ME/CFS Treatment Suggestions

The following is suggested reading,

It gives an extensive list of suggestions with dosages and the studies they are based on, for example

It is a “all on-one-page” that is ideal to discuss with your medical professional.


There are many nuisances in the studies cited that are missed or have misleading inferences. Simple example, “individuals who regularly exercised…. experience less fatigue”… could be restated as “individuals who experience less fatigue…. regularly exercised”. Causality is not in the evidence.

Also, Cognitive-behavioral therapy trials has many more than the single study cited — the majority of studies found that it did not help, or made people worse.

Simplified Suggestions for Microbiome Adjustments

For the last few months I have been working with someone that runs a Long COVID support group. This has resulted in more modifiers being added. One of the outcomes has just been added to the site. She requested that a simplified set of suggestions be added to the site to make her life easier. This consists of items she picked from her experience dealing with the group.

Where to transcribe or upload data (depending on which test)

16s High Resolution tests

These simplified suggestions has been added everywhere (tell me if I missed a page). If you use GI Map or similar reports, it is available after you have transferred and return to adjust suggestions. You should see these options on most suggestion pages now. To get this new condensed report, just click the checkbox.

Common Elements

GI Map and similar

The report is a CDV file (loads into Excel or other spreadsheet programs)

After loading, into Excel, you will need to adjust column widths

First Load
After re-formatting as a table

If an item is a Take, then a clinical dosage is given (if known). Clinical Dosages are those reported from studies listed on the U.S. National Library of Medicine Clinical Trials site.

Example from a 16s Sample

Other sections are shown below.


At the bottom of the page are some essential reminders.

Some of the clinical dosages above may be problematic with some medical conditions.

Dosages should be reviewed by a medical professional before starting.

The suggestions are based on a mathematical model. dosages are from clinical studies.

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.

An email from a ME/CFS reader on Probiotics

This person did a microbiome analysis thru Biome Sight, tranfered the data to Microbiome Prescription where Dr. Artificial Intelligence did an analysis based on over 20 million facts.

I have a set of questions about the selection of probiotics during the course of the microbiome treatment. My first week-and-a-half using the Dr. AI plan went fine, with no notable events. I did recover a significant amount of strength in the same time—from being unable to drive or stand comfortably for long, to being able to drive, walk, do a few chores around the house—but I also have a general capacity to recover so long as I rest, so I can’t say to what extent the treatment was responsible. It’s possible that the rate of recovery was increased. Regardless, I’ve run out of probiotics, so I’m looking to buy new ones. 

For cost per CFU, I am drawn to Custom Probiotics. Having not herxed at all during the initial course of probiotics, I am also thinking I need to crank up the CFUs a little. However, given the unit price, I just want to make sure my decisions are being informed by a reasonable grasp on probiotic use for CFS/Long COVID. Hence, some questions for you, if you have the time:

  • My first dilemma: a singular, large, multi-strain mixture of B&L, or a post-purchase combination of a small number of single-strains of B&L? Generally, it seems necessary to take at least one Bifido. and one Lacto. per treatment cycle, so long as B&L are both recommended and one is not taking a probiotic antagonistic to B&L. My inclination, especially given unit cost, was to request Custom Probiotics make me a mixture of my top B&L. Using Special Studies, for example, I get B. longum, L. plantarum, L. acidophilus, L. paracasei, and B. lactis—so, perhaps I could request a singular mixture of these bacteria. But, I’ve also seen you refer to the use of one or two single-strain probiotics from Custom Probiotics at a time, which, in addition to some other concerns, gives me pause. Would you instead favor, for example, combining separate B. longum and L. plantarum single-strain probiotics, with no other strains in the same cycle, over my big mixture?

Answer: I would advocate just getting a single species bottle and trying for 2 weeks, then rotate to a second and then back. My first choice would be alternating between   B. longum and L. plantarum, noting carefully what the response to each is. Start at a dosage similar to what you were taking and double the dosage every second day until you are at the desired dosage.  The problem with a mixture is that you do not know which one is causing good or bad responses.

  • Is “two weeks on, two weeks off”, or something comparable, a hard-and-fast rule for the pace of the probiotic cycle? Or, are there other good metrics for judging when to stop or start a probiotic? For example, I was wondering whether one might continue a particular probiotic beyond two weeks if it’s continuing to cause a herx at the two-week mark. (Of course, one should stop prematurely if the herx is too extreme.)

Answer: The two week rotation is based on the Jadin’s Protocol for Antibiotics. see Rotation — Essential for Changing the Microbiome. There is no problem stopping early due to herx. Personally, I had to crawl on the floor to get to the washroom from my first taking of Mutaflor, in hindsight, I did not need to push so hard. Rather reduce dosage or stop. A comfortable herx lasting a couple of hours and then fading is what I like — it answers the question of “Is it working” but allows a reasonable day.

  • I noticed E. coli is my top KEGG recommendation, but is weakly recommended (sub-50 Priority) in the consensus suggestions under some circumstances, and not recommended at all in a Special Studies consensus. Is E. coli still favorable in that case?

Answer: Unfortunately we are dealing with fuzzy data everywhere. The numbers do not indicate effectiveness, rather reflects the number of studies that reports shifts of bacteria in a positive or negative direction multiplied by the estimated importance of shifting, hence the term “confidence“. Given you observations, I would suggest trying one bottle of Symbioflor-2 (which is done by drops and persists: (US Source, World Wide Source) ) and include it in the rotation above as a third item (or a fall back if one causes problems)

  • Questioning a previous assumption, is it actually necessary to take both B&L at the same time, each time? I see from the database, for example, that L. plantarum increases both Lacto. species and Bifido. species. This would imply it’s not necessary to take a Bifido. with L. plantarum, right?

Answer: NOTHING IS NECESSARY. The goal is to produce a list of items that have a higher probability of helping (or hurting for the avoids). You can cherry-pick from the list as you finances or situation permits. Doing the avoids is often significant, recently I got an email from someone who cut the avoids immediately while trying to figure out the new menu — she noticed improvement within days..

  • I know biofilm breakers and anti-coagulants are a good idea for antibiotic pharmaceuticals/herbs. But, what about probiotics? I can imagine dissolving biofilms with bromelain is helpful so the bacteria in the probiotics can outcompete what’s hidden too. But, what about the other big players—nattokinase, lumbrokinase, etc.? Do probiotics interact with these supplements favorably?

Answer: I do not know, but I know that some probiotics produce bacteriocins (natural antibiotics), so I would say yes. BUT A WORD OF WARNING — they may also increase or produce a severe herx. So go slow with them. Do not take them until at least day 3 of a new probiotic. Again, the goal is one-item at a time, taking notes; not tossing the kitchen sink into your supplements and hoping something works.

I’d like to thank you for all the support you’ve offered me over the past few months. I truly appreciate the time you’ve spared to answer my questions, and I am sure I will have you to thank when this illness has resolved. I hope you have a great weekend!

Follow Up Questions

  • Regarding your response to my second question: Thank you, this makes sense. I guess Jadin’s protocol can be generalized to anything that modifies the microbiome, give or take. Nonetheless, are there any circumstances where it would be sensible to extend the use of a particular probiotic past the two-week mark? I’m recalling a hypothesis you share in your notes on your 4th relapse, to the effect of, “If a modifier appears to be resolving symptoms, continue using it, even if the database suggests switching in the most recent analysis.” This was proposed with regard to the use of one modifier over another (i.e. keep using L. plantarum if it’s helping, even if the latest priorities from the database suggest some other probiotic would be more helpful). But, I wonder if this could be extended to the choice to cease the use of a particular modifier at the end of a two-week cycle. If L. plantarum is continuing to cause a herx at the end of two weeks, or if my symptoms keep improving with its use, could that (or any other reason you might know of) be taken as a sign to keep using it? I’m assuming no, since other probiotics might help as well and there is a general risk the microbiome develops resistance if one pushes the same modifier too long. But, I am curious where the boundaries of our rules are.

Answer: I would agree that it is a viable path, with the caution being — to monitor that the improvement keeps happening significantly. I would not extend beyond 6 weeks. You will rotate back to it soon enough.

  • Have you heard of anyone having adverse reactions to the anti-coagulants? Easy bruising is the obvious one, but I have in mind other problems. In particular, while not clinically acceptable perhaps, a minority of Amazon reviews of Doctor’s Best “High-Potency Serrapeptase” (at least a fraction of the one-star reviews, which would constitute at most 6% of the 7.2k total reviews for the product) report frightening GI issues, and circulatory issues that do not appear to fall under the category of “easy bruising”. A similar distribution is present for the other brands of serrapeptase. There are many fewer reports of illness for lumbro. and natto. on Amazon, seemingly, but I can’t say for sure. Based on your experience or knowledge of the literature, does this sound familiar, or explicable?

Answer: Yes, it is one reason that I suggest using a MD to determine the appropriate ones. Each ant-coagulant has different impacts on the coagulation cascade. I was able to keep working with over the counter anticoagulants for a while (hoping that things would correct themselves), the moment that I saw easy bruising, or cuts that did not stop bleeding, I bailed from anticoagulants and went on sick leave and then disability the next day. I learnt from deep testing for inherited or acquired coagulation factors (at the former Hemex Labs with David Berg) that my issue was just one (Prothrombin 20210 A/G a.k.a. Factor II mutation). My eldest daughter from an ex-wife had 3 factors (which likely explained some of the cognitive problems and behaviors with her that resulted in her becoming an ex).

Taking anticoagulants that works on platelet aggregation (i.e. aspirin, etc) would not have an effect. Research for substance that impacts the specific issue(s) impacting you is usually advised. I copied a chart below to illustrate the cascade — you may have an issue with just one step.

From Straight Healthcare
  • Any thoughts on the use of bovine organ extracts as a supplement? Heard about bovine thymus extract causing a herx and symptom improvement in a handful of cases, and my naturopath just prescribed me something that contains bovine adrenal extract. The theory, I understand, is that the bovine organ supports the function of the same organ in the human body. So, bovine thymus enhances function of one’s own thymus, leading to intensified immune response to overgrown bacteria in the microbiome (perhaps immune system too weak otherwise under conditions of dysbiosis), leading to experience of herx and symptom improvement. I imagine the mechanism is something analogous for the adrenal glands. Good data is not plentiful as I understand, but maybe there’s something to it. No clue. Saw some papers, but they were mostly theoretical.

Answer: You used several key words: “handful of cases” and theoretical. My first step was going to Clinical Trials to see if there were any. There was NONE. This implies that there are no serious ongoing studies of it. The same results from the PubMed. Doing a wider search I found the following:


So, my impression is that once upon a time, a long long time ago, there was interest in it but its use was abandoned my main stream medicine. There is neither evidence of it being effective nor evidence of it being harmful.

I did a repeated search with “bovine adrenal’, a more specific item. It found 7 in the clinical studies, none involving humans. On PubMed, I searched for “bovine adrenal” supplements and got 12 results, scanning them there was no human studies. So my own take is simple, there is no clean clear science supporting it, hence it gets toss to the back end of things to consider.

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.

CFS Patient after COVID using the Special Studies Results

Foreword – 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.

Back Story

  • Male, 39 years old.
  • Was on antibiotics for 4 years between ages of 16 and 20 for adolescent acne.
  • Severe Onset 4 years ago (around June 2018) after a succession of stressful events.

Symptoms include:

  • Swelling on lymph nodes in throat
  • Cramping
  • Ataxia, unsteady gait, brain fog, trouble thinking, speaking, peripheral neuropathy (tingling in left thumb and index finger)
  • Dizziness
  • Headaches
  • Visual impairment / visual processing impairment
  • Extreme Fatigue / drowsiness
  • Rash on neck and groin
  • Facial spasms
  • Postural hypotension, blacked out many times when standing
  • Have suffered from sinusitis from around 21 years old (seen small improvement lately after taking polyphenols daily)
  • Suffered from anxiety and bouts of depression from around age 16

Since 2018 all forms of dairy have exacerbated my symptoms. Previously I didn’t notice any issue with dairy but in hindsight it might have been one of the triggers for my sinusitis. Having removed it from my diet my symptoms are much improved (less fatigue, more energy), although I still suffer from the cognitive impairment this has been improved by circa 25%.

See below for some more information

High Level Overview

Potential Medical Conditions Detected page found some apparent matches:

  • Metabolic Syndrome
  • Gastroesophageal reflux disease (Gerd) including Barrett’s esophagus
  • Mood Disorders
  • Insomnia

Item like hypertension (High Blood Pressure are define miss — since POTS is typical with ME/CFS.

In terms of bacteria deemed unhealthy

Dr. Jason Hawrelak Recommendations came up at the 89%ile, most were just outside of his ranges.

Looking at distributions, we see a large number of bacteria with just a token presence (0-9%ile)

Looking at Special Studies, we find good matches for several conditions.

Interpreting the updated table shown below can get a little complicated because we are looking at rarely seen bacteria that occur at low levels usually. This can be impacted by the quality of the reads — a low read count will have less of these detected (i.e. both rare and low counts). Getting over 50% is significant, if the top ones are close to each other, use the top 6 or until there is a gap in the numbers.

I contacted this person and asked about some of the above and got this response:

  • I have sleep problems. I am a very light sleeper and get up several times in the night
  • There is a history of bowel cancer in my family. 
  • I have had COVID at least twice, possibly three times in the last 2 years. 
  • my symptoms always flare together. The sinusitis, rashes, POTS, cognitive impairment, aches and pains and fatigue as well as swollen glands. Not sure if that is significant or a regular hallmark. 
  • With alcohol it can cause a flare in my sinusitis. 
  •  a SIBO test in December 2020 that the practitioner said was positive
  • My symptoms saw the biggest improvement after giving up dairy,
Update from person

This results in my doing each of the double matches (i.e. bacteria matching diagnosis) and generating a consensus report. Conerning Long COVID, he wrote “Not sure if I imagined it or a coincidence but my symptoms felt like they improved marginally after it.”

The Consensus Results

I should point out that my preference is shifting to use the a consensus report based on the Special Studies when the results are from or through BiomeSight. The key for the best results are the best identification of the bacteria that has a statistical role (IMHO). It was interesting to note that two different E.Coli probiotics are at the top (which we also get from KEGG Gene data). Choline deficiency means to reduce choline intake.

Top Top To-Take List

Reducing Choline means reducing foods such as those listed below

US National Institute of Health

On the other end (to avoid) are some vitamins that are often suggested for ME/CFS: Vitamin B-12 and Vitamin-B3 (in fact all B-Vitamins are negative!). This is contrary to usual logic because low Vitamin-B levels are common with ME/CFS which causes me to do a rethink. Is the reason that it is low because it is greedily consumed by bacteria causing the problem? If this is the case, then having low Vitamin Bs levels AND avoiding Vitamin Bs make sense.

Probiotics Suggested based on Clinical Studies

KEGG Computed Probiotics

We now take a totally different method of picking probiotics — from the genes in your bacteria and the genes in the probiotics. Above the choice was based on what studies reported that probiotics shifted bacteria in clinical studies. We see E.Coli near the top, the other odd sounding ones are found in Prescript Assist and Equilibrium cited above. In other words, both paths lead to the same probiotics.

Generated from the bacteria in the sample and using KEGG derived data

Bottom Line

What struck me about this analysis is that the picking of bacteria was very simple — just pick the special studies that have high matches and which is reported by the person. The second aspect is that using the data from Kyoto Encyclopedia of Genes and Genomes resulted in a tight agreement on probiotics from two very different ways of selecting probiotics. This gives me a very warm feeling about the suggestions — genomics and studies are in agreement with selecting bacteria using special studies.

Important Note: I did not do suggestions for the two high bacteria cited at the top: Haemophilus parainfluenzae and Prevotella copri. At the moment I speculate they are side-effects and the above will naturally reduce them without needing explicit action. I did run these two bacteria by hand picking with the following being reasonable candidates to reduce them

  • peppermint (spice, oil)
  • thyme (thymol, thyme oil)
  • wormwood(artemisia)
  • cinnamon (oil. spice)

If you wish to take explicit action, I would take the above only for 2 weeks and then pulse them every 2 months.

I should note that there was universal agreement on the following actions:

  • low protein diet (agrees with low choline diet above)
  • bifidobacterium bifidum (probiotics)
  • xylitol (i.e. xylitol gum is an easy way of getting it)
  • chrysanthemum morifolium (a.k.a. Ju Hua)

With no disagreement over most of the top recommendations between the consensus report and the “bacteria hit list” suggestions.

User Feedback

“The foods to avoid are all foods that I eat regularly so it’s great to have clarity on the need to avoid these.” -interesting observation, he is in a no-progress scenario, his regular diet may be contributing to no progress!

“Regarding the B vitamins, another symptom I have is lack of facial hair that is certainly not genetic as every male on either side of my family has strong facial hair. I am wondering if that is an outward sign of biotin consumption from bacteria? I have been taking high dose biotin recently. This might also explain the brain fog via bacterial consumption of niacin.” – this seems to agree with my speculation about the existence of some greedy consumers of B-vitamins being part of the problem.

“Am I right to assume that a plant based diet and avoiding the foods listed should starve out the B vitamin consuming bacteria and help increase those that I am low in” This is a reasonable assumption and one that I would make. I would suggest a minimum time doing that of 4-6 weeks.