ME/CFS Patient – First Microbiome Sample

The Ask

I’ve been reading the site for a few years now and respect and appreciate your work very much! Today I received results from my first test with Biomesight and have uploaded to, however I’m struggling to know where to go from here.

It looks like I have high F. prausnitzii which goes against some of the CFS research. I can also see zero E. coli (I think) and low bifidobacteria/lactobacillus, but not sure there are strep/staph/klebsiella/other pathogens which I was expecting to see, owing to my issues with histamine/bloating, am I correct?

I’m reluctant to go ahead with taking herbal antimicrobials as I’m not sure exactly what I should be trying to kill off. The suggestions that come up mostly seem to be fibres/prebiotics which I haven’t typically responded well to in the past (worsened bloating and oily skin).

My backstory:

My issues started with the persistent abdominal bloating and sneezing/nasal congestion about 5 years ago. The bloating never goes away, and now I’ve progressed into a state of moderate but unrelenting fatigue, muscle pain and inflammatory issues (dry eyes, etc.), made worse by COVID and then the Pfizer jab last year which pushed my ’steady state’ in terms of energy to a lower level than it ever has been. I know that the root cause of this all is my gut. For example, I can eat regular yoghurt and the next day I will wake up with a back ache, 50% more tiredness and very sneezy. I did test positive for SIBO around 3 years ago but multiple rounds of rifaximin did nothing to help, neither did herbal antimicrobials. The bloating seems to be inflammatory/mast cell related rather than actual gas.


  • – Crushing fatigue/muscle weakness/PEM (do not have a CFS diagnosis but the symptoms fit)
  • – General inflammation/muscle pain
  • – Freezing cold hands/feet all the time
  • – Sneezing/nasal congestion/itchy throat especially after histamine containing foods
  • – Persistant abdominal bloating which never goes away 
  • – Brain fog
  • – Acne/very oily skin
  • – Dry eyes

For other analysis of the microbiome of people with ME/CFS, see this index.

First Questions Researched

Low Faecalibacterium prausnitzii is seen in several studies for ME/CFS. This person’s level is at a huge 23.7% of the microbiome — the 93%ile. However, for ME/CFS sibling (Long COVID) we have two studies reporting high levels for Long COVID (with 4 reporting Low) and three for COVID being high and one being low. In other words — atypical levels are to be expected. Note that he had COVID and then the Pfizer jab – so Long COVID is likely a better diagnosis than ME/CFS (at this point). The two tend to merge over time.

Usual Analysis Approach

The percentile x percentage breakdown shows the typical pattern for ME/CFS and Long COVID: Over representation on the low percentiles and under representation of the high percentiles.

0 – 92122
10 – 192225
20 – 291822
30 – 391718
40 – 49919
50 – 591623
60 – 691214
70 – 791016
80 – 8997
90 – 9959

The likely causes suggested are: Faecalibacterium prausnitzii, Phocaeicola coprocola and Bacteroides stercoris. The top one was already flagged by the reader.

Going over to Dr. Jason Hawrelak Recommendations, we see a lot out of range.

TaxonomyRankLowHighYour ValueStatus
Bacteroidiaclass03537.029Not Ideal
Akkermansiagenus130.003Not Ideal
Bacteroidesgenus02033.827Not Ideal
Bifidobacteriumgenus2.550.349Not Ideal
Blautiagenus5104.049Not Ideal
Lactobacillusgenus0.0110.002Not Ideal
Methanobrevibactergenus0.00010.020Not Ideal
Roseburiagenus5102.658Not Ideal
Bilophila wadsworthiaspecies00.250.265Not Ideal
Escherichia colispecies00.010Ideal
Faecalibacterium prausnitziispecies101523.71Not Ideal
Overall Percentile Ranking56.5% 

Looking at PubMed matches we see that he is somewhere between these two siblings

  • Long COVID   (45 %ile) 10 of 204
  • COVID-19   (18 %ile) 3 of 118
  • Chronic Fatigue Syndrome   (66 %ile) 4 of 64

Going Forward

He wrote “For example, I can eat regular yoghurt and the next day I will wake up with a back ache, 50% more tiredness and very sneezy. ” Most yogurt contains large amount lactobacillus acidophilus (probiotics) which is high on his to avoid list. In general lactobacillus should be avoided with brain fog because many species produces d-lactic acid (See my 2019 post Reminder of D-Lactic acidosis and ME/CFS – which contains the name of bacteria that may contribute to the issue). If you cannot find a yogurt free of these bacteria, you may wish to give yogurt up. I would suggest the following probiotics as likely being good choices:

He wrote ” multiple rounds of rifaximin did nothing to help, neither did herbal antimicrobials.” Well, that antibiotic is a negative, and like the lactobacillus yogurt above is likely to contribute to the microbiome issues. He did not specify the herbs that he tried.

-75.8rifaximin (antibiotic)s

Typical herbs used for SIBO [Src] are below. Having no results (or negative results) is not surprising.

  • Allicin – positive
  • Oregano – positive
  • Neem – negative
  • Berberine –  negative
  • Peppermint – negative

The top herbs suggested

He wrote “The suggestions that come up mostly seem to be fibres/prebiotics which I haven’t typically responded well to in the past (worsened bloating and oily skin).’ We see that almost all of the prebiotics are below 100 priority (item #170), so they would not make it into my preferred list (I prefer to keep to the to 100 or less). 25% of these are actually below a -200 priority. We also see low fiber diet is high priority. So his experience and the computations are in agreement

Other Items

In terms of common antibiotics for ME/CFS, near the top we see metronidazole (see this 2017 post) and erythromycin (See Azithromycin in Chronic Fatigue Syndrome (CFS), an analysis of clinical data [2006], where 58% improved). If you can persuade your MD to prescribe.

Supplements of note: Taxifolin (See 2021 post dealing with histamine), glutamine (The Role of Glutamine in the Aetiology of the Chronic Fatigue Syndrome [2011] ). Nothing in the flavonoids, polyphenols list stand out. In terms of prefer sugars: chitosan,(sugar),sucralose, raffinose(sugar beet) – most sugars are marginal or negatives. In terms of Vitamins: Iron and magnesium.

Bottom Line

In my years of reviewing literature on ME/CFS, the typical results are similar to the Azithromycin study above: it works for X% of the people and has no or negative effect for the rest. It is my hypothesis/belief that the microbiome determines if a substance works or not.

Above, you see my preferred approach — look at the top 5-10% of suggestions and then cross reference the literature to see which are known to help some. The alternative of working from studies (without reviewing the microbiome) has failed to produce consistent positive results over the decades that it has been tried. The other key item is to look at the bottom 20% of suggestions and eliminate as many of them that you can.

For “Just give me suggestions”, I prefer the priority to be over 150 if possible for takes, and below 0 for avoids.

Remember this is a multiple path journey. Keep on the suggestions for 6-12 weeks and then retest. The suggestions may shift a bit with each course correction.

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.

2 thoughts on “ME/CFS Patient – First Microbiome Sample

  1. Yes I am in similar situation, I sent my microbiome tests to you a long while back. I too have prausnitzi at 23 percent, along with methane, same symptoms which is unusual for chronic fatigue.

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