uBiome and recovering CFS/IBS patient

A reader that have been following the model with great improvement shared their latest uBiome results. It has some interesting data points which I wish to review.

The patient is not 100% Recovered

My working definition of recovered using uBiome is having a ratio of firmcutes to bacteroides between 2.2:1 and 1.9:1. This patient is at 1.4:1 in April 2017, in January 2017 they were at 1.1:1; they are moving in the right direction but have some distance to go still.

  • Akkermansia (usually low in CFS):   Jan – 1.42% (71%), April 5.68% (287%)


Can you alter your microbiome? Looking at the Order changes shown below over 3 months, the answer is a clear yes!


Bifidobacterium and Lactobacillus at or above normal levels


What is very interesting is that after January, 2017 — there was considerable (major) stress on the person in this period — this may not be the cause of the decline, but personally, I consider it a contributor. Learning to deal with stress, flight or short fight or indifference are essential skills.

Looking at the split between Bifidobacterium and Lactobacillus,

  • Bifidobacterium: 176% in January, dropping to 0% in April
  • Lactobacillus: 3% in January, dropping to 2% in April
  • Diversity dropped from 97%ile to 89%ile.

Diet specific comparisons

uBiome provides comparison with average person and heavy consumers of certain things.


In corresponding with this person, they saw that they were low on the Kefir bacteria chart compared to those  who eat Kefir regularly and (thanks to residue brain fog that is progressively clearing) concluded that they need to eat more Kefir.  They were at the average level of non Kefir people. There is no need to add Kefir (or anything else) when you are at the average level for that.

A surprise on raw milk bacteria

This person does not consume raw milk, but the bacteria associated with raw milk have been increasing. This is a good thing. More diversity.


Interesting factoid on consuming raw honey

Some patients have reported improvement from raw honey. The uBiome cites Clostridium butyricum as being in it; this is available as a probiotic (on my recommended list) Miyarisan.  For this patient, they appear to be low… a little raw honey  or Miyarisan would be suggested.  Honey brings lactobacillus kunkeei which is not available as a probiotic.


Increase of Rare Bacteria also occurred with stress

It seems that a higher number of rare bacteria is an indicator for severity of CFS. This would be expected by the model. In January (pre-stress), these bacteria were seen in 1 of 10 healthy controls. Come April, we had the rare Caldicoprobacter, Gallicola, Mobiluncus suddenly appearing, and a few more common one appearing too: Gelria, Thermoanaerobacteraceae, Atopobium. One disappeared, Acidaminococcus — this bacteria uses amino acids as an energy source and its disappearance may imply the amino acids available in the gut has shifted (either not being produced enough OR some other bacteria hogging them).

Jan 2017 April 2017
janub aprub

Bottom Line

Heading into January, this patient was shifting nicely — correcting the typical CFS shifts. While no significant supplements changed, the appearance of heavy duty stress impacted the microbiome greatly …. the major change was that of Bifidobacterium disappearing!!! A secondary impact was the appearance of several rare bacteria.

Suggestions for the patient:

  • The stress is a hiccup. It has ended and time to get back to the model with a little preparation for the next stress event.
  • Invest in stress-coping techniques — may be prayer, may be yoga, may be self-help books, may be classes.
    • Whenever stress appears — write down plans for how to deal with it
      • Fight – Mark on a calendar when the fight will stop
      • Flight – May be disassociate with people, having excuses to miss meetings, etc
      • Ignore aka let-go of the stress. resignation (What will be will be – Que Sera,Sera!)
  • Resume with heavy dosages of Bifidobacterium
    • Consider adding some Lactobacillus (see this post)
    • Take Ashwagandha regularly for at least 2 months.

As a personal note — I am very aggressive in seeking a low stress workplace. If there are dysfunctional managers or co-worker, I start looking for a new job with the simple rule:

  • If I cannot get the work stress resolved in 2 months (including doing a HR request under ADA if my physician is willing to write a letter), and
  • I am offered a job at a financially tolerable salary which appears to have less stress
  • Then I will take the job and give the minimum required legal notice to my employer.

As a recovered CFS patient, you must protect your health (and uBiome results).