uBiomes before and after a Fecal Microbiota Transplant

Over the last few years I have been in contact with a few people that have had FMT. A common pattern is symptoms disappears for a few weeks or months and then returns. If additional FMT are done, the pattern repeats. In short, it appears that the new microbiota lost the battle with the old microbiota. I have written prior about FMT in my “The poop on Fecal Transplants” post in 2014

I am very delighted to being able to examine the before and after ubiome from a patient was willing to share.

Patient Summary

  • “Under 30, female
  • Weaker immune system from a young age- bronchitis, pneumonia
    • I had mono age 16 [Epstein-Barr virus]
    • Many antibiotics for recurrent UTIs
    • Some antibiotic use for acne
  • Birth control use
  • Got food poisoning or gut infection from traveling to Dominican Republic- diarrhea/flu/severe cramping
    • Took a Zpac one month later for cold
    • Gut started to not function shortly after- not sure if it was a delayed result from the travel bug or from the Zpac
    • I had severe bloating diarrhea and constipation
  • Health started to really decline- fatigue, shortness of breath, food intolerance, weak, developed severe acne
    • Eventually diagnosed with sibo-hydrogen positive
    • Took many different antibiotics for sibo-D
    • Didn’t work, continued many other methods for gut healing
    • My sibo was now methane dominant and I was suffering from constipation
  • Nothing was helping.
    • Tested for lyme, got a positive diagnosis from LLND, went down that path of trying many different natural supplements and treatment
  • Eventually tried FMT, immediate improvements in brain function and lifted depression
    • Tried 20 implants, no real lasting results
  • Continued working on immune system.
  • Low dose naltrexone is the only thing that has made a noticeable positive shift in my health.”

Comments: Positive Lyme is common, especially if you have had mono sometime in your life. The EBV virus is suppressed and not eliminated by your immune system. Lyme tests are well known to give false positive when EBV is involved. — My lyme test was positive on my last CFS occurence and I suspected strongly that it was a false positive — since I was after prescriptions to tetracyclines (see this post), I kept quiet and insisted only on those….

I suspect that your past antibiotics use has been many different classes and likely contributed to your microbiome issues.

uBiome Result

Historic Changes

The changes between samples.


In terms of minor bacteria, this dramatic growth


At the Genus Level


Basic Analysis

Prior After
b1 b2
Diversity: 69%ile Diversity: 86%ile
u1 u2
g1 g2
E.Coli Order

Nothing reported

Akkermansia:   < 0.01x


Akkermansia:   < 0.01x

Initial impression: Things have been shaken up a bit but only marginal improvement (E.Coli order appearing).

  • E.Coli probiotics (Mutaflor, Symbioflor-2) may be worth trying.
  • You have token lactobacillus and bifidobacteia — which is better than the typical CFS patient.

While the overgrowth genus are different (except for Parabacteroides and Thalassospira), I think we should examine both lists to see if there are any distinctive patterns. As before, I’ve numbered each genus for a cross reference and head over to DataPunk.Net for data

  1. Alistipes (genus) 
  2. Bacteroides (genus) 
  3. Blautia (genus) 
  4. Desulfovibrio (genus) 
  5. Dielma (genus) 
  6. Flavonifractor (genus) 
  7. Lachnospira (genus) 
  8. Marvinbryantia (genus) 
  9. Moryella (genus) 
  10. Oscillospira (genus) 
  11. Parabacteroides (genus) 
  12. Pseudobutyrivibrio (genus) 
  13. Thalassospira (genus) 
  14. Victivallis (genus) 







Flaxseed sticks out as a regular (daily) food to intake. Making flaxseed muffins with sucralose and some whole grain barley for snacks appears to make sense. A vegetable diet with fish seems reasonable.

Avoid Walnuts and Resistant starch (type II) because we do not know if they are net benefit or loss.  The rest of the ‘to avoid’ is on the Enhanced By list above.

Resistant starch (type IV) is described in this study as “Foods in which modified starches have been used (for example, breads and cakes)” – which implies that most commercial wheat/gluten items should be reduced or avoided.  Beware of prepared soups — check the labels carefully,

Bottom Line

This is speculative, but I would love to see a study with the following done before the FMT is attempted:

  • One month on tetracyclines and macrolides before (stopped 2 days before the FMT procedure)
    • Inhibit the other overgrowths. Several of those that I have seen in the uBiomes are tetracycline resistant.
    • I know some repeated FMT tried antibiotics to increase the odds — I am not sure if they were the best choices
  • Diet adds Flaxseed for a month before and at least 2 months after
  • Diet low is glucose (i.e. already in the food — if other bacteria generates it, that may be fine)
  • High dosages of probiotics after the transplant that are known to persist. See this post.
    • We want to send in “shock troops” after the FMT in the hope of overwhelming the bad bacteria and giving the native bacteria time to regroup.
    • Lactobacillus Fermentus ME-3 should be included because of it’s strong antibiotics metabolites.

FMT bring immediate remission from MCS (and possibly both MCS and SIBO) strongly suggests that these conditions are due to microbiome dysfunction.  The problem with FMT is that people’s microbiome is connected to their DNA and inherited.  FMT suffers the same risk as organ transplants — rejection! Not only is the bad bacteria fighting the FMT bacteria — but likely the body is also fighting these foreigners!