uBiome progression in ME Flare

This is a follow up to my earlier post: Sudden Onset ME Flare – uBiome One Week Later The purpose of this series is to gain insight on what happens during the early stages of Myalgic encephalomyelitis/chronic fatigue syndrome . A ME diagnosis takes at least 6 months after onset to get usually. In my case, I have been down the full route and I know the early symptoms (which allows rapid intervention).

Ubiome Results

Reports Showing Changes.

There was some improvement over the two weeks, but the lost of microbiome function continued in other areas. This is not unexpected because the microbiome state is a cascade of microbiome changes that takes time to resolve (a Markovian chain to any geeks reading this).

Good News 🙂

Serotonin produces have made a major improvement and GABA is starting to improve.

Bad News 🙁

A delayed major collapse
Alcohol consuming bacteria – Interesting disappearance
Akkermansia continued its collapse
Decreased (more tolerant) – likely because of higher yogurt consumption.
This is likely good news…..

Reports with no change

Production of Vitamin K and Vitamin B9 — still at Zero: Supplement time!

Yogurt has no effect

Despite a liter of yogurt each day — no effect

Microbiome Prescription Site

Over on this site, our news is different from ubiome.

Bacteria Pattern matching conditions

The number of high bacteria associated with known conditions dropped back to almost my prior levels from a year ago. The number of low bacteria associated dropped significantly.

The associated conditions with the most significant drops are shown below:

End Products

In terms of End Products, a number of significant shifts (remember this is an experimental report)

  • INCREASE in:
    • 5-hydroxytryptamine (Serotonin)
      Acetylcholine
      Bacteriocins (natural antibiotics)
      betaine
      Biogenic amines
      Cobalamin (Vitamin B12)
      D-Galactose
      D-lactate
    • Endocannabinoids
      Fucose
      Lactic acid
      Urolithins
  • DROP in:
    • 3,4-Dihydroxyphenylacetic acid
    • Bicarbonate (to zero)
    • Methane

Bacteria Shifts

Remember that there are no ‘norm’, I have the left 2 columns from being in a full (symptomless) remission and the right 2 are from this flare.

The main class of concern is Fibrobacteria, a minor concern for Deltaproteobacteria
For what changes this, click here

At the Genus level,

  • low Staphylococcus is a concern (0,0 -> -98%, -98%)
  • low Anaerococcus also (0,0, -> -45%, – 65%)

Bottom Line

I will be doing another uBiome next week. Overall, I am positive.

  • I am up to 2 – 3 hrs/sessions with a break between for work (i.e. 75% time), using vacation time to keep me at full pay check.
    • Compare to my usual work day (3 hr of commute + 8hrs, I am at 55% of normal)
    • I have tried pressing to a 4 hr session once or twice a week, I can really feel it the next day — so 3 hr work-sessions is my safe zone.
  • Once a week, I do an ‘outing probe’ – that is drive or driven for a hour, then meet with friends for a few hours then head home.
    • Still have ‘day after payback’:
      • often with depression,
      • impaired cognitive function for the following day — which clears by the second day.
      • sleep pattern disturbances
    • This probe helps me keep real with the actual state of recovery (i.e. work from home is fine, a commute to work would worsen the situation).

Two Approaches to suggestions

The normal approach is to upload the ubiome.json to the analysis site and see the suggestions. After doing the above analysis, I can get suggestions based solely on the areas of my concern:

  • low Staphylococcus
  • low Anaerococcus
  • low Fibrobacter

by going to the All Bacteria [Genus] Reported page and just entering those 3. This approach excludes the shifts from population norms, which may be natural shifts (due to DNA) for me. For example, Fibrobacter only occurs in 30% of people — but it was there always prior to this flare — so it’s loss is likely significant .The results are shown below — and very interesting

Looking at probiotics only:

Using the full set of bacteria: