A Reader with mild CFS microbiome

Looking at this uBiome, I noticed that the standard items are far less extreme (today) than most CFS readers. This was not the case a year ago, or 3 years ago. This appears to agree with only 1 uncommon bacteria and just 2 overgrowth bacteria genus (the lowest number that I recall seeing).

Reader Notes

 I’ve been sick so long, and tried so many things, that I’m not easily able to make choices.
I’ve tried many dietary interventions, ranging through Wahls’ Paleo Plus, Crook’s candida diet, high resistant starch, nothing but potatoes, etc.  I recently realized that I have histamine issues, so my latest rotation of probiotics dropped histamine-producing strains.  I’ve had presumed Lyme this summer and last, and did a month of doxycycline each time.  I have always taken probiotics during and after antibiotics.  
I have slow-onset, gradual progression CFS.  In my 30 years of experimentation, the only things that help are a very low carbohydrate diet (but I immediately get severely constipated and give up), and starting in August, 20mg Pyrroloquinoline quinone (PQQ) daily.  The PQQ has bumped me from high-moderate to high-mild. 
I am on day 3 of Bimuno.  I bought 3 packs of 30 because…..shipping from the UK.  If this is a bad idea, I would like to know that.
I have had multi-waking insomnia for decades.  I wake 3-5 times a night (in 8-9 hours), and usually go back to sleep quickly.  I have trouble with mental focus, so I don’t drive in crowded situations, or for longer than 15 minutes, or on highways.  I’m self-sufficient, spend almost all of my time alone, and leave the house 2-3 times a week for groceries and to replenish books from the library.  I can’t handle tv, movies, or any kind of streaming.
Gradual decline 3year ago  => 1 year ago, continuing until about 2 weeks from starting PQQ, then slow, irregular increase in function

Standard Items:

  • Lactobacillus: 0.02x (2014, 2015 – 0x)
  • Bifidobacterium: 0.18x (2014, 2015 – 0x)
  • Akkermansia:  0.28x (2.66x in 2014, 0x in 2016)
  • Diversity:  75%ile
  • Firmicutes to Bacteroidetes:  2.0:1 (Normal 2.1:1)
    • 5.1:1 in 2014
    • 1.1:1 in 2016

Historic Trends


Uncommon Bacteria

Bacteria name Rank % of Samples
Anaerovorax Genus 3.2%

High Bacteria

Subdoligranulum: 3.71 X
Sutterella: 1.96 X


Bottom Line Suggestions

The lists below are done by merging the lists from the deep dives linked above. Some items may encourage one genus and discourage another genus — those are removed (unless it seems that it strongly predominates on one). The impact on Lactobacillus, Bifidobacterium and E.Coli are intentionally ignored [See this post for the logic]. This is all based on applying logic to the results of studies — thus theoretical. This is an addition (not a replacement) to this overview post.


  • Berberine
  • Bifidobacterim Breve
  • BPA bottles
  • Lactobacillus Casei
  • Lactobacillus salivarius
  • Omega 3
  • Saccharomyces boulardii
  • Walnuts


  • Bifidobacterium Longum probiotics
  • High Fat diet
  • Inulin
  • Lactobacillus plantarum probiotics

Personal Comment

The appearance of Lactobacillus and Bifidobacterium, with Firmicutes to Bacteroidetes approaching normal is a very positive sign. I need to revisit “Feeding of Lactobacillus”.

I will be researching Pyrroloquinoline quinone (PQQ) it is not something that I have come across before.

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