The AIP diet was originally formulated to treat patients with Inflammatory bowel diseases (IBDs). IBD includes Crohn’s disease (CD) and ulcerative colitis (UC).  T-cell “dysregulation”, diet, and intestinal micro flora are factors.  Patients saw improvements in various aspects of bowel movements, less abdominal pain and rectal bleeding, and general improvements in well -being.  These general improvements in well being were seen in female patients with Hashimoto’s Thyroiditis who switched to the AIP diet for several weeks.
Foods included in the AIP diet
- any vegetables, except those from the nightshade family The nightshade is a member of the genus Solanum that also includes tomatoes and potatoes.
- high-quality seafood that are rich in omega-3 fatty acids. Species of Solanum produce glycoalkaloids. The general premise is that glycoalkaloids increase intesitnal permeability and markers of inflammation in a mouse model. 
- fermented foods Fermented foods that contain lactic acid bacteria have been shown to improve symptoms of patients with IBD.  One thing we have yet to prove is whether Cu+ promotes the growth of intestinal friendly bacteria versus Cu2+ promoting the growth of “bad” bacteria.
- lean meats and liver Liver is an excellent source of copper, niacin and cobalamin. Some may be okay with eating lean meat but adverse to consuming organ meats.
- small amounts of fruit It is assumed that fruits are only allowed in small amounts due to the production of advanced glycation end products. AGE levels were higher in Hashimoto’s thyroiditis patients (M = 223.18 AU/g prot) than in controls (M = 189.636 AU/g prot; p = 0.020) and inversely correlated with biological antioxidant protein levels (r = -0.196; p = 0.037).  This is where Cu(I)NA2 and Cu/Zn SOD come in.
- oils, such as olive, coconut, and avocado oils Only saturated fats are are suitable for cooking, presumably due to cis-trans isomerization. Olive and avocado oils for uncooked foods.
Foods to avoid in the AIP diet
Many of the foods on this list have lectins, proteins that bind carbohydrates found on the surface of our cells, bacteria, and viruses. The Wikipedia authors point out that nightshade plants, grains, legumes, nuts, eggs, and milk contain lectins.
- nightshades, such as tomatoes, potatoes, peppers, and eggplants
- grains It is not certain if this one is banned because of the starch content and advanced glycation end products and/or the gluten. “Celiac disease (CeD) is defined as a life-long intolerance to dietary gluten that results in small intestinal inflammation, villous atrophy, crypt hyperplasia, and often malabsorption. The ingestion of gluten containing cereal grains, mainly wheat, rye, and barley, drives this T cell driven auto-destructive process within the small intestinal mucosa which usually recovers when these cereals and gluten are rigorously withdrawn from the diet.”  This review discusses thyroid and pancreas directed auto antibodies. but does not discuss link between crypt damage and T cell driven auto destruct process. Surprisingly, little has been written about neurological complications of celiac disease. One review writes, “Neurologic disorders were attributable to malabsorption-induced nutritional deficiency in 6 patients. These disorders included myeloneuropathies (with sensory ataxia) secondary to deficiency of ≥1 of copper, vitamin E, and folate, 5; and myelopathy secondary to copper deficiency, 1 (the patient also had cerebellar ataxia).” 
- legumes Anyone who has ever consumed under cooked red kidney beans knows that these particular lectins can cause intense gastrointestinal pain and other symptoms. Dr Weil contends that legumes when properly cooked can be healthy. An Italian study that compared patients with Hashimoto’s thyroiditis with healthy controls found that the patients that consumed more meat and dairy had greater odds ratios (2.7, 1.5, respectively ) of having thyroid autoantibodies.  Those that consumed legumes were less likely (odds ratio 0.446) to have thyroid autoantibodies (p=0.057) Independent of autoantibodies, the HT patients were found to have higher levels of oxidative sress markers and lower levels of antioxidant enzymes. 
- some vegetable oils
- coffee Is coffee on the “bad list” because it is a bean/seed, the caffeine, or other small molecules? It is noted that green tea is not on the list. The protective and exacerbating association between coffee and autoimmune diseases give reason not to consume it out of caution. 
- nuts and seeds
- alcohol Alcohol dehydrogenase uses NADH. This may play a role in modulating NRLP3 of the inflammasome  that we’ve addressed in another post.
- food additives, such as refined or added sugars
In the AIP diet study to treat Hashimoto’s Thyroiditis study, the investigators used the SF-36 questionnaire to evaluation the outcome. Significant improvements were seen in all SF-36 modules. Scores range from 1= have it a lot to 3= not al all limited.
- Vigorous activities, such as running, lifting heavy objects,participating in strenuous sports
- Moderate activities, such as moving a table, pushing a vacuum cleaner, bowling, or playing golf
- Lifting or carrying groceries
- Climbing several flights of stairs
- Climbing one flight of stairs
- Bending, kneeling, or stooping
- Waling more than a mile
- Walking several blocks
- Walking one block
- Bathing or dressing yourself
The Medical Symptom/Toxicity Questionnaire (MSQ) was also used as an outcome measure. Participants score their symptoms as 0 = never to 4 = frequently have it, effect is severe. The lower the score, the better the quality of life. These are the questions for the joints/muscle module are as follows:
- Pain or aches in joints
- Stiffness or limitation of movement
- Pain or aches in muscles
- Feeling of weakness or tiredness
Not into mineral and B vitamin rich organ meats? Ask the physician that prescribed the autoimmune diet if you might eat regular meats and take mineral and B vitamin supplements. Hopefully this post has given you some understanding of where the diet is coming from.
- Konijeti GG, Kim N, Lewis JD, Groven S, Chandrasekaran A, Grandhe S, Diamant C, Singh E, Oliveira G, Wang X, Molparia B, Torkamani A. (2017) Efficacy of the Autoimmune Protocol Diet for Inflammatory Bowel Disease. Inflamm Bowel Dis. 2017 Nov;23(11):2054-2060 PMC free article
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