Analysis of ex-CFS, now atypical Crohn’s with MCS

Web Site to do Analysis Coming

Over the Christmas holidays I am hoping to write a web site that will allow people to self-serve — with better algorithms where there is a conflict, and report symptoms with their ubiome results. Once that is up, I will discontinue these analysis unless one of great interest appears.

Reader Notes

  • Leaky Gut –> IBS –> CFS with mild MCS –> remission –> atypical Crohn’s with fistulas and severe MCS
  • None of the CFS symptoms (no brain fog, tiredness, etc)
  • MCS
  • Histamine issues

Standard Items:

  • Diversity: 15%ile
  • Lactobacillus:  0.0x
  • Bifidobacterium: 0.01x
  • Akkermansia: 0.01x
  • Firmicutes:Bacteroidetes: 3.6:1 (Normal  2.1:1)

Most aspects of a CFS profile, but as with a prior review, diversity is at the opposite end of the spectrum

Uncommon Bacteria

Fretibacterium Genus 1.3%
Anaerovorax Genus 3.2%
Succiniclasticum Genus 4.0%

High Bacteria

Anaerostipes: 4.54 X
Slackia: 3.54 X
Barnesiella: 2.73 X
Oscillospira:  2.50 X
Gordonibacter: 2.40 X
Clostridium:  2.22 X
Blautia:  2.15 X
Anaerotruncus: 2.02 X
Parasutterella: 1.58 X
Fusicatenibacter: 1.50 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.


  • Arabinoxylans
  • Aspirin (other NSAID’s are fine)
  • Bacillus subtilis
  • barley
  • Berberine
  • Bifidobacterium adolescentis
  • Bifidobacterium catenulatum
  • Bifidobacterium longum
  • Bifidobacterium pseudocatenulatum
  • Bifidobacterium animalis lactis
  • brown rice
  • Butyrate producing probiotics
  • Chicory root
  • Cholic acid
  • CVS Maximum Strength Probiotic
  • flavone
  • Fluoroquinolone
  • Glucose foods (fructose [fruit sugar] appears to be fine)
  • Glutten
  • high grain diet
  • inulin
  • Lactobacillus fermentum
  • Lactobacillus plantarum
  • Lactobacillus rhamnosus GG
  • Lactobacillus salivarius
  • L-sorbose
  • Metformin
  • Oligofructose
  • Omega-3
  • Pomegranate
  • Raspberries
  • Resistant starch (type II, IV)
  • Rosemary
  • Saccharomyces boulardii
  • Safflower oil
  • Sodium butyrate
  • Vitamin K2
  • Walnuts


  • Alchohol
  • Bacillus licheniformis
  • Bifidobacterium Breve
  • Bile supplements
  • Chitosan supplements
  • Enzymatically modified resistant starch
  • Flaxseed
  • Gallate – Tea
  • Grape seed polyphenols,/ Wine
  • Have Chocolate!
  • Lactobacillus Casei
  • Lactobacillus Kefiri
  • Lactobacillus Paracasei (24 BCFU/daily)
  • Lactobacillus Rhamnosus
  • Mutaflor (E.Coli Nissle 1917)
  • Oranges (pectin/flavanones)
  • Polymannuronic acid
  • Prescript Assist
  • Resistant starch (type II & IV)
  • Streptococcus probiotics
  • Vitamin D3
  • Xylooligosaccharide (XOS) prebiotic

A Challenge with Probiotics:

Inulin is on the avoid list and it is unfortunately included with many probiotics. do not add any prebiotics and provide single species, thus a source for:

  • Bacillus licheniformis appears to be only available in mixtures with Bacillus subtilis — so not feasible
  • Polymannuronic acid – is in Sodium Alginate (a food thickening agent) – Amazon


Usually I do not look at the cost and advocate people do what they can

  • Custom Probiotics: US$630 for 4 month supply or $157/month
  • Mutaflor:  $80/month

So taking continuously, $250/month. Alternating in two sets: $125/month, 3 sets $85/month, or lower dosages of each.

After exhausting the probiotics above,  another uBiome should be done. The microbiome would likely have shifted and we want to know if we need to change things.

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.