Hypothesis vs Recent Studies

Some 6 years ago, I documented in a blog post a hypothesis that I had been using and felt sufficiently confidence about to commit to paper. I referenced an even earlier more speculative post from 2012.

” My best hypothesis on CFS is currently a stable dysfunctional microbiota (gut flora) that was triggered by an illness, poor diet, vaccination or chemical exposure.  It is good to put this hypothesis to the test against prior successful treatments that resulted in some remissions. I have already looked at this in an earlier post, but thought a revisit on certain aspects would be good. “

Why Jadin’s Antibiotics Protocol usually work — Pasteur Institute got the solution right and the explanation wrong?[2013]

Infection or even a single Phage changes the microbiome

Phages are specific hunters: each type kills just one type of bacteria. So when the scientists introduced a phage to the mice, they would see a decline in that type of bacteria. However, the impact on other bacteria was more surprising…. They found that when they introduced a phage to the mice and the bacterial composition changed, there were also changes in the levels of certain biologically active chemicals.  If phages make sweeping changes to a mouse microbiome, they are likely to make changes in the human microbiome, too. The changes might be different, but the principle remains.

Gut bacteria: The surprising impact of viruses June 14, 2019

The effectiveness of any ME/CFS treatment depends on the microbiome

Some drugs work well for one person but are ineffective for another; some also produce adverse events for certain individuals but not others. A study, using human gut bacteria and a mouse model, investigates whether our gut bacteria might help explain why.

Gut bacteria may help explain why drugs don’t work for everyone June 6, 2019

Original Article: 3 June 2019 in Nature

Bacteria determines the majority of symptoms

For symptoms like IBS, IBD, Crohn’s, this has been obvious for years for gut related symptoms. For a few others:

  • New Study Suggests an Imbalance of Gut Bacteria Might Be Linked to Restless Leg Syndrome June 10, 2019
  • ‘Using those data, they developed a mathematical model that successfully predicted the role of gut bacteria in metabolizing a second antiviral drug and clonazepam, an anti-seizure and anti-anxiety drug. The study found that the gut microbes were responsible for producing 20 to 80 percent of the circulating toxic metabolites derived from the three drugs.” The gut microbiome may be to blame for the toxic side effects some people experience from drugs that help many others, according to new research. 11 Feb 2019
  • My earlier Eureka Post — found strong statistical relationships between many symptoms and bacteria.

Where Science is at and where I have leapt ahead

Science is just starting to accept the wide effect that bacteria has with the latest studies. In traditional scientific caution, it may take another decade before it is well accepted (look at the 30 years that it too for H. Pylori to be accepted as the cause of stomach ulcers).

Over the last six years, I have seen study after study come supporting my seven year old hypothesis. As more information came in, I moved on to accepting it and the logical consequence: we need to have approaches to modify / correct the gut bacteria. Unlike the usual bad bacteria infection, there is often no good or bad bacteria — rather too much of one and too little of another. Add to this that all of the bacteria interacts with each other.

If you go to DataPunk, and look at Dorea genus, you will see a long list of interactions with other bacteria… a very long list. Any change may have worst cascading effects!

Add to this already complex situation, the absence of research on what various drugs do — I recently try researching what the impact was of three different common histamines. I was lucky to find some material on one of them, the other two has unknown impact.

A reader recently shared this post from my long time friend, Cort Johnson


With my hypothesis, such a drug is likely to impact gut bacteria significantly. It turns out that there was a study on it’s impact and I had add it to my microbiome prescription site. Over 30 impacts. Whether it worked or did not work for a ME/CFS suffer would likely depend on their microbiome!

Suggestions are cutting edge science

I have looked at many sites giving diet advice, even those connected with microbiome testing such as Thryve. The quality of the advice is effectively at general dietitian level, or naive using the microbiome (i.e. used a few studies only). The microbiome prescription site uses a database containing the following information:

The relationships are constantly being updated from new studies.

There was an interesting comment on my facebook page, something like “Correcting the microbiome have never been proven to cure any condition!” – absolutely correct, technically. BUT ALSO:

“There have never been a study published that showed that you can correct the microbiome” – In other words, the above comment was polemics.

My own experience (especially with the ongoing flare) is that you can correct the microbiome to some degree (totally normalize is a different question) and as you correct it, symptoms should reduce (as it has for me).

I know of no other resource, free or paid, that provides suggestions based on as many studies, considering as many factors as being produced by the microbiome prescription site. It may not be perfect, but it is probably more effective than the advice most MDs would hand out — which is often “Take a good quality probiotic” — whatever that means!

Bottom Line

After 7 years, trying a hypothesis, I am still using it and applying it. It holds water. It appears to work — but more importantly, it explains things. Using it and addressing some ‘black holes’ like histamines and mast cell issues are ongoing challenges. We are making progress.

“Hypotheses grow out of explaining empirical data.That is basic science.” Empirical data for me was the published reports of responses to various treatments for ME/CFS, as well as studies on the symptoms reported. All on PubMed or in conference reports. Most of the significant ones were published in 1998-2001.

Some more recent paper that echos historic information

The event that triggered my paying notice to the microbiome was during the 2010’s relapse — I could control all of the other symptoms with things like heparin, etc, herbs etc… but I never had GI issues before. As a result, I had filtered out all of the GI information looking at the literature. This event caused me to re-inspect the literature and lead to this hypothesis (after trying multiple others). It was far better at explaining all of the information and data then any other proposed at that time.