It wasn't that long ago that I thought we might have broken Matthew for good.

He had a really hard winter, but now he's better than he has been in over 8 years.

3 1/2 years on the AIP

Actually, it hasn't been just the Autoimmune Protocol.

That's the point of our new website.

Matthew's healing has required a customized approach.

That's why we're both so keen to share personalized (n=1) experimentation methods: most of us need to try a number of things before we can heal.

However, the AIP has been at the heart of Matthew's progress, and was what enabled his healing process to begin. In addition to reversing all his autoimmune symptoms, it enabled him to clean up his laboratory (he is the laboratory!) so that he could begin to address the symptoms that are not autoimmune in origin.

Quick Recap

  • We both made a long-term commitment to the AIP in 2013. Matthew was very disabled at that time.
  • In early 2014, Matthew also removed all FODMAPs from his diet because that was the only thing that helped to decrease his severe, debilitating and mysterious nausea.
  • It took 7 months on the AIP before improvements became discernible. His brain fog began to lift. His psoriasis improved. His joint pain began to decrease. He was able to decrease his use of painkillers and get off Methotrexate entirely.
  • As time went on, all of his autoimmune symptoms continued to improve, but the nausea got worse. That told us that the nausea was probably not autoimmune in origin. His diet became ridiculously restricted in 2015, as even many low-FODMAP foods began to cause severe spikes in nausea.
  • During this time, he continued to work with his Functional Medicine Doctor (his GP had long since given up, as had all the specialists), and we kept designing and implementing n=1 experiments. Some of which worked. Most of which didn't.

It was a very difficult time.


We try not to get too hopeful when Matthew has a string of good days.

We're so conditioned to his health reversals that sometimes we stay in a bit of unenthused denial even when celebration is definitely called for. Like now.

Matthew is better than he has been in over 8 years.

Since before his health crisis began.


  • His nausea levels are in the 1-3 out of 10 range, compared to 4-10 for the past 3 years.
  • He went back to work full-time in April 2016 after years of disability leave. After barely coping for the first year, he is now thriving, managing exciting projects and functioning at about 90% of his pre-illness capacity.
  • His psoriasis symptoms are better than they have been in at least 10 years.
  • His psoriatic arthritis and other autoimmune joint pain is at a 2-3 out of 10 and he can manage it by taking supermarket painkillers once or twice a week.
  • He walks. Frequently.
  • He's gotten back into golf (!)
  • He now has energy to put into friendships, a previously unachievable luxury.

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The Long Winter

It wasn't that long ago that I thought we might have broken him for good.

This was the winter of Rifaxamin.

Matthew tried a lot of other things before he became willing to try Rifaxamin, which is an antibiotic used to treat Small Intestinal Bacterial Overgrowth (SIBO), but suffice to say that the risk assessment process was rigorous and Matthew tried a lot of other strategies first. 

He did two rounds of Rifaxamin for two weeks each. The first round took 3 months to recover from, but within the first 10 days he was able to reintroduce all AIP-compliant FODMAPs.

He didn't start the next cycle until the he'd recovered from the first.

The second round took 5 months to recover from.

It was around the 4 month point that we started to grapple with the idea that we might have broken him for good. His nausea was severe. He was also experiencing intense depression.

By the 5 month point, we'd kind of accepted the fact that his body may not have been able to handle the experiment.

We had developed and faithfully implemented a risk management strategy. But humans are complex. Especially chronically ill ones.

Then he started to improve.

This is where it gets interesting.


He started taking CBD oil.

He had tried CBD oil in the past, without benefit. Perhaps his body was ready now. Or the quality of the CBD oil is what made the difference.

I'll devote another post to this soon, but here's the quick overview:

  • Matthew's nausea decreased, his psoriasis improved, his brain started working. Really working. Like it used to. Before. After taking CBD oil.
  • He tried an ABAB time series and removing CBD oil for 24 hours results in a severe spike in nausea. Nausea decreases from an 8 out of 10 to a 4 within 20 minutes of taking CBD oil.
  • CBD oil, despite being billed as a cure-all by its proponents, is an 'anti-prokinetic'. I'll elaborate on that soon, but basically it means it may not be the best thing to introduce while trying to get rid of SIBO.

In Summary

Matthew is not healed, but he is as close to healthy than he has been in a very long time.

Q: Did the Rifaxamin help?

A: We don't know. It enabled him to tolerate FODMAPs, but so far the CBD oil seems to be the intervention that is having the most impact on his nausea.

We are aware, of course, that there is a relatively high rate of recurrence of SIBO after treatment with Rifaxamin.

To address this, Matthew has been enjoying fasting during the past month as a way to support the 'Migrating Motor Complex', the natural cleaning function that moves matter from the small intestine to the lower portions of the digestive tract. Including stray bacteria that may wander back into small intestine again.

Q: Is the CBD oil simply helping to manage symptoms or is it addressing the (still unknown) root of the problem that is causing the nausea? 

A: So far it seems to be addressing symptoms. Which is good! Addressing the root cause would, of course, be better.

Featured Resource


The Autoimmune Protocol has been at the heart of all Matthew's progress.

SAD to AIP in SIX is a an online program, facilitated by trained, certified coaches, that supports the process of transitioning to the Autoimmune Protocol (AIP) over 6 weeks. All the diet and lifestyle changes required for the AIP are covered in this step-by-step program.

Enrollment for SAD to AIP in SIX is open 5 times a year.


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