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This 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.

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 on the AIP

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...

Method

Using 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).

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Take the Assessment

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 healing diets 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 pioneers, 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.

Here's an interesting question:

Why 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.

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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."

Results

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

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.

Co-hackers

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.

Featured Resource

SAD to AIP in SIX

The Autoimmune Protocol (AIP) is the elimination diet + lifestyle protocol that enabled Matthew to reverse his autoimmune symptoms and begin to figure out what else was going on.

SAD to AIP in SIX is a an online program, facilitated by trained, certified coaches, that supports the process of transitioning to the 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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