ME/CFS + 3 times COVID + food poisoning

This is part of a continuing series of analysis for ME/CFS or/and Long COVID.


I am contacting you as you may provide a microbiome analysis for you has cfs – long Covid 19.
I have been struggling for years with cfs-me. I also have Covid 3 times (the last one was in December 2023). When I did the test, I just had few days before a food poisoning that led me to ER.
I did a GI map last year because I wanted to have more information after failing to cure a methane SIBO with herbs. I have a very bad infection (enterohemorrhagic e choli).
I was suggested by the functional doctor whom I ordered the test some thyme and probiotics but obviously it had no impact. I redid a stool test (biomesight) but I am really overwhelmed by the results.

Would you mind give me some insight on those tests ?

  • joint pain, neck pain, TMJ, migraines
  • hypothyroidy, insulin resistance, low cortisol,
  • possibly Lyme (low nk57 but negative test)
  • possibly mold intoxication 
  • heavy metal intoxication 
  • brain fog
  • Attention-Deficit/Hyperactivity Disorder (ADHD)
  • skin issues on the face and eczema on my hand 


We have some dysbiosis (i.e. Eubiosis is not 100).

Looking at reported symptoms, we see a number of matches to reported symptoms over 16%ile, with one of the unchecked,  inability to focus eye/vision , being a potential missed item. There are 67 symptoms entered with 58 of them above 16% (the threshold)

Explaining the new Algorithm

This algorithm is similar to the Eubiosis algorithm. We compute the expected number of matches to bacteria shifts associated with the symptoms. The expected number by randomness is 16%. A higher number indicate increased odds, a lower number decreased odds. This is based on the existing annotated samples uploaded. It is not definitive and often there can be multiple subsets of bacteria associated with a symptom. The match is on too much or too few of a collection of bacteria

Looking at Health Indicators

  • General Health Predictors: 11 items, with Veillonella atypica being the greatest concern
  • Potential Medical Conditions Detected: None. I double checked, and there were no significant matches.
  • Dr. Jason Hawrelak Recommendations: 94%ile

Going Forward

Doing just give me suggestion with symptoms gives the following suggestions for items to add (50% of 516 or hgh

The Avoid List

The lowest value was -550, so items below -275 should be the highest priority.

Comparing to Suggestions from GIMAP

The data transcribed is below. Our consensus report above picked 67 bacteria of concern

As expected (See this post) there was agreement and disagreements between these reports on what is high or low, and some agreements. For example,  Faecalibacterium prausnitzii was at the 81%ile on Biomesight data and very low above.

Suggestions will always be different because of the much smaller set of bacteria being used. We do note the following agreement in suggestions:

Many suggestions are not found at all in the GIMap suggestions because there is no literature for those substances and the bacteria reported.

Questions and Answers

Q: Would you have any specific recommendations about enterohemorrhagic e coli (ehec) ?

Q: Another question about the antibiotics protocol for me/cfs (in case I succeed to convince my GP). Dr Jardin suggests : 1 week on with one antibiotics then 3 weeks off, then another cycle with another antibiotics. Is it right ? 

  • Correct for Jadin.  One week on and 3 weeks off… and then change antibiotics.  This comes from old clinical experience at the Pasteur Institute.  I have read studies dealing with sewage plants that found this pattern works better.

Q: On your blog, it also says to pick one of the 4 suggestions of supplements and switch every week during 8 weeks and retest. Does it mean I must choose 4 supplements, take 1 supplement during 1 week then switch to another 8 times and so on. Am I right ? (I am not English fluent so I struggle a little to understand everything)

  • 4 SETS of supplements…. so each week you change sets.  This again is suggested to prevent dysbiosis adapting. I have too often heard “It works for 3 months and then stopped working” . As an analogy, think of cops setting up cameras to stop people speeding, their existence improves traffic — but once people learn that they are always at the same place … bad behavior returns.

Q: Last question : could symbioflor1 help for my enterrococcus faecalis overgrowth? Or is it the opposite?

  • There is nothing that I could find for  symbioflor1 impact on enterrococcus faecalis overgrowth in the 13 studies I have processed. So we are again into the “fuzzy knowledge area”, in general (especially the EU), probiotics are not troubles strains and thus can be used to shift related bacteria.
  • From, we see that it is hard to treat. BUT Curcumin is better than 2 antibiotics tested.

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.