A follow up ME/CFS Analysis

This is a follow up on the prior post below. The reader’s comments are “I am feeling much better but still very fatigued and lately been quite achey.  The recommendations have changed significantly except for whole grain barley.”

For more analysis see: Analysis Posts on Long COVID and ME/CFS

Comparison of Samples

Let us first do the simple numbers. A lot of values are the same (typical) but many of them show improvement. πŸ˜ƒ indicate significant reduction is out of range values See Technical Note: Lab Quality Versus Bacteria Reported We would expect a 15% drop from lower lab quality, the drops shown are well below that).

CriteriaCurrent SampleOld Sample
Eubiosis Index62.8%πŸ˜ƒ59%
Lab Read Quality4.38.4
Outside Range from JasonH88
Outside Range from Medivere2020
Outside Range from Metagenomics1010
Outside Range from MyBioma88
Outside Range from Nirvana/CosmosId1818
Outside Range from XenoGene4242
Outside Lab Range (+/- 1.96SD)9πŸ˜ƒ16
Outside Box-Plot-Whiskers38πŸ˜ƒ98
Outside Kaltoft-Moldrup56πŸ˜ƒ139
Bacteria Reported By Lab494752
Bacteria Over 90%ile20πŸ˜ƒ82
Bacteria Under 10%ile66πŸ˜ƒ232
Shannon Diversity Index1.4651.701
Simpson Diversity Index0.0350.028
Chao1 Index747417093
Shannon Diversity Percentile28.561.4
Simpson Diversity Percentile30.221.5
Chao1 Percentile28.987.7
Lab: BiomeSight
Pathogens18πŸ˜ƒ39
Condition Est. Over 90%ile44
Kegg Compounds Low969πŸ˜ƒ1242
Kegg Compounds High5πŸ˜ƒ23
Kegg Enzymes Low272284
Kegg Enzymes High17πŸ˜ƒ75
P or P Chi2.9999245.999999999
Percentages of Percentiles Chi2 is a proxy for severity of abnormality, it has decreased.

Health Analysis Comparisons

I have not created an automatic compare yet (on to do list). Many values were similar, some interesting ones with improvements are below. Jason Hawrelak Criteria got worse, but I have deep reservations on using his criteria on Biomesight tests (he based them on a very different test method).

RecentPrior
General Health Predictors: Flagged Bacteria8πŸ˜ƒ10
Anti inflammatory Bacteria Score14.4%ileπŸ˜ƒ13.3 %ile
Lactate (controls many bad bacteria) πŸ“š33.1 %ileπŸ˜ƒ20 %ile
L-Lactic Acid (controls many bad bacteria) πŸ“š47.1 %ileπŸ˜ƒ25.2 %ile
NADH (Typically low with ME/CFS) πŸ“šπŸ“š26.5 %ileπŸ˜ƒ13.7 %ile
Hydrogen peroxide (controls many bad bacteria) πŸ“š17.3 %ileπŸ˜ƒ5.8 %ile
D-Lactic Acid (Associated with brain fog) πŸ“š6.5 %ileπŸ˜ƒ7.9 %ile
Potential Medical Conditions Detected2πŸ˜ƒ7
Bacteria deemed Unhealthy7πŸ˜ƒ22
Jason Hawrelak Criteria56.4 %ile75.8 %ile

Going Forward

A review of the Health Analysis was done above, with the two items: Mood Disorders and COVID-19 (a proxy for ME/CFS IMHO). A secondary review of all the items on [Changing Microbiome]/[US National Library of Medicine Studies] for high items not flagged. Nothing added.

Doing what is becoming a regular pattern: “Just give me suggestions” and then using given symptoms under Special Studies using these items:

Note: items like age and gender are omitted as well as any other symptoms that we do not have sufficient data.

First the filtered PDF suggestions. The list is much longer than usual:

And the to avoid list is more typical.

Let us go over to viewing the consensus to get some priorities


The highest value was 485 (so 240 for cutoff), lowest value was -574 ( so-287 for cutoff)

So in summary, shift a diet to low sugar, gluten free with moderation in meat (no guidance on chicken or fish). If your MD is willing, I would suggest reviewing Cecile JadinπŸ“š approach with antibiotics and rotate with those suggested above. IMHO Continuous on a single antibiotic is more likely to complicate the microbiome.

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about β€œappearing to practice medicine”.  I am safe when it is β€œacademic 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.

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