An early twenties CFS Patient Analysis

The patient is in the mid 20’s male and under treatment with a very well known CFS specialist. “although he is stable we aren’t seeing any further improvement….  He doesn’t meet the official CFS definition since he only has the PEM (Post-exertional malaise), general on-going fatigue, and maybe some sleep issues.”

This is the first of two parts, the second part is after the first Pfizer covid shot. This will be interesting to see the shifts.

“Also, after this sample was sent into Thryve he had his first Pfizer covid shot and then had a crash – so I got another sample at that time that I should get results for in a few weeks.”

Walk thru of this blog

KEGG Results

KEGG Probiotics

I am going to do a multiway compare in the hope of clustering a consensus from different algorithms. Using advance suggestions

I tend to favor KEGG because the data it is working from is significantly complete. Using Net Benefit and Advance suggestions — we got only weak results (usually against) or no results, except for Lactobacillus paracasei. This would be my first choice for trying a probiotic except it is a histamine producer.

Probiotic (available commercially)
Bacillus thuringiensis or
Bacillus mesentericus
Clostridium butyricum
Lactobacillus paracasei (D-Lactic acid producer [2013] )
Bifidobacterium adolescentis

Enterococcus faecalis
Lactobacillus kefiri

Probiotic Suggestions Analysis

Look at the Lactobacillus Genus, we see that this person is at the 87%ile (i.e. much higher than most people). Bifidobacterium is 29%ile, i.e. in the normal range. It is not surprising that these two are low as suggestions. On the other side, there was ZERO bacillus reported (not unusual, Thryve only reports Bacillus 45% of the time) which seems to be reflected in the top suggestions being Bacillus probiotics.

Having high lactobacillus can contribute to ME/CFS Symptoms. In general, lactobacillus probiotic should be avoided unless verified to not be d-lactic acid producers (if no information, assume they produce!!)

KEGG Supplements

As with probiotics, I tend to favor KEGG suggestions for similar reasons. The list below is where their generated values falls in the bottom 5%. All of them are available on Amazon, iHerb and other suppliers

As always consult with your medical professional. A pattern to discuss: start at 1/8 of the suggested dosage and increase every 4 days (usually doubling). Do one at a time, keeping those that have apparent benefit. If you stop giving one, wait 4 days before starting the next, on occasion, stopping may reveal that it helped — just slowly.

Most of the suggestions above appears to agree with studies as illustrated above. We have 3 suggestions that are novel (unstudied) for ME/CFS: Phytase, Molybdenum, L-Lysine.

This strong agreement to studies is reassuring for using the KEGG model. The model knows only the bacteria, no lab tests or diagnosis. Far more critical (for modelling), it appears to explain that the lab results can be reliability attributed to the ME/CFS microbiome population!

Core Supplements

While core supplements has largely been replaced by KEGG, it is still available. There was only one supplement computed that strongly suggests supplementation, DAO. There is no studies on PubMed for CFS and DAO, however DAO does reduce histamine levels — it is a possible experiment to try. I know several people with ME/CFS that have histamine issues, in some cases, severe hay fever. There is some literature in this direction:

The second lowest is Vitamin B6

The third lowest is Vitamin D, a well establish lab result for CFS. Generally “low level” supplementation does not work because the ME/CFS microbiome does a poor job absorbing it. A collection of PubMed Studies, and my prior blog posts

An important observation

All of the above suggestions came solely from the microbiome of the person (no diagnosis information at all!!!). The suggestions agree with significant subsets of ME/CFS patients. Using the microbiome, we appear to be able to be uber-specific to the person. We are not working off “general treatment suggestions” for ME/CFS. The suggestions in this post may not apply to a different ME/CFS patient — they have a different microbiome! Likely similar, but different!


The concept is to supplement what is not being produced by reduced bacteria creating a more normal environment. The hope is that a more normal environment will trigger feedback loops in the microbiome that will increase the reduced (or excessive) bacteria. The microbiome is a city – with a city, reducing the crime rate can often be the result of eliminating causes like: poverty, education, job opportunities, etc.

National Library of Medicine Comparison

In general, the bacteria identified for Chronic Fatigue Syndrome in Studies is not suitable for strong pattern matching. Chronic Fatigue Syndrome has a spectrum with many subsets. This variety is reflected in the studies.

I went to the Component Analysis / Medical Conditions page and then clicked under the Count Column, i.e. by the 📚 for Chronic Fatigue. I then Clicked on Direction to put all of the flagged items (💥) at the top. I then put checked the checkbox besides them (family, genus, species). On this page the 💥 is NOT outside of the Kaltoft-Moltrup Normal Range, but above 75%ile or below 25%ile. The Change Your Microbiome / Medical Condition (PubMed) Outliers applies the 💥 with the K-M ranges (in this sample, there were actually zero outliers!!!)

Only 5 matches.

Why this change? The studies reported averages were above or below for Chronic Fatigue Sydrome compared to controls. The studies did not report extreme values (which is the K-M goal).

Using Hand-picked Bacteria

Above we have the Hand-Picked Suggestions (which uses only the above).

First, we see that two of my favorites (as a person who has dealt with ME/CFS personally) is at the top of the list: Slippery Elm and Triphala. All of the probiotics suggested are non-lactic acid producers: Bifidobacterium. We do have a disagreement with CORE suggestions on Vitamin B6 (CORE says levels may be low, above says avoid). Given that the avoid list is full of B-Vitamins, I would tend to avoid.

Other ways of Getting Suggestions

Since ME/CFS often have cognitive challenges, I have a canned computation ( Changing Your Microbiome / For Chronic Fatigue Syndrome./ Brain Fogged ). The suggestions are below.

Above I did the path that I felt was best focused a person for Chronic Fatigue Syndrome. The scopes here is less bacteria and also flags high Lactobacillus. We could add Lactobacillus to the hand picked bacteria (exercise for the reader), but I am inclined not too because lactobacillus will dominate suggestions because there are so many studies for it, the other bacteria will fade off the suggestions.

Bacteria NameAnalysis
  Dorea longicatenaToo Low
  LactobacillusToo High
  Odoribacter splanchnicusToo Low

There are some others options on the site:

Dr. Jason Hawrelak Guidance

His results are based on general health and not ME/CFS. With this sample, we see these bacteria being selected. There is nothing in common with our first analysis, and only lactobacillus with our one above.

Bacteria NameAnalysis
  AkkermansiaToo Low
  BifidobacteriumToo Low
  BlautiaToo Low
  Faecalibacterium prausnitziiToo High
  LactobacillusToo High
  RoseburiaToo Low

I would not run with these suggestions — they are simply not focused on ME/CFS.

Symptom Prediction – Citizen Science

The bacteria pattern found with some 1700 prior samples appears to match. This implies that many symptoms are microbiome bacteria caused — something that may be modified. Many of the prediction agrees with what we know. One item is new, Carbohydrate intolerance which is hinted at by our Phytase (Enzyme) recommendation from KEGG.

It also lines up with the iron recommendation and suggests the mechanism for iron being low:


The physician being worked with is not dogmatically opposed to using antibiotics. So I did antibiotics only suggestions with the results shown below. Remember this is off label use of these antibiotics.

From the original handpicked selection
From Canned ME/CFS suggestions
Using Dr. Jason Hawrelak’s Significant Bacteria

We have everyone agreeing!!! The Tetracycline family (which includes minocycline and doxycycline). My personal preference in minocycline. Not only do we have agreement between methods — we have agreement with protocols reporting success (to various extents) with ME/CFS. [Success or failure is likely connected to each patience’s microbiome]. This approach fell out of favor during the crackdown on “inappropriate use of antibiotics to prevent antibiotic resistance”, and appears to be considered again in 2021.

In this case, “prescribing antibiotics to address a microbiome dysfunction” (which is exactly what we are doing), would likely fly with most medical review boards 🙂

Bottom Line

We have come up with some very specific suggestions based on the person’s microbiome and ME/CFS as a condition. We have also looked at some less specific approaches. These approaches would often be the “stock-in-trade path” that many medical professional will walk. IMHO, they are “ok” but not as “good” or “awesome” as a really focused approach.

Remember, all suggestions should be discussed with a medical professional before doing. The Microbiome Prescription site goal is to model a variety of diseases and compute theoretical candidates for treatment. In some cases, like this post, we find that many candidates have been tested with positive results. Other candidates have not been and thus are potential ones (with logic and studies inferring their benefit).