Flare Report #5

This is part of the ongoing tracking of the flare or loss of remission from myalgic encephalomyelitis through microbiome studies. You may view my prior reports below:

I have added a lot to the site and analysis over the last month — so this will be a very long post.

First Symptom Prediction – almost 100% accurate

The artificial intelligence agent that does prediction continues to astound me for it’s general accuracy. The results of the latest microbiome uploaded is below:

#1 is reasonably correct, I live with two of them (excluding myself) — and #3 comes in because both have histamine and mast cell issues… Does this mean no more snogging with the wife?. #2 and #4 (confirmed by conventional lab tests) are definites, as are 5,7,8,9 (been known for 30 years), 11,12,13,14,15. The only possible miss is #6. So 14/15 for correctness (for AI that is awesome).

Some symptoms missed that it got right on earlier samples:

For Data Science Nerds out there, there are 161 1-tuple symptoms (covering 77 symptoms) . That is, some symptoms are associated with different shifts in different bacteria — but still the same symptoms.

Why is this important?

If we can predict symptoms accurately from bacteria, this implies (does not prove) that the bacteria are causing the symptoms. This implies if we shift the amount of the bacteria we may reduce symptoms. Getting a high success rate on predicted symptoms (in spike of some nasty issues with having good samples) means that not only is this viable — but that the method being used is reliable and not vaporwear or speculation.

I have gotten rid of symptoms by following the suggestions

If you read the prior reports, I have a lot less symptoms now. I have been following the suggestions determined by the same artificial intelligence process. It appears to be working.

Back to MY Symptoms

The physical fatigue is massive after any activity. I would not attempt to walk to the local bus stop — or even down and back on our long driveway. If I am in town, I figure that I am good for about three city blocks. Symptoms when I push things include massive sweats, hiccups, clumsiness etc.

On the bright side, there were no neurological symptoms like brain fog predicted — and as you can see by recent enhancements and these posts. There is no sign of cognitive issues — purely physical issue. For someone in information processing — that means working remotely is viable. Doing a commute into the city for work is not. “If it ain’t in my Zipcode, it is too far!”

Key Bacteria Shifts

I have covered Lactobacillus and Bifidobacterium in my post on Seed Probiotics failing to persist. I will switch to selective charts for this section:

I have zero of Akkermansia muciniphila (35.27% of Samples) just other species
High levels are associated with super athletes and it converts lactic acid into fuel for the body. … I have almost zero
Lactobacillus collapsed and making some comeback
Bifidobacterium went from median levels to zero and still has not returned
Betaproteobacteria attempted to rally and then collapsed.
Sutterellaceae (family) followed a similar pattern
Actinobacteria class (class) also collapsed

Faecalibacterium boosts the immune system. It’s collapse result in increased risk of multiple conditions.
Candidatus Soleaferrea went sky high while on Seed Probiotics.

Some Ubiome Charts

Anti-inflammatory Microbes

Butyrate producing microbes are starting to recover, quite a distance to go
Polyamine producing microbes are back to prior range
Propionate producing microbes are moving upwards (traditionally I have been high for this one). So some distance to go still
Serotonin has made a good recovery, but GABA is way below my past levels

Incidental Charts

Diversity did not change — there was a shift in the population.

Firmicutes/Bacteroidetes Ratio

This is a ratio that is often cited in research articles — I view it as a hang over from pre-16s data when measuring bacteria was much harder. I did a post on this ages ago and have largely ignored it due to a statistical gut feeling that it was not very useful. I decided to look at these numbers manually and perhaps automate a chart or report in coming days.

Bottom 95% of samples — remaining values were huge

From this chart, I computed the percentile for each measure and got the chart below for my samples.

Dramatic Changes with onset, reversed and perhaps, overcorrected


When I added the probiotic mixture feature to the site, I saw that Seed was a bad choice. I took a sample (the one above) and sent the ubiome sample off. The next day I stopped taking it because if was NOT on my recommended probiotics list for my specific microbiome.

The ones on the list FOR ME are shown below. I find that I must remind people that this is specific suggestion for MY MICROBIOME results — your list may be very different.

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I also added AOR / Probiotic-3: the best of the Mixed list with a net value of 3.0

Where as Seed was negative

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What happened when I changed probiotics?

I was definitely willing to change because symptom improvement had stopped. The main symptom was having a 15-20 minute window of even mild physical activity before severe fatigue sets in.

Switching to the above probiotics, a lot of changes within 48 hours:

  • Sore throat (same as when I started with Barley porridge) – my body is fighting something
  • Niacin flushes whenever I take some (suggesting that vascular constriction is happening from toxins released by dying bacteria)
  • Night sweats stopped. Running hot at night but without sweats.
  • Nose started running, sneezing
  • Groggy feeling starting about 1 hr after taking them and lasting for 2-3 hours. Reminds me of an antibiotic herx.

You will have to wait until the next installment for the microbiome changes.

Recently added Bed Time Oral Probiotics based on this post about ME/CFS oral bacteria being different than controls. Two of those in the list and on hand, were pressed capsules so I could just let them dissolve solely in the mouth:

With both, I slept hard and had night sweats when I took them (but none if I did not). This has been reported also by another reader.

What is next?

There were a few significant changes on the suggestions from this sample, so I will do those for 7-10 days and then take another sample. Each sample results in a change of course, especially when additional data has been added to the artificial intelligence database.

I am not happy with the very limited physical activity. My three dogs are even more unhappy — they have not had any of their customary weekend walks in the Cascades for months.

Maurice, Winston, Angie