Biohacking Update: 17 months on the Autoimmune Protocol

Biohacking Autoimmune_CoverThis is part 2 of a 2-part post (but it can also be read alone). Find part 1 here.

Here’s the dramatic beginning:

After 16 months on the Autoimmune Protocol (AIP), we were back where we’d been at the worst of Matthew’s autoimmune crisis: he was almost completely incapacitated & unable to care for himself.

Despite that, the AIP is working.

All Matthew’s autoimmune symptoms are reversing, and he is still experiencing results that are consistent with my 12 month update, even though he’s just come through the winter & spring, which are his worst times of year.

Here’s a recap of that 12-month progress:

symptoms_12 months

Even though he hasn’t experienced any improvements in autoimmune symptoms since December, the fact that he experienced only a slight increase in those symptoms during the winter is significant (& counts as improvement).

But the nausea, which started in October of 2013, has not responded to the AIP. Even a low-FODMAP AIP.

In fact, after an initial reprieve during the first months of removing FODMAPs, Matthew’s nausea got steadily worse. But that wasn’t easy to discern at first, due to the other symptomatic improvements Matthew was experiencing.

For fun, let’s look at it on a graph:

Matthew's Symptoms until May 2015

Decoupling the nausea from Matthew’s other symptoms & tracking it over time helped us conclude that his nausea is not autoimmune in origin. We know that healing from a complex (wicked) health condition is non-linear, so it took time before we felt confident about this hypothesis.

We now attribute the nausea to SIBO, which means it is likely a symptom of the same overall gut dysbiosis that contributed to his autoimmune crisis in the first place.

In other words, his nausea & autoimmune conditions are both symptoms of a common problem. As is his long-term issues with Irritable Bowel Syndrome.

It’s all connected!

Now we’re getting somewhere…


Scientific MethodUsing the language of the scientific method, we’re treating the first 16 months of the AIP as one experiment: let’s call it experiment A (A for Autoimmune).

To complete this particular cycle of experiment A, I’m reporting our findings (this post is the report~).

Based on our findings, we’re going to continue with experiment A in the long term. And based on our new hypothesis, we’re also starting experiment B (B for Bowel). (I just totally made that up).

We’ve decided to give experiment B an 8 week trial. Then we’ll analyze, do research, and hypothesize again.

Experiment B: a New Protocol

As I mentioned in my last post, 5 weeks ago Matthew started a new protocol. It’s the most restrictive one yet.

We adapted this new protocol from the one recommended by ‘s Jacobs in her book Digestive Health with Real Food.

Although the elimination phase of Agalee’s protocol makes a low-FODMAP AIP look like a 24/7 birthday party, Matthew’s nausea was so extreme when he started that he was hardly eating. So the new restrictions didn’t phase him.

 adapted her protocol from:

  1. The Specific Carbohydrate Diet (SCD), which was one of the first ‘weird diets in the quest for health‘ we ever tried, way back in 2006; &
  2. The Gut & Psychology Syndrome (GAPS) Diet, which, itself is an adaptation of the  of the SCD.

Both the SCD & GAPS, interestingly, were created by women who were desperate to help their children with debilitating health conditions when the medical system couldn’t.

N=1 biohackers, for sure~!

As is . And Dr. Allison Siebecker, a leading SIBO expert, who has devoted her career to this work as a result of her own attempts to heal from this condition.

So, we’re in good company.

‘s protocol is entirely adaptable to the AIP (the only thing you need to remove is green beans).

I highly recommend book to anyone who needs radical gastrointestinal healing. Which, on reflection, might include most people.

But here’s an interesting question:

Biohacking update_17monthsWhy did a low-FODMAP AIP improve Matthew’s nausea at first, but lose it’s effectiveness over time?

16 of the 17 months Matthew has been on the AIP have been low-FODMAP (he’s technically still on a low-FODMAP version of the AIP, just an extremely restricted version of it).

At first, there was an improvement in his nausea without the FODMAPs (you can see that in my jolly graph, above). This initial progress was aligned with the other symptomatic improvements he was experiencing, so seemed to be linked.

But a low-FODMAP AIP, though better than a regular AIP for people (like Matthew) who have inappropriate bacteria in their small intestine, still nurtured those bacteria and helped them flourish in the long-run.

The low-FODMAP AIP made Matthew feel better at first because he was no longer eating foods that were inappropriately fermenting in his small intestine. But the bacteria that were loitering there were still being nurtured by many of the carbohydrates he was eating (Especially after his 1-year AIP-iversary, when he started investigating AIP baking).

SIBO experts Allison Siebecker & Steven Sandberg-Lewis describe this in their paper The Finer Points of Diagnosis, Test Interpretation, and Treatment:

“The FODMAP diet is not specifically designed for SIBO and therefore does not eliminate polysaccharide and disaccharide sources… Eliminating these poly- and disaccharides is essential in SIBO. In SIBO, well-absorbed carbohydrates, foods that usually go to feed the host, feed instead the increased small intestine bacteria, creating symptoms and fueling more bacterial growth. Any diet will need to be individualized by trial and error over time. Providing a food chart or particular diet prescription merely offers a place to start.”


As I mentioned in my last post, after just 9 days on this new protocol, Matthew’s nausea was reduced from a range of 7-10 to a range of 4-6. And stayed there.

What’s the difference between 7-10 and 4-6?

  • He can cook. For himself. And for me.
  • He can think.
  • He can plan.
  • He can exercise.
  • He can take an interest in life.
  • He has an improved relationship with food.
  • I am no longer chronically stressed. Worried about him, the future, and how I’m going to run our life by myself forever.
  • We have more sex.
  • We have more hope.


Hope is a dangerous thing. We know because we’ve had it before.

We’re trying not to have too much.

Especially because it seems as though there are circumstances in which SIBO can be untreatable, one of them being historic daily use of opiate painkillers. Something Matthew has done over the years in an attempt to manage the chronic pain associated with psoriatic arthritis.

Which is ironic, because it is quite possible that SIBO caused the intestinal permeability that led to the development of psoriatic arthritis that necessitated the daily use of the opiates.


Other AIPers are also hacking SIBO, including Rory Linehan, an AIP blogger who is treating SIBO with antibiotics.

You can read Rory’s interview with Angie Alt, another AIP blogger who has successfully treated SIBO with anitbiotics, about her treatment here.

And find Angie’s excellent ‘SIBO Saga’ series of posts here.


24 thoughts on “Biohacking Update: 17 months on the Autoimmune Protocol

  1. Pingback: Dietary treatment for SIBO (low-FODMAP isn’t enough~) | petra8paleo

  2. Petra-
    Have you ruled out salmonella or e coli food contamination for the set-backs? I was having major setbacks last year that I finally linked to the raw almond butter I was eating (when it was recalled). I eliminated all nut products, added them back one at a time, and then started monitoring every nut/seed product I purchase now to make sure symptoms of fatigue, brain fog and diarrhea don’t reappear. I’ve experienced bad sunflower seeds, walnuts, almond, filberts and pecans.

    • Yay, Ruth~. Thanks for joining the team! Yes, Matthew has had extensive testing done to rule out those things. And hasn’t eaten nuts or seeds since he started the AIP in December 2013.

  3. Best of luck with this new venture. I had pretty good results from SCD but I think the fructose in the allowed treats pushed me into diabetes. Or it’s just my age and my lifelong indulgence in “healthy treats”! Anyway, good luck!

  4. Petra and Matthew,

    I am sure you are inundated with advice of the concerned well-wishers. Please, accept another one.
    Have you looked into the MTFHR mutation and often resulting B12 deficiency (and many other problems when both the gene and enzyme do not function fully). One of the many symptoms of this mutation is persistent nausea.
    Matthew, it is apparent that your problem is multi factorial and truly a journey of thousand steps. Methylation problems – when undiscovered – can impede the best nutritional regiment. Perhaps this is the link.

  5. Pingback: Biohacking Pioneer: Elaine Gottschall | petra8paleo

  6. I’m wondering if you have considered autoimmune liver disease as a cause of the ongoing nausea? or perhaps eating a food daily that you are intolerant to?

  7. Pingback: Chronic Illness (& the ‘Stockdale Paradox’) | petra8paleo

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  9. You probably already know this, but Dr. Siebecker mentions that bone broth made with joints/tendons etc can be high FODMAP. She also lists spinach as being high FODMAP if you consume more than 10-15 leaves at a time. (For many months I was trying to heal my toddler’s SIBO, and until I ran across Allison Siebecker’s site I didn’t realize that bone broth could be high FODMAP.)

  10. Pingback: Healing Autoimmune | petra8paleo

  11. I’m also battling sibo and have had symptoms for many years. Previous issues with IBS and also rheumatoid arthritis- symptoms were largely controlled for some time by dietary changes. However the symptoms of what I now understand to be SIBO did not improve and in the last few months following a very stressful period in my life it was almost intolerable. I could not work, could not enjoy food, and was generally feeling depressed. I began to follow the combination low FODmap /SCD diet and got some relief. For the last 3-4 weeks in the fight against SIBO I have been eating meat and organ meats only (along with some herbs, spices, coconut oil, beef tallow, bone broth) and using herbal antimicrobials to fight both candida and sibo. Initially some low FODmap veg was ok but I soon realised I felt better without any veg. I started using haritaki to help the MMC and enteric coated peppermint oil. I also tried to breathe slowly for at least a minute before eating and eat slower to aid digestion. All these things helped but I would still have bad days. Right after a particularly bad episode that kept me awake ALL night I visited a Chinese Traditional Medicine practitioner. She gave me herbal granules, taken twice daily and performed acupuncture. Her diagnosis was of “damp heat” and/or leading to poor liver function. Well…. it’s only day three but I am absolutely thrilled to say my tummy is quiet, no belching, passing wind, grumbly noises, bloating for three days. Fingers crossed that this will continue. I was excited to have the most normal bowel movement I’ve had for a while! ( I tend toward constipation) I reintroduced carrot yesterday and again today with no adverse effects. I will try spinach tomorrow! Incidentally, I decided to try the TCM approach after reading a couple of inspiring stories on the internet from others. I’ve temporarilly ceased all my other supplements, and have to say- it is so much easier to take these herbs than my former regime!

      • Hi again,

        It’s now been almost 3 weeks since my first visit to the Chinese herbalist/acupuncturist and I feel I can say for sure that this approach is working!!
        I had a second visit 8days ago and since then I’ve not had a single attack of *the burpies*!!
        My stomach feels calm for the first time in years. This is especially good news as on the day of my last visit (right afterwards in fact) I got on an airplane and have been away from home since. I have continued to cook all my own food although that has been a little challenge all on its own. I have introduced oyster mushrooms,button mushrooms, cauliflower, sweet potato and butter without any ill effects.
        That’s exciting because not only do I love these vegetables (and butter!!) , they are not low fermentation potential veggies!! I really feel I am on the road ro recovery. I have my third acupuncture treatment coming up in two days. I am just absolutely mind-blown at the difference this has made!

  12. Hi,

    I wonder if a SCD/LowFodmap diet combination would be beneficial to help heal my seborrheïc dermatitis.
    I did the gaps diet, but didn’t notice any benefits back then.
    I was eating a lot of onions, garlic, broccoli etc.
    I wonder if it’s true some people said you could get sick from bone broth and that it also containes fodmaps.
    Now I just eat whatever I want, but I want to try this diet and see if it can help with the right probiotics or probiotic foods.

    Thanks in advance,

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