Biohacking Update (& a New Hypothesis)

Biohacking updateMatthew has been on the Autoimmune Protocol (AIP) for 18 months.

17 of those have been low-FODMAP.

For the last 2 months, he’s been doing the most extreme low-FODMAP AIP variation yet: a gut-healing protocol outlined by Aglaée Jacob in her book Digestive health with Real Food.

The only carbohydrates he’s been eating for the past 9 weeks are carrots and spinach. And he drinks gallons of bone broth~.

The Results

This is the reporting part of the Scientific Method.

  • Nausea: As I mentioned in my post Dietary Treatment for SIBO, after 9 days on this new Protocol, Matthew’s unexplained and debilitating nausea went from a 7-10 on a scale of 0-10 to a 4-6. And stayed there. Two months later, his nausea is still in the 4-6 range. This reduction has enabled him to participate in life, including cooking for himself (and me), engaging in moderate exercise, and doing things around the house. But the nausea has plateaued at the 4-6 level and that is barely tolerable much of the time.
  • Brain Fog: Over the past 2 months his brain fog lifted further. He’s winning at scrabble again. For the first time in years.

A New Hypothesis

Our Functional Medicine Doctor, Dr Cline, was as perplexed as everyone else about Matthew but (unlike everyone else) he didn’t give up.

Dr Kline talked to several colleagues and has a new hypothesis: yeast colonies protected by biofilms in the gut.


Biofilms are communities of microscopic organisms, such as bacteria and yeast, that produce their own protective matrix.

Organisms inside a biofilm are highly resistant to eradication attempts and, it seems, are also capable of complex, coordinated behaviour like quorum sensing.

The hypothesis that Matthew is colonized by biofilm-protected yeast colonies in his gut comes from a re-analysis of the results of a comprehensive stool analysis that Dr Kline ordered last year.

As Matthew had been on a low-FODMAP AIP for quite some time when that test was conducted, his results were better than any Dr Kline had ever seen.

Apparently, he should have been feeling great!

But he wasn’t.

The trace amounts of yeast in each of the three tests didn’t seem consequential at the time. But the specialist Dr Kline consulted with, Dr Tom O’Bryan, thought they were. Quite.

Vratislav Šťovíček, Libuše Váchová and Zdena Palková explain: “Pathogenic yeasts can colonise various surfaces within the human body, including host tissues… and form biofilms that resist otherwise effective drug therapy. Biofilms are thus very difficult to eliminate and serve as a source of serious systemic infections.”

Apparently yeast can grow roots, called hypha, which can puncture the intestinal wall and thereby create intestinal permeability (leaky gut). So even though Matthew has been on increasingly restrictive gut healing protocol for a year & a half, if the yeast is armored inside biofilms and putting down roots, his gut is still leaky.

It makes sense~.

A New Protocol

Dr O’Bryan has recommended a 3-month protocol designed to attack the biofilms and eradicate yeast colonization, with supplemental colostrum for gut-healing.

Biohacking modes: Reporting, Current biohacking modes: Reporting, hypothesizing & designing a new experiment~

Current biohacking modes: reporting, hypothesizing & designing a new experiment~

He has also recommended an ‘Intestinal Antigenic Permeability Screen’ from Cyrex Laboratories to measure Matthew’s gut permeability before and after the protocol. That will enable us to get a baseline and then measure any improvement.

Dr Kline has suggested that we may want to consider a fecal microbiota transplant at the Taymount Clinic in England after that, to repopulate Matthew’s micobiome. Maybe even as soon as this winter.

We might have sell our house to finance that, but hey~.

If I want to go on losing at scrabble for the rest of my life, that might just be what we have to do…

16 thoughts on “Biohacking Update (& a New Hypothesis)

  1. Before you sell your home, Petra, I wonder if Dr O’Bryan referred you to Dr Jack Tips? He is an expert on gut health and biofilms. They have both greatly contributed as experts on Christa Orecchia’s online program, Gut Thrive in 5.

    You may consult directly with Dr Tips at Wellness Wiz. He is based in Audtin, Texas.

  2. What a breakthrough and excellent find!! What plan does the new 3 month protocol consist of? Wishing you guys expedient healing.

    • The protocol consists of: 1.) Biocidin, a plant chemical that erodes biofilms; 2.) Fluconazole, a 3-month pharmaceutical treatment for yeast that needs to monitored with regular bloodwork as it is very strong; and 3.) A bovine colostrum product called GI Restore from NuMedica for gut healing. We are still waiting for all of these to arrive in Canada from the States, as none of them are available here. And the ‘Intestinal Antigenic Permeability Screen’ from Cyrex Laboratories to measure gut permeability before and after the protocol.

  3. I hope Dr O’Bryan’s plan helps your hubby feel better. I too am interested to know what his biofilm protocol is.

  4. I wondered if you’ve heard about SIFO? If you look up small intestinal fungal overgrowth there are interesting articles. One on mentions nausea as present in SIFO… I’m on a similar quest with my husband. Having Dr. O’Bryan in your corner should be huge!

  5. Good luck. I really hope you find a cure. I had serious morning sickness-i.e. hyperemesis, worse with each of my kids…six months of it with the third, so I can sympathize even if I can’t imagine *years* of incapacitating nausea. Anyway, fingers are crossed for healing Matthew!

  6. Petra I am wondering if you have come across “the Gut Health” protocol? It is highly researched and there is an associated Facebook group of committed core members led by John Herron who put the protocol through many rounds of testing and has recently released it as a self published kindle book. There is an extensive section on SIFO and SIBO and associated bio films with enzymatic approaches to getting rid of them. I think you would enjoy reading it with your background. And best of luck

  7. Petra – I have all my digits double crossed that this new Dr O’Bryan-sanctioned protocol is the answer for Matthew. Fingers and toes crossed (x2), my friend.

  8. I also recommend the “Gut Health Protocol”, as does Cheryl. Working on my own Biofilms, using Interfase Plus supplement. Keep doing what you are doing, you are helping so many of us. THANKS!

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