In August, Matthew started a three-month protocol designed to tackle biofilm-protected yeast colonies his gut.

Five months later we are feeling optimistic.

The Back Story

The symptom: debilitating nausea with no apparent cause.

The nausea first occurred in October 2013 after an autumn feast of chanterelle mushrooms I had picked.

It happened again when we ate chanterelles a second time that month.

And then just kept recurring. And getting worse. Until it gradually became Matthew's most problematic symptom.

In fact, it was the severe nausea that finally prompted Matthew to take the leap and commit to the Autoimmune Protocol (AIP).


After a few test runs, we both committed to the AIP long-term in December of 2013. Almost immediately, Matthew moved to an even more restrictive low-FODMAP version of the protocol to reduce his nausea.

The AIP:

  • Improved all of Matthew's other symptoms, including arthritis pain, psoriasis and severe brain fog;
  • Enabled him to get off Methotrexate, a toxic medication that he had been taking for 10 years that caused its own host of nasty side effects;
  • Helped him significantly reduce prescription and non-prescription pain medication; and
  • Caused me to feel younger and more vital than I had in my adult life.

But Matthew's nausea kept getting worse.

He was, of course, poked and prodded and tested by a bunch of doctors, all of whom lost interest as soon they ran out of diagnoses.

Meanwhile, his tolerance for carbohydrates continued to decrease, with even low-FODMAP AIP foods dropping out of his diet because they exacerbated the nausea.

The fact that all of his autoimmune-related symptoms were improving on the AIP, while the nausea continued getting worse suggested to us that that the nausea was not autoimmune in origin. But that was pretty much all we knew.

The Yeast Hypothesis

By the time our Functional Medicine doctor consulted with an expert and brought back the biofilm-protected yeast colony hypothesis in May 2015, the nausea was so severe that Matthew was debilitated.

He could tolerate only two well-cooked carbohydrates (spinach and yellow zucchini) and was avoiding most fat. He had been eating one meal a day for over six months.

His situation was dire and he'd been dropped by everyone he'd sought help from inside the mainstream medical system.

Probably the only reason he was still functioning was the high quality of the food he was able to eat, including daily bone broth and pastured meats.

Biofilms & Yeast

Biofilms are communities of microscopic organisms, like bacteria and yeast, that produce their own protective matrix that makes them highly resistant to eradication.

They basically build their own party bunkers and settle in to breed.

Inside biofilms, yeast can grow roots called hypha, which can puncture the intestinal wall and create intestinal permeability (leaky gut). So no matter how targeted a gut healing protocol is, if the yeast is armored inside biofilms and putting down roots, the gut is still leaky.

Which is still causing systemic inflammation.

Which is exacerbating autoimmune response in the body and brain.

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Take the Assessment

The Treatment

The recommended treatment was a three-month protocol designed to attack the biofilms and eradicate yeast colonization, with supplemental colostrum for gut-healing.

It included:

  1. Biocidin, a plant chemical that erodes biofilms in three forms: drops, nasal spray and pills;
  2. Fluconazole, a pharmaceutical treatment for yeast that needs to monitored with regular bloodwork; and
  3. A bovine colostrum product called GI Restore from NuMedica for gut healing.

Also recommended was an ‘Intestinal Antigenic Permeability Screen’ from Cyrex Laboratories to measure Matthew’s gut permeability before and after the protocol.

I love data, so I was keen include this test, but it was only available in the United States.

Matthew wasn't well enough to travel across the border, and we were really struggling financially. It's a pricey test. As we're pretty good at gathering data in other ways (its kind of our thing), we decided opt out of that part of the protocol.

Fluconazole was readily available by prescription, but the Biocidin and colostrum weren't available in Canada, so it took a number of months before we assembled all the components. Even then, the nasal spray didn't arrive until two months in.

Near the end of August, he started, minus the nasal spray.

The Results

Within a few weeks, Matthew was able to reintroduce some carbohydrates.


Broccoli is amazing when you've been eating only well-cooked spinach and yellow zucchini for months.

Chard. Plantains.

He started slow, but as the months past he realized he was tolerating almost all AIP carbohydrates, including some higher FODMAP ones.

It has taken this long for us to feel confident that he has improved.

He has felt quite unwell since he finished the protocol at the end of November, but that is starting to lift. We expected it may take time for him to recover from the Fluconazole, which is known to cause both nausea and dizziness, but we didn't know how long that might take.

The fact that Mathew is feeling better at a time of year when he usually starting to feel much worse (winter is the hardest time for year for him) is heartening.

If we had done the Intestinal Permeability Screen before he started and after he finished the protocol, we would have had some accurate data about changes in intestinal permeability.

If the treatment was successful, the yeast colonies should be reduced or eradicated, and no longer puncturing the intestinal wall with their hypha. His gut should be less permeable.

Because we don't have that data, we have looked for other indicators.


  • His increased tolerance for carbohydrates and new-found ability to eat fermented vegetables, which is enabling him to reinoculate his gut microbiome.
  • The fact that his brain fog continues to lift.
  • The reduction in nausea. Two months after completing the protocol, it is now 2-6 on a scale of 0-10. At it's worst he rated it a 7-10. Reduced nausea has enabled him to get healthy fats back into his diet.
  • He now sometimes eats two meals a day. We are no longer worried that he is malnourished.
  • He can now cook, and participate in life. We've started making fun AIP meals again, and have been loving The Healing Kitchen cookbook by Alaena Haber and Sarah Ballantyne.

So we're ready to tentatively call the experiment a success.

And we're deeply grateful to Dr Cline for sticking with us.

We'll wait to see what happens as Matthew continues to recover. He's gaining strength now that he can eat a diversity of nutrient-dense foods again.

If the experiment was a success, and the yeast colonies are no longer puncturing his intestinal wall with their hypha, his gut will be able to heal.

What's Next?

Now that he has started to stabilize from this last big experiment, Matthew is testing something new.

A supplement called MitoQ to address the issues he expects he has as a result of being homozygous for the Rs4880 gene mutation. He's trying to keep all of the other variables stable (as much as one can in real life with a chronic illness) to help him discern what effects that supplement might have.

N=1 Reporting

By reporting the results of our experiments, including our successes, failures and new questions, we hope to be able to add to the body of knowledge available to others in the n=1 community.

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