More Before and After Fecal Microbiome Transplants uBiomes

Fecal Microbiome Transplants(FMT) had great promise when the first ones happened — almost immediate remission of CFS symptoms. With time we have discovered that the FMT benefit fades, sometime quickly, sometimes slowly. I fear that it may be a similar problem as blood transfusions and organ transplants — compatibility is needed, but we still do not know how to determine it.

There have been attempts to do high dosage antibiotics prior — which according to reports from readers — have not made significant changes in the pattern.

Patient Summary


  • Respiratory tract infections as a child
  • Pneumonia twice as an adult (hospitalised once)
  • Reflux and IBS symptoms on and off through the 2000s
  • In sept 2011 I came down with flu type symptoms may have been ebv. Looking back in retrospect I was overexercising at the time and probably not supporting it nutritionally so there were a number of stress factors contributing. I gradually went down hill. Diagnosed with CFS December 2011.
  • Had a small recovery in 2013 due to lots of relaxation techniques (breathing and mindfulness) strict paleo diet.
  • 2014 started back to work. Things were pretty bad(full blown SIBO symptoms) had bioscreen gut test done (attached) was given emycin.
    • Post emycin[Erythromycin] histamine  symptoms went away and mood/energy improved.
    • 3 months after did a course of flagyl,rifaxmin and nistatin followed by FMT (10 rounds).
    • Improvement for a few months then bronchitis required AB and gut symptoms came back.
  • 4 more rounds of AB combinations of Flagyl, neomycin,cipro and rifaximin.
    • Each time less benefit from the AB each time followed up by FMT.
    • In 2016 stopped work did elemental diet 2 rounds of 14 days.
    • Improvement of gut problems but lots of inflammation symptoms.
    • Things have been very bad since I have tried lots of different herbal protocols in the last 2 years with a limited amount of success.
    • My liver is struggling to process things (based on experimentation and a functional not supported by mainstream medicine test).

Current symptoms:

  • Fatigue is not that bad.
  • Constant cycling of gut symptoms: burning, cramping gas, bloating.
  • I react to many things I eat both foods and supplements but it is inconsistent. Histamine is definitely a problem and I think High salicylate/phenol also seem to be a problem.
  • Inflammation symptoms.
  • Tingling in face hands and feet.
  • Whole body trembling
  • Sharp pains in feet
  • Feeling like head will explode
  • Headaches
  • Mental state: Extreme depression and anxiety


Time Line

Phyllum Changes


Genus Changes



1/10/2017 3/07/2017

E.Coli Parent:Enterobacteriales:  < 0.01X
Gordonibacter:   0.04

E.Coli Parent:Enterobacteriales:  < 0.01X
Gordonibacter:   0.08
Diversity: 86%ile Diversity: 86%ile
Unique Bacteria
Unique Bacteria
B/F Ratio: 4.8x normal
B/F Ratio: 4x normal
Sleep Deprived Genus
Sleep Deprived Genus

Initial Impressions

  • EMycin: Erythromycin belongs to a group of drugs called macrolide antibiotics.  (one of the recommended ones, see this post)
  • cipro – Ciprofloxacin is fluoroquinolone antibiotic (one of the recommended ones, see this post)
  • Rifaximin: Does not reduce Bifidobacteria [2010] [2007] [2002]
  • Neomycin is an  aminoglycoside antibiotics.

I am unhappy to see that Bifidobacteria decreased, and happy to see the histamine issue disappear.

Analysis of Overgrowth on Both uBiome

  1. Akkermansia (genus) 
  2. Alistipes (genus) 
  3. Butyricimonas (genus) 
  4. Desulfovibrio (genus) 
  5. Odoribacter (genus) 
  6. Parabacteroides (genus) 
  7. Phascolarctobacterium (genus) 
  8. Victivallis (genus) 








The FMT did not result in positive significant change of the microbiome — same diversity, similar bacteroidetes/firmicutes ratio, etc.

There was one interesting change at the family level was those related to the Melatonin /sleep bacteria went down. Items #3 and #4 are my greatest concern — but all available information on inhibitors is zero.

The only thing common with the nutrients is D-Glucose — a familiar theme in many uBiome studies, has a helpful table here of foods low or without glucose. There are no common inhibitors 😦 .

One question that arises, does a FMT result in “noise” in the microbiome for N weeks after the FMT — resulting in instability of the microbiome (i.e. is this the cause of an absence of clustering seen above?)

Bottom Line

There was no mention of probiotics in the patient notes. Given the number of rounds of antibiotics I would suggest starting with Prescript Assist and then add in Equilibrium.  The E.Coli probiotics OR Lactobacillus Fermentum ME3 would be the next ones to rotate to.

The reader also supplied results from Genova Diagnostic test done before either of the above.

This would suggest:

  • butyrate supplements
  • Miyarisan (Clostridium butyricum) probiotics

As always, consult with a medical professional before altering diet, changing supplements or probiotics.