2 year follow up: ME/CFS back to work

This is a follow up to this analysis ME/CFS after trying suggestions from Dr.A.I. from 2 years ago. The goal of MicrobiomePrescription is not to cure any condition — rather to generate suggestions that have a high probability of mitigate a person’s symptoms. Mitigate means reduce severity or eliminate. With some condition, it could result in a technical remission (i.e. no longer matches a diagnostic criteria). The term remission and not cure should be used always — because the microbiome could return to a dark place due to future events or inadequate ongoing care.

Update Story

I’ve been doing MUCH better for the last two years. I feel nowhere near the “normal” levels of energy that a 36 years old man should have and a lot of things are difficult, but I’ve been better and I’m able to work full time as a web developer, remotely. I know live with my significant other, and working + living with someone takes absolutely all of my energy, so I usually have no resources left to meet friends or do extra activities, but the fact of being able to work full time is a huge improvement compared to two years ago. Most of the brain fog has lifted. It comes back on my bad days, but it’s really not as bad as it used to be

I feel that my energy levels are going worse these days and it’s getting harder to work full time though. That’s why I’ve done another microbiome analysis, and it seems to be even “worse” than 2 years ago, according to Biomesight’s score. 

I still have trouble digesting things (even though it’s been a bit better the last two years, it has never been “normal” I think) and get diarrhea quite often. I usually have to go to the toilets 5-6 times a day. I’m still very skinny.

I take much less dietary supplements than I used to, but I’m still taking :

  • Acetyl L-Carnitine
  • Ubiquinole
  • R Lipoic Acid
  • B12
  • Vitamin D
  • Nattokinase

I’ve also done another round of “Spezzata”[Licorice] recently, but it definitely makes my blood pressure go up. I also eat a lot of dark chocolate and drink a lot of coffee.

My diet has changed a bit since I’ve started living with my Significant Other about a year ago. I eat a lot more rice than I used to now.


The first thing that I noticed was the lab quality is down a lot. Lower quality means less bacteria types (793 dropped to 334) are identify and the estimated costs have greater uncertainty. On the plus side, all measures are the same or are significantly better.

CriteriaCurrent Sample
Old Sample
Lab Read Quality25.4
Lab Quality Adjustment Percentage85.9100
Outside Range from GanzImmun Diagostics1919
Outside Range from Lab Teletest2525
Outside Range from Medivere1515
Outside Range from Metagenomics99
Outside Range from Microba Co-Biome66
Outside Range from MyBioma88
Outside Range from Nirvana/CosmosId2121
Outside Range from Thorne (20/80%ile)327327
Outside Range from XenoGene4141
Outside Lab Range (+/- 1.96SD)710
Outside Box-Plot-Whiskers43118
Outside Kaltoft-Moldrup2468
Bacteria Reported By Lab334793
Bacteria Over 90%ile099
Bacteria Under 10%ile031
Lab: BiomeSight
Condition Est. Over 90%ile03
Standard Items

Looking at new features added. Note that the drop in number of bacteria reported impacts many of these values)

“Leaked” from Oral Cavity [LOW is better]21.1%ile65.7%ile
General Health Predictors [More is better]617
Jason Hawrelak Ratio 10%ile14%ile
Potential Medical Conditions Detected03
Bacteria deemed Unhealthy031

The charts show similar patterns but with a group of bacteria dominating (80-90%ile) range

Conclusion: He is better than 2022 in many measures but is worse in a few (especially newer ones).

Let us look at some recent feature additions. First key bacteria — we see improvement we a lot of key bacteria dropping down below the threshold. (see Technical Note: Identifying Key Bacteria to Address for background)

“Leaked” from Oral Cavity is based on this study Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes, 2024. As with above, we see improvement.

  • 2024: 21.1 Percentile.
  • 2022: 65.7 Percentile

Going Forward

As usual, I start with “Just give me Suggestions include Symptoms” with the new refactored algorithm (see Algorithm for “Just Give Me Suggestions”). The items were similar but with just a change of order.

First, let us look at what is currently being take. Microbiome changes over time. The highest for non-prescription items is 327 and lowest -516.

  • Acetyl L-Carnitine: 152
  • Ubiquinole: AKA COq 10, Not on current suggestions
  • R Lipoic Acid: Not on current suggestions
  • B12: 82
  • Vitamin D: -152
  • Nattokinase: looking at bacillus subtilis natto -39
  • Spezzata [glycyrrhizic acid (licorice)]: -42
  • chocolate : 11.5
  • coffee/ Trigonelline (found in Coffee): 152

None of the above is clearly a bad choice. The worst, vitamin D tend to be a slow acting supplement. This illustrates that doing a retest every 6 months to reset your course to recovery is likely good practice.

Some observations on suggestions:


Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.