Another Microbiome Analysis of a ME/CFS person

This person has an interesting set of symptoms for ME/CFS. 40 yo male. I am following the same pattern as the two previous analysis. Every ME/CFS person share some factors and are different in other factors. There is nothing that works for all ME/CFS people.

  • Symptoms
    • Depression
    • Irritability
    • Brain fog
    • Post exercise malaise
    • Tinnitus
    • Post nasal drip
    • Stuffy nose
    • Cold extremities & insensitivity to cold
    • Fragmented sleep
    • Low libido
    • Low appetite
    • Frequent bowel movements
  • I’ve had different tests and bloodwork done over the years and these were the common outliers:
    • Low DHEA-s
    • Very high B12
    • High Vitamin D despite not supplementing
    • Low Estradiol (E2)
    • Mild blood coagulation
    • High(ish) eosinophils% (~5%)

Looking at Naive Predicted Symptoms From Bacteria table, we have:

There are more hits than the last person (who reported that fatigue has improved) – and gender prediction is wrong.

Enzyme Analysis

The awesome results in a past post on an autism child, where the enzymes were identified as coming from bacteria species constantly reported as high with Autism, is causing me to look at enzymes shifts as a good strategy to identify the key bacteria to look at.

So the next step is to look for probiotics that can also produce these enzymes.

Any of the probiotics with a 5 is good and sufficient. A higher BCFU is desired.


The easiest combination to obtain retail from the above are clostridium butyricum (Miyarisan ) which produces all 5 enzymes! or any of bifidobacterium adolescentis, bifidobacterium animalis subsp. lactis bb-12, and bifidobacterium longum. The latter ones (without additives) are available at Custom Probiotics (with a recommended daily dosage of 320-400 BCFU/daily) at the lowest cost per BCFU that I have seen.

KEGG Module Analysis

This is another way to evaluate the functions of the bacteria in a microbiome sample. There are less items then with Enzymes and, to be honest, I have not examined the results much after adding the code and data to compute them. There was nothing there.

End Product Outliers

Nothing was found outside of the ranges, and looking at Core Supplements there was one item of concern, high d-lactate production. High D-lactate is associated with neurological issues. (See these posts: Killing Lactobacillus to improve Brain Fog, Approaches to D-Lactic Acidosis). We also see that the microbiome suggests high B-12 (at 76%ile) which the labs report.

Unlike my last post on an autism child, there were no high enzymes to indicate the troublesome bacteria.

We turn to the Advance Suggestion engine and apply some filters.

Pass 1 for suggestions

First from Citizen Science we look at filtering for neurological decision making and drive a blank until we widen the search as shown below

The prior ME/CFS person require a 9% level to get any suggestions

Looking at the suggestions, we only find one item in common with the prior ME/CFS person: inulin (prebiotic).

Vitamin B12 is called out explicitly as a to-avoid.

Top probiotics suggestions all contain  saccharomyces boulardii. Flavonoids are a short list

This is close to my usual breakfast for many months: Barley porridge with walnuts!

Pass 2 for suggestions

We change the filtering to CFS/ME and drop back to the most extreme 3% – where we get results

There was no items over 0.5 for to take, we just have a critical list of items to decrease,

We have a conflict on triphala. One subset of bacteria says to use it, a different subset says not to use it. Given that it’s the highest value in both cases we need to do an experiment. I would advocate doing triphala for 4-6 weeks to see if it improves neurological issues, then stop it and re-evaluate.

We have a long list of probiotics, all with appropriately the same value

Rerunning with only probiotics, we find just one lactobacillus plantarum (probiotics)

Bottom Line

Remember this is strictly on the basis of the microbiome and our current state of knowledge in interpreting and being able to act on it. It is important not to view microbiome analysis as a magic silver bullet. A summary of suggestions to discuss with your medical professional.

In summary, clinical studies have tested some substances on various conditions which have been reported on PubMed. Microbiome analysis is based on microbiome shifts reported on PubMed by consuming some substances (ignoring medical conditions usually). If you construct a full list of both sets of substances, you will likely have only 10-20% of the substances in common. What has been studied in one context, has not been studied in the other context. Microbiome analysis is complimentary, not a replacement.

As always, to be reviewed with your medical professional before starting. There are algorithm/artificial intelligence generated suggestion based on data that has been entered (usually from gold standard sources).

Postscript on High Vitamin D

See these posts:

Feed back from person

” Indeed very insightful! Strangely enough, walnuts, tea and inulin both made me feel better despite not knowing why and your analysis make a lot of sense.”