Autoimmune protocol - making the best of it!

Answered on August 19, 2014
Created June 14, 2013 at 2:28 PM

Dear all,

I am thinking about starting autoimmune protocol, but I am afraid I won't be able to be 100% compliant with it.

It would be of huge help if you could rate each of the following "gray area" foods on 10 scale, 1 being ok and 10 extremely dangerous for autoimmune conditions. Please, also tell what's your opinion is based on: your personal experience, some expert's positions or a study.

  1. White rice
  2. Buckwheat
  3. Cheese (good quality Parmesan) - if one is dairy tolerant
  4. Milk - if one is dairy tolerant
  5. Eggs
  6. Nuts: walnuts, almonds and Brazil nuts
  7. Nightshades: potatoes
  8. Nightshades: tomatoes
  9. Nightshades: eggplants
  10. Nightshades: bell peppers
  11. Coffee
  12. Chocolate
  13. Huckleberries
  14. Spices derived from seeds (Anise, Annatto, Caraway, Celery seed, Coriander, Cumin, Dill, Fennel, Fenugreek, Mustard, Nutmeg, Poppy, Sesame)

Also, do I understand correctly that ALL fruit, ALL meat, ALL fish, almost ALL berries, mushrooms, radishes, celery, cauliflower, broccoli, spinach, green tea, are totally fine?

Also, consumption of which foods one should consider INCREASING if he/she has autoimmune issue?

Could you please also share how long it took you to get better on autoimmune protocol?

Please, also consider posting here http://paleohacks.com/questions/199791/autoimmune-protocol-for-kidney-disease#axzz2WCgmeAJk

Thank you very much!



on June 14, 2013
at 05:39 PM

Nice answer dude.

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5 Answers



on June 14, 2013
at 04:54 PM


I actually came here to get some of the same information as you, but I think I have a few references and personal experiences that might help. Then, I'm also following and I get answers, too!

I have been doing a 99% strict autoimmune protocol for about 1 month; I have been TRYING to do this protocol for about 3 years with periods of doing it more strictly than others. I am a caretaker of a cancer patient who "forgets to eat" unless we have palatable less-than-strict paleo food (rice, fruit, some cheeses, etc.) which makes it difficult for my own dietary habits. I have multiple autoimmune diseases, and paleo alone helped 1 of 3 of them, but the one I'm trying to "get rid of" at the moment is a particularly troublesome spot of LP that has not responded to "paleo" alone or any other hack I have found online. Also, it's a good AI indicator for me (i.e. I know when it's flaring or when I've eating something stupid).

I'm sure there will be a lot of disagreement over the list below, but I'm going to rate them as to how I have noticed these foods make my LP flare.

1) White rice -2 I have had white rice a few times while on AI protocol, and have never noticed it causing a flare in my LP. From what I understand, as a whole, it is one of the least immunogenic of the cereals. However, it's not impossible for it to be an immunogen.

2) Cheese, milk -10 Cheese and Milk both flare my LP, even though I am generally lactose tolerant. I have done another super-strict paleo version before and seemed to do OK on goat cheese, but I haven't introduced it on the current AI protocol. These can also be relatively high in estrogens, which are bad for autoimmune diseases.

3) eggs - 7 I've a few things with eggs during this AI protocol; I definitely had a noticeable increase in itchiness associated with LP, but not like cheese, milk, and nuts trigger it.

4) nuts - 8 Definite LP trigger for me. Almonds are the worst. Macadamia nuts aren't so bad.

5) potatoes - 2 I personally have never noticed any responses to potatoes, although I usually don't eat them just because of glycemic load alone.

6)coffee - 2 I drink coffee black still. (I'm a grad student so I don't have too much of an option there). I like the upgraded approach to; I use ghee and it makes my "fasting" days easier to tolerate. I haven't noticed it causing me any problems. I cut it out for about 6 months a while back and got no appreciable benefit, although I was eating other things like eggs and nuts at the time. A lot of people like to reference this "coffee and gluten cross reactivity study" that has been circulating around for at least 3 years now and appears to be propaganda from the company (Cyrex) trying to sell the assays/ELISAS. I have never see a reputable study that confirmed this "fact," which is sold under the guise of the pretty-idea-of-but-not-well-demonstrated "molecular mimicry." (It is believable that if you are gluten intolerant and have a leaky gut, you are more likely to be sensitive to multiple foods, but I highly doubt this is because your body "sees" gluten, coffee, cheese, and casein in the same manner, and that by continuing to eat these foods you are in some way propagating a gluten-specific response). On that note, if anyone reading has actually seen a REAL source confirming this that isn't reposted from the same original propaganda article, I would legitimately appreciate it, because if coffee is actually cross-reactive with gluten, I want to know.

7) chocolate 7- I eat 90% chocolate ~ 2x per month and sometimes put cocoa in protein shakes. I only noticed a flare in response to chocolate when I ate a "real" chocolate bar, but that of course has a lot of other s*it in it.

I can't comment on the tomatoes, eggplants, and bell peppers because I haven't been eating them at all. Not for any reason other than my partner hates the taste of all 3, so I just don't cook with them. Also can't comment on buckwheat and huckleberry from a personal standpoint. Source of huckleberry probably matters (i.e. what kind of huckleberry? Garden huckleberry, etc).

The biggest help for all of my AI diseases is maintaining strict ketosis long term. Pathogenic T cells depend on glycolysis; while regulatory T cells rely on fatty acid oxidationsee here. I don't think it has ever been demonstrated that eating more sugar vs. eating more fats can actually skew these populations within the body, but I figure, why take a chance? We (i.e. partner & I) use the same approach for dietary cancer therapy.

I have known other AI suffers who have clear reactions to nightshades. I haven't noticed these in myself (but maybe that's why my LP isn't totally gone!)

I am 4 weeks in of being 99% strict with the diet, and my LP has JUST begun this past week to start to fade. That said, since about 1 week into the diet it has only itched after I eat something not on the protocol (nuts, eggs). I also ate a very small amount of popped popcorn once and it flared. The only person I know who has done AI successfully reported that it took her 8 months of being extremely strict with the diet. This likely has to do with the turnover time of inflammatory cells, and the time it takes to "re-educate" the inflammatory processes going on. I wish I could reference the previous sentence, but I can't, so take it with a grain of salt.

I think all the fruit, meat, fish, berries, mushrooms etc is mostly correct. I would say from experience however, the more you are able to limit fruit the better (I mean like high glycemic fruit & fructose). I stick to just a few slices of apple & the berries most of the time. Also, I choose fish & chicken over red meat & other seafood. I try to reduce purine content of foods because uric acid (what purines break down into) directly activates the inflammasome. Similarly, uric acid and fructose compete for excretion via SLC2a9. So, theoretically, if you limit fructose your body can handle the purines/uric acid better, and therefore limit inflammation arising from these sources. I'm not sure if practically it can change things, but it can't hurt.

Increase leafy greens & fermented foods (sour kraut) as much as you can tolerate; but do it slowly. Many people with AI can't tolerate a lot of these all at once. I feel like I have the flu if I eat more than a 1 or 2 cabbage leaves at a time.

I've heard a lot of good things about Dr. Wahl's protocol for AI disease (particularly of the neuro type), but I haven't tried it or bought the book, so I am not recommending it, just putting the info out there.

I do not currently take a probiotic, but I have several multiple-AI friends who swear by them... I'm a little skeptical, but I'll leave that there. A lot of the no-no foods on AI protocol are not only aimed at limiting gastrointestinal inflammation, but also promoting growth of so-called "beneficial bacteria", which might systemically affect inflammation. I also take L-carnitine and L-glutamine which may or may not be actually doing anything, but I think they can't hurt. L-carnitine in particular is very important for proper immune functioning (again, in theory, I'm not sure if supplementing is doing anything). I am skeptical of L-glutamine actually doing something, because if intestinal cells are participating in inflammation they likely not be taking up the glutamine (i.e. participating in nutrient absorption -- see Matzinger 2011). That said, ALL intestinal cells aren't going to be participating in inflammation, so maybe it's good for the ones that aren't taking a bath in TNF or IFNg.

Also, if you still drink alcohol, I would stop it. Alcohol definitely causes flares in me and has been demonstrated to be all around bad for your guts, as I'm sure is covered elsewhere in these forums in great detail.

Ok, cheers. Hope your AID's get better. Kudos for taking your health into your own hands. Excited to see what others have to say.


p.s. - my post looks poorly referenced because I'm a watcher but not a poster and was capped at 5. I tried to link more than 20.. whoops!

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on June 14, 2013
at 05:39 PM

Nice answer dude.



on June 14, 2013
at 03:19 PM

My digestion (as judged by the Bristol stool chart and by color) seems to be directly and positively correlated to cooked vegetable consumption and the degree to which it is cooked. Different vegetables have different effects, I'm liking broccoli but there are a plethora of vegetables to pursue I'm sure.. If autoimmune problems start in the gut then I figure maybe that's a good place to start. Maybe that soluble fiber is feeding some cool bacteria that decrease inflammation by up-regulating the bacteria that produce anti inflaming omega 3s.

I've never had great digestion myself and finding a system that works for me has taken time.



on July 10, 2014
at 10:57 AM

I'd say at least elimate all dairy except ghee, buckwheat, egg yolks, nightshades, chocolate(rather use natural cacao products but that may also be rather eliminated)

You can check thepaleomom.com for the protocol, though I think some things are spoken more bold than they should be. The book is rather cheap on Kobo.

How's your progress ? Tell us about it.


on June 15, 2013
at 02:57 AM

I think the point of the autoimmune protocol is so that you can establish which foods you can handle and which give you trouble for yourself.

My experience with discussing these foods amongst friends who've all tried the exclusion then reintroduction of these foods has been that we're all very different. I know that's not a convenient answer, but something worn considering. Any way, best of luck!



on June 14, 2013
at 03:09 PM

Have no idea why "Nightshades" is highlighted as a link. Please, don't click it.

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