizes/binds to (called the antigen). The classic analogy is that the antibody is like a lock and a 15-20 amino acid section of a protein/antigen is the key. There are 5 classes (or isotypes) of antibodies, each with distinctive functions in the body. The IgE class of antibodies are responsible for allergic reactions; for example, when someone goes into anaphylaxis after eating shellfish. The two classes IgG and IgA are critical for protecting us from invading pathogens but are also responsible for food sensitivities/intolerances. Both IgA and IgG antibodies are secreted by immune cells into the circulation, lymph, various fluids of the body (like saliva!) and tissues themselves. And both IgG and IgA antibodies are found in high concentrations in the tissues and fluids surrounding the gut (this is part of why the gut is considered our primary defense against infection).

The formation of antibodies against an antigen (whether this is an invading pathogen or a food) is an extremely complex process. When antibodies are being formed against a protein, the antibodies recognize specific (and short) sequences of amino acids in that protein. Depending on how the antigenic protein is folded, certain amino acid sequences in that protein are more likely to be the target of new antibody formation than others, simply because of the location of that sequence in the structure of the protein. Certain sequences of amino acids are more antigenic than others as well (i.e., more likely to stimulate antibody formation). This is also part of why certain foods have a higher potential to cause allergies and sensitivities.

Understanding that antibodies recognize short sequences of amino acids and not an entire protein is key to understanding the concept of cross-reactivity (and molecular mimicry, but that’s a topic for another post). It also is the reason why many different antibodies can be formed against one protein (this redundancy is important for protecting us from pathogens). Many different antibodies can also be formed against one pathogen or, more relevant to this discussion, one specific food.

So what happens in cross-reactivity? In this case the amino acid sequence that an antibody recognizes is also present in another protein from another food (in the case of molecular mimicry, that sequence is also present is a protein in the human body). There are only 20 different amino acids, so while there are millions of possible ways to link various amount of each amino acid together to form a protein, there are certain amino acid sequences that do tend to repeat in biology.

The take home message: depending on exactly what antibody or antibodies your body forms against gluten, it/they may or may not cross-react with other foods. So, not only are you sensitive to gluten, but your body now recognizes non-gluten containing foods as one and the same. Who needs to worry about this? Any of the estimated 20% of people who are gluten intolerant or have celiac disease, i.e., have formed antibodies against gluten.

A recent study evaluated the potential cross-reactivity of 24 food antigens. These included:

Rye
Barley
Spelt
Polish Wheat
Oats (2 different cultivars)
Buckwheat
Sorghum
Millet
Amaranth
Quinoa
Corn
Rice
Potato
Hemp
Teff
Soy
Milk (Alpha-Casein, Beta-Casein, Casomorphin, Butyrophilin, Whey Protein and whole milk)
Chocolate
Yeast
Coffee (instant, latte, espresso, imported)
Sesame
Tapioca (a.k.a. cassava or yucca)
Eggs

They did not find cross-reactivity with all of these foods (as is implied by the Cyrex Labs gluten cross-reactivity blood test, a.k.a. Array 4). But, they did find that their anti-gliadin antibodies (antibodies that recognize the protein fraction of gluten) did cross-react with all dairy including whole milk and isolated dairy proteins (casein, casomorphin, butyrophilin, and whey)—this may explain the high frequency of dairy sensitivities in celiac patients—oats, brewer/baker’s yeast, instant coffee (but not fresh coffee), milk chocolate (attributable to the dairy proteins in chocolate), sorghum, millet, corn, rice and potato.

While not all people with gluten sensitivities will also be sensitive to all of these foods, they should be highlighted as high risk for stimulating the immune system. Just like trace amounts of gluten can cause a reaction in at least those with celiac disease (the threshold for a reaction has not been tested in non-celiac gluten sensitivity), even a small amount of these foods can perpetuate inflammation and immune responses. This is important when you think of the small amounts of corn used in so many foods and even the trace milk proteins that can be found in ghee.

Beyond this gluten contamination is common in the food supply and many grains and flours that are inherently gluten free may still contain gluten once processed. Commonly contaminated grain products include millet, white rice flour, buckwheat flour, sorghum flour, and soy flour. As these are commonly used ingredients in commercial gluten-free baked goods, extreme caution should be exercised.

Cyrex Labs offers a simple blood test that is referred to as their gluten ross-reactivity panel, a.k.a. Array 4. It tests for reactions to the gluten cross-reactors mentioned above as well as the non cross-reactors evaluated in the paper. Cyrex Labs reported to me that they see positive sensitivities frequently (many as high as 25%) in many of those foods in people with diagnosed gluten sensitivity. This may reflect that when you have a leaky gut, food intolerances are quite easy to form.

If you have autoimmune disease (which has a very high correlation with gluten-sensitivity), celiac disease, gluten-sensitivity, or are simply not seeing the improvements you were hoping for by following a standard paleo diet, one or all of these foods may be the culprit. You have the choice of either cutting these foods out of your diet and seeing if you improve or get tested to see if your body produces antibodies against these foods.

When I first wrote this blog post, it made so many pieces of the puzzle come together. I stopped eating chocolate (I had already given up coffee), fermented foods like sauerkraut and kombucha (because of the yeast content), eggs, and tapioca. Over the months that followed, I was able to definitely discern that I am very sensitive to chocolate (perhaps because it is extremely high in phytic acid, discussed in this post) and eggs (discussed in this post). I have successfully reintroduced fermented foods and have not been particularly inspired to test my sensitivity to tapioca (I test by eating a bit and seeing if I have a reaction, most typically my reactions are acne, but sometimes trouble sleeping, mood issues, joint aches, or increased itchiness and redness of my lichen planus lesions). So, will I give coffee a try now? Maybe, once in a while as a special treat, but removing gluten cross-reactivity from the list of ways coffee is suboptimal, really only removes one potential problem. Coffee still has effects on cortisol and still correlates with increased inflammation. Oh well. Whether I can drink coffee again or not, I am glad to be able to share this updated information with all of you!

A great overview of proteins and antibodies (and source of protein folding image): http://publications.nigms.nih.gov/structlife/chapter1.html

A fairly technical review of food IgG-mediated food sensitivities: http://www.usbiotek.com/Downloads/information/criticalReview.pdf

Cyrex Labs Array 4: http://www.cyrexlabs.com/CyrexTestsArrays/tabid/136/Default.aspx

Image of antibody binding taken from http://classes.midlandstech.edu/carterp/Courses/bio225/chap17/ss2.htm

A. Vojdani and I. Tarash, “Cross-Reaction between Gliadin and Different Food and Tissue Antigens,” Food and Nutrition Sciences, Vol. 4 No. 1, 2013, pp. 20-32. http://www.scirp.org/journal/PaperInformation.aspx?PaperID=26626

Thompson T et al. Gluten contamination of grains, seeds, and flours in the United States: a pilot study. J Am Diet Assoc. 2010 Jun;110(6):937-40. doi: 10.1016/j.jada.2010.03.014.

Tags: array 4, avoiding, celiac, chocolate, citation, coffee, contamination, cross-reaction, cross-reactivity, cyrex labs, Gluten, Gluten-Free, grains, information, intolerance, mimicry, molecular, paleo, Paleolithic, potato, reference, science, seeds, sensitivity, sesame, tapioca, the paleo approach, update
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AIP FAQ: “I am confused about fruit on the paleo autoimmune protocol. Could you explain?”

February 4, 2013 in FAQ

I am going to be addressing many Frequently Asked Questions about the Autoimmune Protocol in some posts over the next few months. If you have a question that you think should be answered, you may e-mail me at thepaleomommy@gmail.com.

I get asked about fruit on the AIP very frequently. I am intentionally vague with my recommendations for and against fruit in the Autoimmune Protocol because tolerance and need are highly variable. The short answer is, it’s individual.

I will, of course, be going into extreme detail to answer this question in my book. However, I feel like this question also needs to be answered here.

There are a couple of factors that are going to determine whether or not fruit is okay or beneficial for you to include in your diet, which fruits and how much fruit.

Many autoimmune diseases are very sensitive to blood sugar changes. This is more likely to be true if you’ve had a history of obesity or metabolic derangement. In that case, limiting to one serving of fruit with each meal seems to work well. Lower sugar fruits like berries tend to be better for blood sugar regulation. Berries are also high in several vitamins and antioxidants, which can be very beneficial for resolving inflammation. Other good low-sugar fruits include grapefruit (one of my personal favorites) and other citrus, melons (except watermelon), kiwis, apricots, and tart green apples.

For others with better blood sugar regulation, fruit can be an important source of carbohydrates in the absence of starchy vegetables. Because of the high frequency of gut dysbiosis in autoimmune disease, most people with autoimmune diseases need to be very careful about starchy vegetables, at least at first. But, going too low carbohydrate can also be problematic (increases leptin resistance which stimulates inflammation). So, increasing fruit intake can be very helpful for anyone who is underweight to normal weight (and not needing to lose weight) but who also doesn’t tolerate starchy vegetables. In this case, higher sugar fruits and larger portions are typically well tolerated. High glucose content fruits will be the most helpful for those who want to gain weight. These include bananas, grapes, apricots, figs, plums, cherries, and pineapple. Citrus, berries and melon (except watermelon) also tend to have more glucose than fructose.

Fructose contributes more to inflammation than glucose. So, keeping portions of very high fructose content fruits on the small and infrequent side is a good idea even for those who don’t have FODMAP sensitivities (they aren’t explicitly banned, but do be aware of how you feel after you eat them). These include mango, red apples, papaya, and watermelon. Dried fruits tend to concentrate the sugars so extra caution is required in terms of portion size.

As a quick aside (but seems relevant here), starches are avoided for everyone with overgrowths (bacterial or yeast), which is the majority of those with autoimmune diseases. But, some people suffer undergrowths in which cases starches are very valuable (starches tend to be high in “prebiotics” which is anything hard for you to digest but easy for your gut bacteria to digest). That mostly applies to people with gut disorders like celiac disease and IBD, but also anyone who has frequent diarrhea as a symptom of their disease.

More information on starches:

More information for anyone who is underweight: