Biohacking Update: 6 months on the Autoimmune Protocol

Matthew & I started the Autoimmune Protocol (AIP) on December 23, 2014. This is a quick update.

Fry up w crispsPain & medication

When we started six months ago, Matthew (who I adore) was taking 4-8 hardcore prescription painkillers a day for psoriatic arthritis & other inflammatory pain.

Here’s the amazing news: he’s off Methotrexate & he hasn’t had  any Tramadol or Dilaudid for a few weeks. He’s taking just 2-4 over-the-counter ‘Tylenol Arthritis’ a day & no other pharmaceuticals.

He still has substantial pain, but he can manage it with virtually no drugs. Comparatively speaking.

A dietary deviation at the 2½ month point set him back significantly, but he has recovered the progress he’d made before the divergence & has now surpassed it.

The moral of that is: no cheating on the AIP.

Baked Sockeye Salmon, Roasted Kuri Squash, Avocado

Nausea & Dizziness

Six months ago Matthew was also suffering from extreme, undiagnosed nausea & dizziness.

He still is.

Despite every diagnostic test the western medical system could throw at it (he’s been biopsied & scoped every possible way) no one has any ideas. At first they thought his liver was declining. Then they thought ulcers. Then Ménière’s. Though it’s good news that all of those tests came up negative, he’s still very debilitated, and still on disability leave from work.

We suspect it may be Small Intestinal Bacterial Overgrowth (SIBO), which the gastroenterologist assured us does not exist. But the gastroenterologist seems to be fresh out of other ideas, so we recently found a Functional Medicine doctor who does believe in SIBO & seems to be approaching this in a rational way.

Four reasons we suspect SIBO:

  1. The only relief from nausea was after being on a low-FODMAP version of the AIP this Spring. When he put the FODMAPs back in, the nausea slowly returned.
  2. wrapsIf the nausea & dizziness was autoimmune, you’d think it would have also responded to diet, given that other autoimmune symptoms have.
  3. Matthew had Irritable Bowel in his twenties & thirties. Until he met me, really.
  4. I’ve told Matthew we’ll keep trying things until we figure this out.


Hey, I’m just living in a state of peak experience all the time & I’m evangelical about how great I feel.

Read my update here.



18 thoughts on “Biohacking Update: 6 months on the Autoimmune Protocol

  1. Petra – thanks for the update. I hope you continue to find answers for (and with!) Matthew.

    I know all about the consequences of falling of the AIP wagon. I love that we have a community of people who ‘get it’ here in blog land.

  2. In my experience just about every patient with autoimmune disease has some degree of SIBO. They generally all benefit from a diet low in FODMAPS, but also low in starch in general (ie. parsnip, turnip & swede are low FODMAP but most patients feel better when avoiding those foods).

    I’m so happy to hear how wonderful you feel! 🙂

    • Thanks for the SIBO tips! From what I understand, SIBO can’t be cured from diet alone & if that’s what’s going on, we need to find a way to knock it back because it’s wrecking Matthew’s life. Our experience is that a low-FODMAP version of the autoimmune protocol is so restrictive that it is difficult to get the nutrient density over a prolonged period, though he’s back on it again now. It’s ALOT of chard, bokchoy & cucumbers!

      • There are studies to show that herbal anti-microbials are as effective as prescription antibiotics, and Chris Kresser has said he agrees.

        Most people can tolerate fermented vegetables well on a low FODMAP/starch free diet. The fermentation breaks down the carbohydrates, therefore they won’t feed SIBO.
        Fermented vegetables are extremely nutrient dense, and it allows a greater variety of vegetables in the diet.

        Most people benefit from taking digestive enzymes, betaine hydrochloride and ox bile while eradicating SIBO.

        I enjoy all your blog posts. 🙂

  3. Thanks for the update,Petra. I’ve fallen off the AIP wagon and can feel the deteioration. But with kids and grndkids coming for the next7 weeks, I probably won’t get back on very soon. So I’ll do my best to stick to low-carb Paleo. (That’s how I feed them when they’re here.) I’m glad to hear you’re feeling fantastic and I have great hopes for Matthew’s improvement.

  4. Petra, I’m really happy for you and Matthew! The progress both he and you have made must be very validating and rewarding. Keep up the awesome work and the great posts!

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  7. Enjoying your blog very much. I experienced severe nausea and vomiting and eventually moved away from the gastros toward the neuros. An MRI and bloodwork confirmed that I had swelling on my brainstem causing the nausea and I have a diagnosis of a rare auto immune condition called NMO. Not sure how deep you’ve gone into the neuro side of things but could be something to consider. Because of the potentially serious effects from the condition I do have to take medication (6 monthly dose of Rituxan) but I also do AIP and have found my energy levels significantly increased with it. Still on the journey. Best of luck to you.

    • Thanks so much for passing that on. After a quick google search, it doesn’t look like Matthew has the other symptoms associated with Neuromyelitis Optica, but it’s helpful to know as much as possible, especially given that specialists specialize, by definition. Our experience has been that most doctors only know what they have been taught to know & only see what they are looking for. We have to do most of the research ourselves. I’m really glad to learn that the AIP has resulted in increased energy for you. Of course, the hope is, that over time the remission of autoimmune symptom continue, resulting in continued improvements. I hope this is the case for you.

    • Hi Deb,
      My 7 year old daughter was diagnosed with NMO this year. She was also diagnosed with coeliac disorder too, which has to do with your gut. So she is on a gluten free diet and as iv been doing my research, i came across this site. What sort of diet are you on now and how are things going for you? My little girl has lost sight in one eye and even though she lost power in her legs twice this year, they have returned back to full strenght. I do believe we will be able to control this disorder through diet and healthy living. Hope alls good with you and what ever you are trying works for you.

  8. I didn’t have any of the other symptoms either and God willing, hope I never do. Its why for so long they thought it was gastro related. I wouldn’t wish the diagnosis on anyone but some of these weird brain auto immune things don’t enter the sphere of our docs very often and yes, totally agree with you we are left doing our own research and seeking out our own healing. Like you, I am smart and enjoy research but gosh what if we weren’t/didn’t I ask myself. I have yet to lose any weight from eating this way and have been heartened by your encouragement that it takes months to see real results. Many many thanks for documenting all your research, so very helpful to those of us looking for optimal health. Best of luck to you and Matthew.

  9. Wonderful to read your progress Petra and so glad of your continued support for Matthew. i can relate, I have doing AIP now sincerely since May and have seen some great things but have also been having symptoms relapses which have been frustrating. I know that a histamine intolerance is part of the issue and I now also suspect fodmaps, so am starting the low fodmaps AIP version of the diet. i’m following you and so impressed by your lovely recipes.

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  11. Is it possible he has POTS? I copied this from a site:

    Postural Orthostatic Tachycardia Syndrome (POTS) is a form of dysautonomia. POTS is a subset of orthostatic intolerance that is associated with the presence of excessive tachycardia on standing.1 The current diagnostic criteria for POTS is a heart rate increase of 30 beats per minute (bpm) or more, or over 120 bpm, within the first 10 minutes of standing.1,2,3,4 In children and adolescents, a revised standard of a 40 bpm or more increase has recently been adopted.4,5 POTS is often diagnosed by a Tilt Table Test, but if such testing is not available, POTS can be diagnosed with bedside measurements of heart rate and blood pressure taken in the supine (laying down) and standing up position at 2, 5 and 10 minute intervals.

    While the diagnostic criteria focus on the abnormal heart rate increase upon standing, POTS usually presents with symptoms much more complex than a simple increase in heart rate. It is fairly common for POTS patients to have a noticeable drop in blood pressure upon standing, but some POTS patients have no change or even an increase in blood pressure upon standing.1 POTS patients often have hypovolemia (low blood volume) and high levels of plasma norepinephrine while standing, reflecting increased sympathetic nervous system activation.3 Many POTS patients also experience fatigue, headaches, lightheadedness, heart palpitations, exercise intolerance, nausea, diminished concentration, tremulousness (shaking), syncope (fainting), coldness or pain in the extremeties, chest pain and shortness of breath.

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