uBiome changes after a year

A reader for over a year did a 2nd uBiome recently. I have included some of their notes over the last year.


“As always I’m enjoying and learning much from your latest posts. I’ve been on some version of your basic cookbook/protocol off and on for a few years now. While I’ve had some symptom relief and a few extended weeks and even a month or two of improvement, I keep having setbacks. I am still disabled to the point of not being able to work more than 5-10 hours a week. …. I’ve had parvo, coxsackie, both confirmed via blood tests, and then influenza-a confirmed via nasal swab. The doctor who diagnosed the influenza immediately put me on Tamiflu, which I took for ten days. I honestly felt better on Tamiflu than I have in years. By day three of the Tamiflu course, after being bedridden and sick with very high fever and some of the worst body pain I’ve ever experienced, I was full of energy and strength. I did things that haven’t been possible for me for years, like take down and pack up the Christmas tree and lift the entire thing and haul it out to the street alone. I traveled across the country alone with my daughter and felt fine the next day, even energetic the same day I got home, unpacking and doing more chores. I even wanted to exercise. This level of physical exertion would normally have me, at best, resting for a few days to recover. More than likely they would result in a full week of pain and exhaustion before finally returning to “normal bad”. I was wondering how Tamiflu might fight in your model? Or, if you think that its effects aren’t microbiome related, that I may see more health gains by pursuing and possibly even rotating antivirals.”

—— a month later ———-

“Here’s some more grist for the CFS Remission mill. I had been much improved by upping my Vitamin D and adding Symbioflor-2. I was even working 20+ hours a week, a huge amount for me over the last five plus years. On top of those two mainstays, I rotate in another probiotic. Since I’m always low in Lactos and Bifidos via many stool tests over the years, three of which are featured on your blog, I aim for your recommendations on those. I’m no longer usually that sensitive to most supplements and probiotics and usually react well to Bifidos, especially for a slight but very elusive change in brain fog. But last Friday night I took ONE of these puppies and have been suffering ever sense. The next day I could barely move and had to resort to pain killers, the histamine reaction is still going strong with blocked sinuses and runny nose and constant sneezing. Here is a link to the Bifido only probiotic I took, which I believe is mentioned on one of your posts. There are several versions of this 25 Billion Bifido only option from Renew Life, but they seem to contain the same ingredients. http://www.renewlife.com/probiotic-supplements/ultimate-flora-daily-immune-probiotic-25-billion.html

————- a month later ————

“As part of my monthly or so rotation of herbs, I added in Black Cumin seed a few days ago. Big mistake. I swore I read about it on your blog, but could actually only find one reference to it on your site and that was on the Bibliography
————-2 months later———
“I had been taking Symbioflor-2 off and on for the last six months. I didn’t think it was doing much and didn’t reorder. What a big mistake! My pain and stiffness has come roaring back. I of course ordered more but it’s a two week wait to get it shipped from Germany. Is there anything else I can do in the meantime? I’m in so no access to Mutaflor either “
———————- this month —-
My symptoms haven’t been getting better overall, though they have been changing over the last year, more towards muscle cramping, rigidity and spasms as well as a continued worsening of my brain fog towards major difficulties in thinking and understanding. I went to see a neurologist because of this and had an MRI with contrast. The results weren’t enough to confirm MS, but there were several white matter lesions and I was told it was a “somewhat worrisome” finding for someone my age (38) and possibly early MS.

uBiome Results

2016 2017

Enterobacteriaceae:  0.01X

Biodiversuty 69%ile


Enterobacteriaceae: not reported

Biodiversity: 59%ile

Thalassospira: 2.30 X
Parasutterella: 2.27 X
Subdoligranulum: 2.14 X
Faecalibacterium:  1.83 X
Anaerostipes: 1.45 X
Hespellia: 1.40 X
Anaerostipes: 3.24 X
Alistipes:  1.95 X
Subdoligranulum: 1.76 X
Thalassospira: 1.71 X
Oscillibacter: 1.48 X
Bacteroides:  1.47 X
Faecalibacterium:  1.45 X
Parasutterella: 1.38 X
Bacteria name Rank % of Samples
Anaerobacter Genus 2.5%
Acidobacteriia Class 3.5%
Acidobacteria Phylum 3.7%
Asteroleplasma Genus 9.0%
Bacteria name Rank % of Samples
Anaerobacter Genus 2.5%
Cloacibacillus Genus 6.3%

I must admit that I was disappointed not to see major change in the uBiome. The reduction of rare bacteria, decrease of several over growths(4 went down, 1 went up), decrease of biodiversity (as measured by uBiome) — I view as an improvement. While significant changes in the uBiome did not happen the impact of the probiotics was significant according to their reports.

Bottom Line Theoretical Items

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 placed in inconclusive. 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.


In general, should try to avoid (helps some, inhibits some — we do not know the balance). These could be tried in isolation to other changes to infer their impact on your own uBiome.



Concerning  Multiple Sclerosis concerns , none (not one) of your high bacteria genus are reported to be high with MS. I was read as early Alzheimer’s disease on my SPECT scan. The bacteria induced changes appear to mimic some other autoimmune diseases (which may be caused by different bacteria shifts).

In my own experience, I ascribed my brain scan clearing to the following:

  • Nattokinease (note the Bacillus subtilis natto cited above)
  • Lumbrokinease
  • Serrapetase
  • Minocycline


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