Update and Recap

Ideas on this blog has evolved as more and more information have become 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 that I am working off and my thought process.

Microbiome Definition of CFS/FM/IBS

A condition that results from:

  • Low or no Lactobacillus
  • Low or no Bifidobacteria
  • Low or no E.Coli
  • A marked increase in number of bacteria genus (as measured by uBiome) to the top range
    • Most of these genus are hostile to/surppress 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.

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.

Other Supplements Reported to Help

Bootstrapping Bifidobacterium and Lactobacillus

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

Unless the bifidobacterium and lactobacillus (B&L) are human sourcedthere is almost zero chance of taking up residency. Taking probiotics will not allow B&L to get established — 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. The 2017 paper by Peterson, Klimas, Komaroff, Lipkin (and a stack of other CFS researchers) makes that clear in it’s title: “Fecal metagenomic profiles in subgroups of patients with myalgic encephalomyelitis/chronic fatigue syndrome”

The best way at present to proceed is to get uBiome.com done.[No financial interest]. When the results come in, click on the Compare tab, then go to Genus, click on ratio twice so the results are in descending order.

This is the “hit list” of what you are trying to reduce. DataPunk.Net provides a nice summary of what we know about these. For example, Alistipes: https://www.datapunk.net/substrata/display.pl?239759+S

At this point, we hit a cognitive challenge.  You want to avoid items that are “Enhanced By” which is in common across all of the high items, 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 some uBiome.

  • 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 (no surprise there) and have started creating posts based on it’s data and then added studies from 2016 and 2017 to the page. Current pages are below (I will add more links as I research other genus)

  • Adlercreutzia: https://cfsremission.wordpress.com/2017/10/14/decreasing-adlercreutzia-genus/
  • Akkermansia: https://cfsremission.com/2017/10/14/decreasing-akkermansia-genus/
  • Alistipes: https://cfsremission.com/2017/10/09/decreasing-alistipes-genus/
  • Anaerostipes:   https://cfsremission.com/2017/10/07/decreasing-anaerostipes-genus/
  • Barnesiella: https://cfsremission.com/2017/10/15/decreasing-barnesiella-genus/
  • Bilophila:   https://cfsremission.com/2017/10/14/decreasing-bilophila-genus/
  • Butyricimas: https://cfsremission.com/2017/10/14/decreasing-butyricimonas-genus/
  • Caldicoprobacter: https://cfsremission.com/2017/10/15/decreasing-caldicoprobacter-genus/
  • Collinsella: https://cfsremission.com/2017/10/10/decreasing-collinsella-genus/
  • Clostridium :  https://cfsremission.com/2017/10/07/decreasing-clostridium-genus/
  • Dorea :  https://cfsremission.com/2017/10/18/reducing-dorea-genus/
  • Faecalibacterium: https://cfsremission.com/2017/10/11/reducing-faecalibacterium-genus/
  • Gordonibacter: https://cfsremission.com/2017/10/09/decreasing-gordonibacter-genus/
  • Herbaspirillum: https://cfsremission.com/2017/10/12/reducing-herbaspirillum-genus/
  • Oscillospira: https://cfsremission.com/2017/10/15/decreasing-oscillospira-genus/
  • Parabacteroides: https://cfsremission.com/2017/10/17/decreasing-parabacteroides-genus/
  • Prevotella: https://cfsremission.com/2017/10/14/decreasing-prevotella-genus/
  • Pseudobutyrivibrio: https://cfsremission.com/2017/10/15/decreasing-pseudobutyrivibrio-genus/
  • Robinsoniella: https://cfsremission.com/2017/10/12/decreasing-robinsoniella-genus/
  • Sarcina: https://cfsremission.com/2017/10/12/decreasing-sarcina-genus/
  • Slackia: https://cfsremission.com/2017/10/15/decreasing-slackia-genus/
  • Subdoligranlum: https://cfsremission.com/2017/10/10/decreasing-subdoligranlum/
  • Sutterella: https://cfsremission.com/2017/10/13/decreasing-sutterella-genus/


Src: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4754147/

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.


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

Probiotics should be rotated (2 weeks on a specific one, 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 each other!!!]

Why 3x per day? Simple: 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 appears to actually help. Some probiotics may make your symptoms worst! Unfortunately, most commercial probiotics contains some of those.

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) are Lactobacillus Plantarum


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

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.

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 CFS. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.