Repeat IBS + Vaccine + COVID

This is a follow up to the January 2022 post, IBS + BioNTech COVID Vaccine -> ME/CFS? For discussion on vaccination changing the microbiome see that post (ANY thing that changes the microbiome has a risk of cascading into ME/CFS — an innocent kiss could result in result in the kissing disease( Infectious mononucleosis) which is usually Epstein-Barr virus and well associated with ME/CFS!).

[Revised: Jul 27th,2023 There was a mix up on the sample for some analysis]

The Request

One biomesight test failed and then I got Covid again, so I had to wait.

There are some improvements since last time: I can listen to music again. I can play cards with my brother a little bit in the night when it’s quiet. I was also able to breathe freely again while doing most things, but in January I had an exhausting doctors appointment and some improvements were lost.

A few specific questions:

  •  Are the “mold bacteria” you mentioned last time still a problem?
  • Have there been any important/significant new treatments or scientific findings recently that you are aware of that would help me with my issue (CFS from biontech vaccination)?

Things I am taking continuously right now: Magnesium malate, Coenzyme Q10, Acetyl-L-carnitine, Vit. D+K2, Piracetam.


“In one study researchers were able to classify 83% of the ME/CFS patients correctly based on their dysbiosis in gut and increased inflammatory markers in blood as a consequence of microbial translocation” 

Reduced Diversity and Altered Composition of the Gut Microbiome in Individuals With Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. Microbiome [2016]

We have three samples, the first one was at the start (and used in the above post). I mentioned in the earlier post that he had not had the symptoms long enough to be deemed ME/CFS. The table below seems to show that the typical ME/CFS and Long COVID pattern is not an immediate result but is cascaded into over time. The pattern of over representation of the percentage in the 0-9 percentile showed up in subsequent samples. We see agreement with his subjective opinion of improvement and then loss of progress in the numbers below.

Nov 2021Nov 2021May 2022May 2022Jun 2023Jun 2023
0 – 9111056814354
20 – 29121315211711
30 – 3916191211818
40 – 499132117913
50 – 59192415261414
60 – 69131915171719
70 – 79232012211111
80 – 89141814161212
90 – 991212912514
Shannon Diversity Index79%ile83%ile42%ile
Jason Hawrelak96%ile95%ile56%ile
COVID %ile83%ile71%ile83%ile

The “mold bacteria” is a reference to Prevotella. This often grows excessively when there is mold or fungi. His latest sample had a low percentile, so unlikely to be an issue. 

Going Forward

Doing “Just Give Me Suggestions” executes the following four individual approaches:

On the simplified summary (intended for those with severe cognitive impairment) there is a button that takes you to the full details (the consensus report)

This gives a list of 1800+ different items that were evaluated. I am not a medical professional and do not have clinical experience. My choices from this tend to arbitrary but with the following guidance:

  • To take items should be at least 50% of the highest value (in this case, 553 /2 =277)
  • To Avoid items should be below 50% of the lowest value (in this case, -541/2 = – 270)
  • If the person has ME/CFS or Long COVID, and I know from reading the literature that studies found that it helps people, I will tend to pick those items
  • In general, I will not suggest prescription items because most patients will be stonewalled by their MDs on doing prescription items off label. If I do (because the patient reported having a cooperative MD), I will tend to keep to items documented to help ME/CFS patients.

I then checked what is he taking against the results:

So handpicking from the suggestions (with value):

Because the reader is in the “Land of Mutaflor” (Germany), I checked that explicitly in two ways:

  • Using KEGG Data — it was the top probiotic (but the value was lower than usual)
  • Using Consensus Data — it was very slightly positive (0.3).

So it does no apparent harm (except on pocket book), and I would consider trying it after the above bifidobacterium because low E.Coli has been reported in studies (16s does not provide data).

Checking KEGG suggested supplements against the consensus, we have the following in agreement:

  • Arginine, Consensus:40
  • Leucine, Consensus: 85
  • Vitamin B1 Thiamine, Consensus: 201
  • Vitamin B2(Riboflavin), Consensus: 32
  • Vitamin B7 biotin, Consensus: 184
  • Glutamine, Consensus: 158
  • Histidine, Consensus: 31

Remember we are dealing “fuzzy data on sparse data” and use the consensus approach to improve odds of picking things that will actually do positive changes. By comparing KEGG identification of metabolites that appear to be at low level (and thus starving some bacteria) with the same items that will improve the bacteria balance, we add another layer to consensus building for suggestions. One more layer is taking substances shown to help ME/CFS which are not in our database. He appears to be making use of my CfsRemission site for that purpose. Consensus and layered is the most likely to produce good results.


This person reports a friendly medical professional. So:

I would do the first one only. I have a pending post with a video with Cecile Jadin which may be helpful.

To Avoid

This is usually selecting items that are likely to be taken by some. If it is below -270, it should be consider to reduce of eliminate. We have a long list, my arbitrary selections are:

Questions and Answers

  • Q: “Vit D is negative”: My vitamin D is in fact over 150 nmol/l already should I stop?
    • A: Yes. If a value is negative it is likely that taking it will be shifting things in the wrong direction.
  • Q: “Grapefruit daily”: I quickly develop food intolerances. Would every 3 days be reasonable?
    • A: Start with every 3 days, if issues arise, try the supplements. Remember these are just suggestions to be considered and may need to be filtered by your tolerance and costs. This applies to your next question too “The same problem for the herbs: Would every 3 days be enough? Also can I just add multiple herbs to my food or are these also “One thing at a time, no juggling”?
  • Q: This might be a dumb question: Is the suggestion all three bifidobacterium in a row, or just pick one of them and then Mutaflor?
    • A: There are never dumb questions. The sequence is arbitrary. Proceed as you feel comfortable. Bifidobacteria is likely to have a greater effect.
  • Q: B Vitamins and Amino acids: Also one thing at a time? I know I’m asking this question again, but I am really unsure because if I do all the suggestions in a row it seems it might take like a year..
    • A: Do them all at once or in groups. The reason for doing things in rotation are for items that bacteria are likely to adapt to (i.e. bacteria resistance). These items are typically probiotics (which produce natural antibiotics), antibiotics and a herbs/spices with significant antibiotic like effects. These are not such items.
  • Q: My mom suggested me N-Acetyl-L-Cysteine which helped her a lot, and I want to look that up.
    • A: It is there, N-Acetyl Cysteine (NAC), with a solid positive value (247).
    • Feel free to inspect that list and create your own set of suggestions. These are suggestions only based on your microbiome and computation. For ME/CFS, I try to highlight items seen to have positive effects in studied. You may wish to search CFSRemission for literature on items you decide to try.

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 can compute items to take, those computations do not provide information on rotations etc.

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.

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