A review of a ME/CFS Microbiome

Every ME/CFS microbiome is different. IMHO, the root cause is a bad mixture of chemicals and chemical signals being produced by a dysfunctional microbiome that has reached a stabilization point.


This reader provided detail background which is always desired.


35yr Male have had ME/CFS for about 7 years now since 2015. In 2018 after first child and really bad sleep it got really bad..would wake up with anxiety for no reason. Major brain fog depressed and tired all the time. Sometimes had to be in bed multiple parts of the day. When I would exercise I would crash 5 hours after exactly for 24 hours which were an extreme version of my symptoms …plus temperature dysregulation, flushed feeling in the face, vision sometimes blurry (blood sugar looked normal), eyes squinty/heavy, felt very rundown, stomach would get inflamed with water, weight gain instead of loss, felt dehydrated even though I drank electrolytes, night sweats, etc. Strangely the period immediately after exercise leading up to the crash I would feel fine. Seen a lot of different doctors, but never felt like the root cause of it all was found. Made a lot of progress working on mental health, positive circle of friends, church/prayer, methylation, detox, nutrition, neurofeedback/ EMDR, and Perrin Technique (lymp drainage massage daily). Tried of other strange out of the box treatments like frequency therapy, applied kinesiology, red light therapy, self learned some acupuncture.   


Child hood trauma, but no serious health problems growing up minus strep throat a few times and bad food poisoning in 2013. Always struggled with a bit of brain fog and ADD like symptoms (can start tasks, but difficult finishing them). I’m an entrepreneur and before my health issues started would play basketball 3x a week for a decade, gym, and martial arts…sometimes all on the same day.  In 2015 went through a stressful mental and physical time starting another business. I really burned the candle at both ends. 

Initial onset was panic attacks , felt like I was going to die driving even though I know that wasn’t logical (fight or flight stuck). EMDR stopped the panic attack issues. Overall made lots of progress, but haven’t healed PEM yet.

Initial Onset Labs/Tests:

-Salivary Test showed tanked Cortisol and Low Neurotransmitters w/High DHEA.

-Blood Sugar and A1C barely a little over normal range.

-High Cholesterol / Trig /LDL and Low HDL

-Gi Stool Test showed candida, pseudomonas, low Bifido..naturopath put me on klaire labs bifido probiotic, super restrictive diet , and grape seed extract to kill candida all for 6 months. (Bifido still low per last 16s years later)

-Mold Test showed Ochrat toxin at 35/17..took some charcoal and glutathione for a while. House tested very low for Mold.

-Non Alcoholic Fatty Liver per Naturopath …corrected in latest lab

Brain Scans QEEG:

-Low power overall in the brain

-Was using Delta waves during the day at times and had a hard time getting into Alpha (neutral gear)

-Never seen anyone with a scan like me nor in their global database

– Lots of stuff going on in subconscious and abnormalities all around


On my pending projects list is a database linking microbiome to lab results – still waiting for volunteers (I do not have sufficient bandwidth at present to start the population of data). I have done prior posts on some related items:

The Microbiome

Looking at probable symptoms, entered symptoms and the above history we have a high number of matches with a few items suggested but not listed above (i.e. issues that should be checked)

  • Infection: Epstein-Barr virus Associated Bacteria (re-activation of EBV is common in ME/CFS)
  • Comorbid: Methylation issues (MTHFR)

From an autism group that I follow,  Prevotella copri goes high with the presence of mycotoxin [2020], which may explain this rather dramatic chart below. There does not appear to be a significant active mycotoxin issue at present.

Scanning thru My Microbiome view I note the following:

This produced a very short list of suggestions: Iron, Zinc and lactobacillus reuteri (probiotics) with some interesting avoids:  folic acid,(supplement Vitamin B9),  quercetin,resveratrol, boulardii (probiotics), glycyrrhizic acid (licorice). Adding in items known for parents/children we see some more probiotics suggested:

It is clear that a B-Complex may have questionable results.

Pro Forma for ME/CFS

My usual advice for ME/CFS when brain fog is not too severe is to use advance suggestions and slowly work up from 3%ile until you get at least 10 bacteria identified.

  • 6% –> 6 bacteria
  • 9% –> 10 bacteria
  • 12% –> 15 bacteria

At 9%, we have relatively few to take over 0.4 confidence:  iron, linseed(flaxseed),omega-3 fatty acids and some interesting avoids:  soy, inulin (prebiotic), Cacao, resistant starch,  resveratrol (grape seed),mediterranean diet, lactobacillus casei (probiotics). I say interesting because the avoid items are often seen as to take with ME/CFS. For example,  High cocoa polyphenol rich chocolate may reduce the burden of the symptoms in chronic fatigue syndrome Nutrition Journal [2010].

I increased to 12%, and a lot of items appeared.

Finding a good list of suggestions is an iterative process, I usually want to see a good list of items over 0.4 as suggestions — going up to 12%ile produced the desired goal.

Among the interesting items was:

  • Aspirin – it has the same effect on platelets (one factor of blood coagulation) as reservatrol (an AVOID), and should help with cognitive issues. They impact on the microbiome is different. in my own story, aspirin had a dramatic positive effect taking the maximum dosage of aspirin for the maximum duration had on me, and resulted in my MD becoming a believer that hypercoagulation was part of the CFS condition and ordering tests from Hemex Labs (a specialty lab on coagulation) — a significant part in terms of brain fog.

Neither Kegg suggested supplements nor Kegg suggested probiotics returned anything,

Bottom Line

Compare to others with ME/CFS, their microbiome is not an extremely shifted as is often seen. For probiotic dosages, I recommend looking them up here — often people take insufficient to effect change.

The dominant probiotic suggestion is: Lactobacillus Salivarius. Which is available from several sources. My own favorite source is Custom Probiotics (bottle price can be a shock, but the cost per BCFU is a fraction of competition).

Beginner Guide to Getting Suggestions from Microbiome Part 2 – YouTube

Questions from Person and Answers

  1.  iron – very strange. I eat a lot of red meat and take liver supplements. Did you take iron on your journey and what type?
    1. A: Iron uptake depends on the bacteria present. This article goes into the mechanisms. More related studies [2021] [2021]
  2. EBV – sorry actually have this test. I did a protocol for a month but maybe didnt nuke it enough?  My attached isn’t clear if it’s past infection or reinfection though. 
    1. A: This does not indicate an active case (it could be), it indicates that the microbiome has had signs of an EBV shift….
  3. On my Nirvana Biome – does it distinguish good e coli From bad? It said it was high there as well as c.diff ..on 16s test don’t think either showed up as a concern.
    1. None of the 16s tests distinguish good e coli From bad. It is important to know that most E.Coli are good.
  4. Coagulation – your aspirin comment made a big light bulb go off. I remember a few times I would take aspirin right after basketball which may have been for some other issue but I remember feeling like I didn’t crash/get PEM.  Is there any studies on what a good dose might be for this.
    1. A: “baby aspirin” (up to 100 mg) daily is well accepted (see this summary). I would suggest (in consultation with your medical professional), trying to find an effective daily dosage each day. Ideally, it would be taken with food to reduce risks. Take aspirin over other items like acetaminophen.
  5. Looks like I can rule our mycotoxins. I had a bit of elevated ochra a …worked on it a bit. Good news 
    1. A: Reasonable intrepretation
  6. I have a friend who has similar issues and I directed him to your site. He’s getting a 16s and just had a spect scan. Let me know if you’re looking for more blog cases. Happy to ask him. Please let me know if there is anything I can do to help you too!
    1. Yes, please do.