I have been observing the Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) community for almost 35 years. I have been an active member of this community. I have also been in remission for it, but deeply interested in understanding it; I have had several relapses. I wanted to prevent future relapses hence great interest in reading and researching.

Microbiome Analysis as a path with good results

My main focus in 2023 is on the microbiome of ME/CFS people. I have a collections of reviews of individual microbiome samples reviews available. The data from the suggested tests are processed using the free expert system at Microbiome Prescription. So far, every person who has done this route and repeated the microbiome tests have reported subject improvement and objective improvement. It can be a long journey, we take one step at a time.

During those decades I have seen a huge number of theories, suggested treatments and clinical findings. I have seen many “this cured me” which failed to deliver remission for anyone else. I have seen treatment plans proposed / sold by well-meaning MDs that worsen the condition and persisted for years. I see this still going on today for both ME/CFS and Long Hauler COVID.

My training is in science: mathematics, statistics, general sciences. I have been an instructor in those areas at many universities, colleges and even high schools. My remissions resulted from following gold or silver standard evidence. I have read several thousand published papers on ME/CFS (with and without brain fog).

What is on this site?

Most of the posts results from reading a new paper, readers asking questions, seeing a question asked on some online groups. The posts follow this pattern:

• The question or concern that started the post
• A review of all literature on the US National Library of Medicine, conference papers, etc.
  • Quotes provided from papers or their titles
  • Links to the paper so people or their medical professionals can read for themselves
• A bottom line section which are my conclusions inferred from the literature.

To quote Seargent Friday from the old Dragnet TV Series, “All we want are the facts, ma’am“.

Use the site as an Encyclopedia

There is another similar site, Encyclopedia Myalgic encephalomyelitis, [me-pedia.org], which I also use. I actually have had more page views than that site! What the difference? I seem to cover things in more depth. I just searched for “grapeseed” on that site and found nothing. I searched on this site and literally had dozens of posts cited. Resveratrol Revisited [2015], Resveratrol Recap [2017], Mast Cell Moderators — non-drugs and suspect bacteria [2023]

The fastest way to find information is to go to google search, enter site:cfsremission.com followed by what you are interested in.

I Promote No Protocol, I promote evidence based treatment.

As a statistician, I recognized that ME/CFS consists of many, many, many, different subsets. To treat successfully means getting information. I know that my own ME/CFS was usually triggered by the interaction of an inherited coagulation defect (Prothrombin G20210A a.k.a. Factor II Mutation) interacting with stress and a microbiome that goes bad with stress. What works for me may not work for another with ME/CFS.

My Unified Model of ME/CFS and Long COVID

I have a hypothesis on the causes of ME/CFS and a treatment approach (not a protocol) that is likely to reduce the severity of ME/CFS. Some may go into remission.

The Cause of ME/CFS

The cause is rather simple: anything that causes an alteration of the microbiome. This may be food poisoning , an infection (COVID, Flu, Lyme, Epstein-Barr virus), a vaccination, a prescription or over the counter drug, pesticides, bad diet. This alteration and happenstance cascade into a microbiome dysfunction that mucks up your system. Too much of some metabolites /chemicals are being produced, too little of others, the chemicals used by the body are “hacked” and the body manifests a huge variety of symptoms.

Treatment Approach

Over the 30+ years, I have been a good mathematical modeler. Trying to find a model that agrees with all of the facts, explains all of the observations and last, can make predictions that are testable. Not that many years ago I came to the realization that the microbiome dysregulation model was an extremely good fit. More important, it made predictions that could be tested.

A 1999 study in Australia found a common pattern with ME/CFS patients microbiome. If something helps ME/CFS then it is likely that this same thing would influence the bacteria found to move closer to normal. This post from 2013, Finally! Someone verified the 1999 Studies – Thank you Kenny De Meirleir! shifted me further down this path. Finding that the most effective antibiotic protocols for ME/CFS and Lyme would also correct the reported microbiome function (see Why Jadin’s Antibiotics Protocol usually work — Pasteur Institute got the solution right and the explanation wrong? ).

I keep monitoring ME/CFS studies. My current effort is dealing with improving the ability to correct the microbiome. This is done on a separate site, Microbiome Prescription, and a separate blog site.

I have a page linking to people experience with this approach. Each person is different.

Analysis Posts on Long COVID and ME/CFS

I believe that most ME/CFS people will improve significantly with microbiome testing followed by appropriate adjustments. This is often an iterative approach (test-adjust-repeat).

My ideas on this blog have evolved, as more and more information becomes available. This post is an attempt to bring readers up to date with my current thinking. I am striving to be transparent in my logic — showing the evidence I am working from, and my thought processes.

Notes to Treating Physicians     Quick Self Start on treating CFS

Analysis of Microbiome/stool with recommendations

Site: has moved to https://microbiomeprescription.com/

• Over 30 different tests are supported. See this page

The data is available in an online collaborative python workbook for analysis. See this post.

Microbiome Definition of CFS/FM/IBS

A coarse condition that results from:

• Low or no Lactobacillus, AND/OR
• Low or no Bifidobacteria , AND/OR
• Low or no E.Coli , AND/OR
• A marked increase in number of bacteria genus (as measured by uBiome) to the top range
  • Most of these genus are hostile to/suppress Lactobacillus, Bifidobacteria, E.Coli
  • Several are two or more times higher than normally seen
  • The number of bacteria genus goes very high (using uBiome results), but most of them are low amounts.
    (“Death by a thousand microbiome cuts” and not “Death by a single bacteria blow”)
• The appearance of rarely seen bacteria genus in uBiome Samples.

A finer definition would be a condition with a significant number of abnormalities in the ‘Autoimmune profiles see this page for the current criteria (i.e. over 25%).

The specific genus and their interactions determine the symptoms seen — likely due to the over- or under-production of metabolites (chemicals). Other autoimmune conditions may share these core shifts. The specific high and low bacteria determine the symptoms if the person was the DNA/SNP associated with the symptoms.

Replace the metabolites produced by the missing bacteria

Replacing the metabolites should result in the reduction of symptoms associated with a deficiency of these metabolites.

See this post for the study references. These items should/could be done continuously.

• Acetylcholine  See this post
  • Warning: lots of writing on the web. Some suggestions are contraproductive.
  • Regular eating of almonds
  • Repeated administration of almonds increases brain acetylcholine levels and enhances memory function in healthy rats while attenuates memory deficits in animal model of amnesia [2016].
• Riboflavin (B2) [1999]
  • 400 mg/day [Src]
• Biotin (B7)
  • 100 mcg/day [Src]
• Folate (B9)
  • 6,000 mcg and 13,000 mcg of Folate, OR
  • 15 mg of Folininc Acid [src]
• Vitamin B12
  • 1000 mcg/ 1 mg [post]
• GABA
  • 1000-3000 mg often cites on various sites
  • Up to 0.8g/kg day [Src]
• Urolithins requires bacteria and dietary ellagic acid (pomegranate juice is a source).
  • Bifidobacterium probiotics should be taken (at same time) WITH pomegranate juice.
    • While the bifido will not stay around, they may utilize the pomegranate during their transit in your body)
  • No dosage information.

Other Supplements Reported to Help

• Vitamin D3 -15,000 IU/day
  • “Baseline vitamin D level was found to moderate treatment effect on several outcome measures. Dry mouth and sleep disruption were reported more frequently in the placebo group. [Control took Lactobacillus helveticus and Bifidobacterium longum]” [2017]
  • Vitamin D deficiency changes the intestinal microbiome reducing B vitamin production in the gut. The resulting lack of pantothenic acid adversely affects the immune system, producing a “pro-inflammatory” state associated with atherosclerosis and autoimmunity[2016].
• Thiamine Vitamin B1
  • 100 mg 2 times a day
• Bacopa monniera and Cognitive Function
  • Impacts GABA, acetylcholine

Bootstrapping Bifidobacterium and Lactobacillus

The items below were found in studies to increase bifidobacterium and lactobacillus:

• Almonds/ almond skins: Enhances Bifidobacterium, Lactobacillus 
• Sesame seed: Enhances Bifidobacterium Enterococcus  Lactobacillus
• Dark Chocolate
• “heparin- or heparosan-treated animals were different from those of the saline-treated animals, with increased Lactobacillus spp. and decreased Enterococcus sp….heparin or heparosan may be used as an effective gut microbiota modulator by increasing the subpopulation of Lactobacillus.” [2013] – Note: Berg’s anticoagulant therapy for CFS used heparin
• “After the intake of apples (2 apples a day for 2 weeks) by eight healthy adult humans, the number of bifidobacteria in feces increased ” [2010]

Unless the bifidobacterium and lactobacillus (B&L) are human sourced, there is almost zero chance of taking up residency. Taking probiotics will not allow B&L to get established. In fact, there are grounds to believe that most commercial probiotics actually reduce your  native B&L. You want to encourage your native B&L. See this post for citations.

Bootstrapping E.Coli

The E.Coli probiotics below are human sourced and known to take up residency in the human gut.

• Core: D-Ribose a preferred food that it uses
• Mutaflor probiotics — E.Coli Nissle 1917
• Symbioflor 2 — multiple strains

Dealing with the other microbiome shifts

The other microbiome shifts appear to be in different clusters of microbiome shifts. This 2017 paper by Peterson, Klimas, Komaroff, Lipkin (and a stack of other CFS researchers) makes that clear in its title: “Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome”.

The best way at present to proceed is to order an analysis from uBiome. (Disclosure: I have no financial interest in this company.) When your get your results back, log in, click on the “Compare” tab, then go to “Genus,” and click on “ratio” twice, so the results are in descending order.

This is the “hit list” of what you are trying to reduce. DataPunk provides a nice summary of what we know about these. See, for example, Alistipes:

At this point, we run into a logistical challenge.  You want to avoid items that are “Enhanced By” (which is in common across all of the high items) and take the items that are “Inhibited By” (which are not on any of the “Enhanced By” lists).  You may also wish to reduce foods that are high in items listed in “Nutrients/Substrates.”  It becomes a jig-saw puzzle! I have done this exercise for many readers’ uBiome results:

• https://cfsremission.com/2017/09/11/ubiomes-before-and-after-a-fecal-microbiota-transplant/
• https://cfsremission.com/2017/09/03/ubiome-result/
• https://cfsremission.com/2017/09/18/another-ubiome-review-with-bifidobacteria-overgrowth/
• https://cfsremission.com/2017/08/27/ubiome-of-a-mcs-with-cfs-person/

I have discovered that DataPunk is not absolutely current, and have started creating posts based on its data, and then added studies from 2016 and 2017 to the page. Past pages are below, for current list MicrobiomePrescription site.

General Suggestions (no uBiome results)

Some of these items are contraindicated with a few uBiomes that I have reviewed. This likely is why person B reports no results while person A reports improvement. Example: Magnesium is usually very helpful — but there are a few cases where it encourages overgrowth of undesired  bacteria.

Probiotics

Most probiotics do not take up residency. They are “here today, gone tomorrow”. Their primary role in my model is producing natural antibiotics against other bacteria. For example:

• Inhibition of Clostridium perfringens by an antibiotic substance produced by Bacillus licheniformisin the digestive tract of gnotobiotic mice: effect on other bacteria from the digestive tract [1976].
• “Among those, seven Paenibacillus polymyxa strains showed the highest antibotulinal activity and the largest antimicrobial spectrum against C. botulinum strains. ” [2002] – this is in Prescript Assist Probiotics

Probiotics should be rotated: 2 weeks on a specific one, then several weeks off. As a general rule, you want about  6-12 B CFU taken three times a day (or 2-3 times the recommended dosage) — but work up slowly because you may get be a major herx! In general, do not take Lactobacillus with Bifidobacteria or with E.Coli etc. Keep to one family per cycle. You do not want them to kill off one another!

Why 3x per day? Because almost none of them are detected after 12-24 hrs. So to keep them — and the production of natural antibiotics — going, you need to keep taking them during the day. See this post for citations.

The following probiotics commonly seem to help people with CFS/Lyme/Fibro:

• Symbioflor-2
• Mutaflor
• Lactobacillus Fermentum ME3
• Lactobacillus Kefiri LKF01
• Lactobacillus Reuteri
• Lactobacillus Casei
• Bifidobacterium infantis
• Bifidobacterium Longum
• Bifidobacterium bifidum
• Bifidobacterium Breve
• Prescript Assist
• General Biotics Equilibrium

Some probiotics, however, may make your symptoms worse! And, unfortunately, most commercial probiotics contains some of these. At the moment Bifidobacterium animalis, Saccharomyces boulardii and Lactobacillus acidophilus are on my best to totally avoid list.

• “. The findings show that the six species of Bifidobacterium differed in their ability to relieve constipation. B. longum, B. infantis and B. bifidum were the most effective in relieving constipation, B. adolescentis and B. breve were partially effective and B. animalis was not effective. Furthermore, edible Bifidobacterium treated constipation by increasing the abundance of Lactobacillus and decreasing the abundance of Alistipes, Odoribacter and Clostridium. .” [2017]

On my neutral list (no clear benefit) is Lactobacillus Plantarum.

Teas

Some teas can also be antibiotics (among other roles). There are two teas that seem to produce significant results quickly:

• Rosehip Tea
• Tulsi Tea

Again, rotate and, if practical, change brands too. Their antibiotic compounds are different from different sources.

Herbs and Spices

The best choice needs examination of your microbiome (i.e. uBiome results) and doing the work cited above.  Survey results found:

1. Neem and Oregano with 80% improving
2. Olive Leaf and Licorice with 56% improving
3. Thyme with 50% improving
4. Wormwood and Tulsi with 33% improving

Other things

If you do not know your microbiome, then see https://cfsremission.com/reader-surveys-of-probiotics-herbs-etc/  for suggestions. Your results will vary because your microbiome vary.

Thick blood is an issue also — but here things gets more complicated and not suitable for this recap.

Antibiotics can have a role — but getting prescriptions for the right ones can be a major challenge.

Metabolism Shifts

From volunteered data, we can identify some distinctive shifts, see Metabolism Explorer Summary

Bottom Line

Working with the microbiome and autoimmune is like working with fragments of the dead sea scrolls. For many bacteria we can identify it — what inhibits or encourages it is not known to modern medical science.  We have extremely thin slices of knowledge –Almonds enhances Bifidobacterium, Lactobacillus (B&L)  as do sesame seeds. What about sunflower seeds? Peanuts? Cashews? We find that Walnuts help the bacteria that inhibits B&L — so we cannot safely generalize to “all seeds/nuts are helpful”.

In many cases, we find that healthy diet or supplements demonstrated to work for normal people have the opposite effect on CFS and other altered microbiome conditions. This is made even worst because most of the studies were done on males and most people with CFS are females. We end up having to swim up-stream thru good and valid suggestions — that are just wrong for us.

My model is simple to understand and allows us to filter many suggestions and candidates. With the availability of uBiome testing (without needing a prescription!) we have entered the age of explicit treatment based on your unique microbiome. We do not know the role of many bacteria involved. We do not know what will inhibit or enhanced all of these bacteria. Frustrating little knowledge!

On the flip side, many readers have reported significant improvement, reduction of prescription medication, etc. so the model and suggestions have potential and thus hope of remission! Microbiome studies are exploding on PubMed, a lot of research is being done and we can often borrow their results.

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any medical condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.