ME/CFS Microbiome after 5 years

This is a follow up for a reader from 2017 (yes FIVE YEARS ago). It was when I was attempting to work suggestions by hand, before I handed that process to Dr. Artificial Intelligence.

Reader Back Story

I have not taken any probiotics for over 1 year. My medical treatment is pharmacological for type 2 diabetes, levothyroxine, hydroaltesone[Hydrocortisone], hydroferol[vitamin D3 analog] 1 a month, statins, Omega 3 and fenofibrate, I have not taken probiotics.

Symptoms persist, abdominal bloating, tiredness, unrefreshing sleep, PEM, sore throat, lack of energy, exercise intolerance, visión changes, all symptoms of ME/CFS

Also the increase un body weight has been considerable and it is not possible for me to lose weight, my complexion was thin.

The latest sample was from BiomeSight so the number comparison below is more out of interest than being a truly valid comparison (which would be same lab to same lab). On the surface of the comparison we see what appears to be significant improvement on high percentile bacteria but an increase of low percentile bacteria.

Using the various canned criteria (Jason H, Medivere, Metagenomics, MyBioma, and XenoGene), there has been no change. By “canned”, we mean the bacteria picked by various sources that are important –usually at the genus or family level. The criteria below these lines are sensitive to the lab and the quality of the sample.

CriteriaCurrent SampleOld Sample
Lab Read Quality6.98.4
Bacteria Reported By Lab543203
Bacteria Over 99%ile122
Bacteria Over 95%ile1040
Bacteria Over 90%ile2651
Bacteria Under 10%ile26231
Bacteria Under 5%ile20518
Bacteria Under 1%ile1472
Different Labs – Items Skipped
Outside Range from JasonH88
Outside Range from Medivere1313
Outside Range from Metagenomics1010
Outside Range from MyBioma99
Outside Range from Nirvana/CosmosId1313
Outside Range from XenoGene55
Outside Lab Range (+/- 1.96SD)920
Outside Box-Plot-Whiskers6147
Outside Kaltoft-Moldrup23689

Comparing Samples (limited)

In the old analysis I was using ratios to mean. I have since moved on to percentiles. The table below looks at the top items and compare to percentiles. Note: there can be differences between labs on what they called bacteria (see The taxonomy nightmare before Christmas… (2019)).

Bacteria (Ratio to mean)Old Sample
New Sample
Parasutterella: (14.2x)99.8%ileNot Reported
Adlercreutzia:  (6.84x)99%ile0%ile
Bilophila:  (6.36x)99%ile88%ile
Butyricimonas: (5.28x)99%ile40%ile
Oscillibacter: (3.69x)94%ileNot Reported
Intestinimonas: (3.36x)97%ileNot Reported
Odoribacter: (3.20x)97%ile40%ile
Flavonifractor: (3.1x)99%ileNot Reported
Parabacteroides distasonis88%ile97%ile
Bacteroides ovatus36%ile98%ile
Phocaeicola massiliensis95%ile99%
In general, there has been little significant change on the extreme bacteria between the labs

Going Forward

We are doing suggestions from the following:

The goal of doing consensus are two fold:

  • Identify items that will help all issues, instead of helping one and making another worst
  • Doing what is called Monte Carlo simulation to have more confidence because the data we are dealing with is fuzzy

As a FYI, the PubMed are done via the Research Features / Advance Suggestions. Some produced no suggestions (for example Diabetes — which may be due to the diabetes drugs normalizing the bacteria)

Top Items From Consensus

The top items (in descending order) are below. Unusually, every single one was a take recommendation for each set of suggestions generated above. There is a rather clear theme on fibers.


The top suggestions are below in decreasing order.

I noticed that both lactobacillus plantarum (probiotics) and bifidobacterium longum (probiotics) are in the list, as it was for the ME/CFS person in this post: An email from a ME/CFS reader on Probiotics. As with that person, symbioflor 2 e.coli probiotics (US Source, World Wide Source) is lower down on the list. I checked the KEGG AI Suggested Probiotics [revised], and got a low 4.9 for Escherichia coli (with the highest value being just a 7 – indicating reasonably good balance). Using uBiome data, Escherichia coli was the top choice with a big 108.1. I would be inclined to offer the same advance as I did with the email, “because this probiotic is known to persists, use one bottle as part of probiotic rotation” – even just taking once a week is fine.

REMEMBER: The order does not reflect effectiveness — it reflects the amount of research available, hence the term Confidence.

Avoid Items

We have a variety of items listed that are usually suggested for ME/CFS. The reason that they are suggested is that blood tests show low levels. I am becoming inclined to suspect that the low levels in the blood is because of greedy bad bacteria in the microbiome that consumes them before it get to the blood. SPECULATION: Taking them as a supplement, feeds the bad bacteria and keeps ME/CFS going.

Vitamin B injections are likely fine, probably good! “ Patients with myalgic encephalomyelitis (ME, also called chronic fatigue syndrome) may respond most favorably to frequent vitamin B12 injections” [2015]

The thing that I have noticed with analysis is that two people have the same diagnosis and common symptoms, but their microbiomes are different and the AI generated suggestions are very different.

Bottom Line

With no active work on the microbiome, the microbiome stayed similar. Some of the changes may be due to the drugs being used;  fenofibrate,(prescription) – reduces Odoribacter, Bilophila, Flavonifractor and Butyricicoccus (which we saw above)

I would suggest trying the above suggestions (after it is reviewed by your MD), and retest every 4 months. Looking at A History of Several 16s Tests and Suggestions which was done on another ME/CFS person, we saw improvements in the he various canned criteria (Jason H, Medivere, Metagenomics, MyBioma, and XenoGene) after 3-4 months.