ME/CFS Person: 6 mos since last test / not much movement – IMPROVEMENT!!!

Prior Post: Another ME/CFS person has gone to Firmicutes!

This just came in on Dec 4, 2023

I wanted to share some good news with you.  In the last 3 weeks I’ve noticed my time going to the bathroom has decreased in half and my gut has been less irritable.  Over the last 2 weeks, my mood has steadily improved and I’ve enjoyed more energy than usual.  It appears that your guidance has pointed me in the right direction! 

Note:  I didn’t end up performing the FMT.  

I thought about why my Firmicutes would get to 97%+.  It’s most likely because the majority of the foods I eat are continually pushing my gut towards Firmicutes.  And it could also explain why after adding 5+ daily supplements to push my gut the other direction, it hasn’t worked.   You noted that my being a vegetarian may be acting as a significant counter balance to the direction we’re trying to go.

Besides adding a small amount of meat in the morning, I cut out the foods I eat most frequently.  Bananas, raspberries, blueberries, nut bars.  And then I added in the Seaweed you recommended.  I think the seaweed has made a massive difference and with all these changes implemented collectively, the boat has begun to turn around!
I’m hoping this continues


I’m 39 and have suffered from moderate CFS since i was an early teenager.  My major 3 symptoms are low energy, brain fog, and IBS.  My CFS didn’t affect me as much when I was 18, but combined with the effects of aging, I’ve been feeling the fatigue more impactfully the last two years.  

Journey over last 10 months

When I first began working on this in January, my samples showed my Firmicutes at 98%.  That seemed to be the smoking gun as you described it, and I was eager to begin shifting my microbiome.  Over the next 6 weeks I felt markedly better but unfortunately I now believe that was merely a placebo effect.  Once I started to believe the benefits I had received were from a placebo, I rapidly returned to baseline.  Over this time period, I cut out many of the foods that pushed my gut in the wrong direction, and I was taking 4 supplements 2-3x a day.  By my second test 2 mos later, my firmicutes adjusted downwards from 98% to 93%.  In terms of how I felt, it was difficult to assess whether it was better than my baseline.  I was hopeful that it was, but I couldn’t say for sure.

Over the last 6 mos my Firmicutes has reduced from 93% to 89%.  During this time period I continued to cut out foods that were counter-recommended.  I ordered 4 more vitamins & supplements that were in my consensus list, and I was taking 4 supplements 1X/ day, while also rotating the supplements every 4 weeks to prevent resistance.

Once again, it’s difficult to assess now how i feel versus my baseline.  I don’t feel significantly better, that I know.  And while I’m disappointed my sample isn’t improving drastically, the upshot from my perspective is that at least my sample results match how i’ve been feeling.

Reader Addendum After reading

“I’m mostly vegetarian… which may help to explain why after 9 months of supplements I’m partially moving in the wrong direction.  I’ll incorporate the seaweed and increase my red meat.”


We have three samples to compare.

Percentage of Percentiles

We see significant shifts between samples with chi2 values increasing (meaning more abnormal) instead of decreasing. What is interesting is that the two earlier samples does not the typical ME/CFS or Long COVID pattern, but the third sample shifted to the pattern of spikes in the 0-9%ile range. This is open to many interpretations; some good and some concerning.

Evaluation Criteria

The numbers below are mixed, some showing improvement, others showing loss.

Lab Read Quality4.35.98.7
Outside Range from JasonH336
Outside Range from Medivere181820
Outside Range from Metagenomics887
Outside Range from MyBioma9915
Outside Range from Nirvana/CosmosId232324
Outside Range from XenoGene383843
Outside Lab Range (+/- 1.96SD)181510
Outside Box-Plot-Whiskers545356
Outside Kaltoft-Moldrup85125181
Bacteria Reported By Lab431553591
Bacteria Over 90%ile493234
Bacteria Under 10%ile4372174
Shannon Diversity Index2.8522.9372.49
Simpson Diversity Index0.0830.0980.101
Chao1 Index85921180715969
Condition Est. Over 90%ile1172
Kegg Compounds Low8217311190
Kegg Compounds High13425199
Kegg Enzymes Low359204259
Kegg Enzymes High208311243
Kegg Products Low201124170
Kegg Products High130199158
Kegg Substrates Low195114156
Kegg Substrates High149216162

Forecast symptoms

The top 3 forecasted items are below. See this post: Post Exertional Malaise (PEM) with diminished ME/CFS for more information on forecast symptoms in use. The earliest sample had no forecasts being reliable (i.e. > 60% match). What we also see in that the symptom patterns are becoming stronger. Again, this is usually not desired.

  • 2023-01-06
    • 54.3 % match for Neurological-Vision: Blurred Vision on 35 taxa
    • 52.4 % match for General: Headaches on 42 taxa
    • 50 % match for Immune Manifestations: new food sensitivities on 56 taxa
  • 2023-03-29
    • 65.9 % match for Pain: Pain or aching in muscles on 44 taxa
    • 56.2 % match for Immune Manifestations: Diarrhea on 89 taxa
    • 56 % match for Neurocognitive: Brain Fog on 50 taxa
  • 2023-09-12
    • 65.7 % match for Neurocognitive: Difficulty paying attention for a long period of time on 70 taxa
    • 62.3 % match for Neurocognitive: Can only focus on one thing at a time on 53 taxa
    • 61 % match for Neurological-Vision: Blurred Vision on 41 taxa

Impression and Possible Model

This is the first follow up sample where there was neither clear objective or subject improvement. What we see clearly above was that the microbiome has changed. Subjectively, there was no deterioration reported.

Objectively it seems that the microbiome has been de-noised. This person has had ME/CFS for 20+ years and thus the microbiome dysfunction will evolve. His latest sample changed to the typical pattern for ME/CFS for percentage/percentile chart above. The forecasted symptoms values are increasing for what are likely correct forecasts. The bacteria associated with ME/CFS and IBS are showing themselves better and other bacteria causing noise are diminished.

Going Forward

I first looked at the US National Library of Medicine studies for bacteria reported for the conditions he reported.

  • Chronic Fatigue Syndrome   (1 %ile) 9 of 64
  • ME/CFS with IBS   (9 %ile) 4 of 18

Symptom matching on these is a clear miss. I did note some high matches that are typical symtpoms so I add in the results from these selections:

The result was just 84 unique taxa and we have 5 sets of suggestions in our consensus.

So we fall back to the “Just give me suggestions”. The high priority value was 300 and the low priority value was -405. Adding in special studies suggestions moderated the ranges but most items stayed the same.

It looks the a modified Surf And Turf diet, i.e. Steak and Seaweed (our local Costco does sell a nice seaweed salad that is a regular for me)


The avoid values are so high compared to the takes that we need to review them to try reducing or excluding them. The threshold value is -300 (-600/2).

Bottom Line

This has been a challenging set of samples to do an analysis on. I have often used the analogy of going from the port of sickness to the port of health in a sailing ship along a rugged coast. There may be a long series of course corrections needed.

The suggests above are very atypical. Given that there appear to be a lot of noise in his microbiome, we may have some more denoising to do (bring out more the ME/CFS and IBS bacteria into the light). I would advocate attempting to get a course of rifaximin. It has been well used for his IBS diagnosis so there should be little push back from his MD.

Questions and Answers

Q: I’ve read through my new Simplified Suggestions List, and The suggestions of what I need to take and avoid are the same as before…. but the impact score of each was adjusted.  Although you’ve noted in the past that a higher impact doesn’t indicate it works more effectively, it looks from your suggestions that you stick to the highest impact items as there are the most studies to support them, right?

  • Correct. One study may report honey increases a bacteria, and another study report that it decreases the same bacteria. To determine the confidence of a suggestion we look at all reports. If you have 10 honey studies (8 increases and 2 decreases) and one study alone for roasted whale increasing the bacteria; most people will have greater confidence that honey is a better choice to try.

Q: One initial inquiry comes to mind- for complex cases, have you given any additional consideration to (probiotic) enemas as a way to make a big impact, and then to adjust with oral supplements from there?

  • I work from published clinical studies and not from influencers opinion. There is a good summary on WebMD, What to know about probiotic enemas that gives pros and cons.
  • I found Clinical trial: probiotic treatment of acute distal ulcerative colitis with rectally administered Escherichia coli Nissle 1917 (EcN) which had no results (” the number of responders was not significantly higher in the EcN group than in the placebo group”) or results depending on the statistical method used. Thus there is uncertainty about it’s effectiveness.
  • Using commercial/retail probiotics have two significant risks:
    • Very often the declared species is not what is in the bottle, the exception is for those strains that are owned by someone.
    • Often they contain fillers that will be well consumed before they reaches the nether regions. These fillers being inserted here may give a feast to some bacteria that usually do not get much, sparking an unexpected overgrowth.

Q: Below are the supplements I’ve been taking each day.  My plan is to cut out everything that doesn’t have an impact score north of a 150.  Does that sound like a reasonable approach?

  • ground flaxseed.  I took this every day for 4 months and had to stop because it began to make me nauseous. — Try it again at low dosages after one month
  • Luteolin – low positive
  • carboxymethyl cellulosedefinite take
  • Dietary Fiber Cellulose definite take
  • partially Hydrolyzed Guar Gum (SunFiber)remove
  • licorice rootremove
  • Vit B1, B6, B7 — low positive
  • Gaba definite take
  • Vit C remove
  • Melatonin — low positive, suggest you try removing for a week then trying for a week to see if it still help sleep
  • Diosmin – low positive
  • Astragalus – low positive

Answer: The logic is good but I would restrict to only items that are negative. You may wish to revisit the reason that you started each; if it was symptom related and improved — then monitor that symptom and return it if the symptom returns. I have annotated the list above


Suggestions could also be described as influencers. There is no need to get religious about taking everything. Take what you are comfortable with is my usual advice. In this case, the person being a vegetarian may have significantly counter-indicated the other influencers. Once the microbiome is normalize, a return to be a vegetarian is viable.

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.

4 thoughts on “ME/CFS Person: 6 mos since last test / not much movement – IMPROVEMENT!!!

  1. You seem to like the “percentage of percentiles” measurement, but I’m not convinced it’s being analyzed appropriately. As I understand it, you first convert to percentiles, getting numbers in [0, 100]. I think this is fine. Then you histogram these percentiles. Because each lab will perform the same measurements every time, I think this is also fine. However, the result is compositional data in the sense of Aitchison, and it should be analyzed in a manner consistent with that. For compositional data, a chi^2 test is inappropriate because it relies on the number of species (or genera) measured.

    My suggestion is to apply a centered logratio transform to each person’s percentages and fit a normal distribution to the transformed data. To determine whether someone’s microbiome deviates significantly, calculate a multivariate normal tail probability. Beware that the covariance matrix will be rank deficient (you’re in a ten-dimensional space, but there are only nine parameters because percentages sum to 100). You may want a robust fit because it’s reasonable to expect that the microbiome of someone ill might be an outlier.

    For more information about compositional data, see Aitchison, J., “The Statistical Analysis of Compositional Data,” Journal of the Royal Statistical Society. Series B (Methodological) Vol. 44, No. 2 (1982), pp. 139-177; Aitchison, J., “The Statistical Analysis of Compositional Data,” Chapman & Hall, London, 1986; and Aitchison, J. “A Concise Guide to Compositional Data Analysis,” unpublished manuscript, 2005, available online (just Google). For other approaches to compositional data analysis, see Greenacre, Michael; Grunsky, Eric; Bacon-Shone, John; Erb, Ionas; Quinn, Thomas, “Aitchison’s Compositional Data Analysis 40 Years On: A Reappraisal,” arXiv:2201.05197, 13 Jan 2022, to appear in Statistical Science.

    1. Many thanks. I will review the article in the coming weeks. I may need to increase the intervals so that the expected numbers are higher.

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