ME/CFS Patient- Ongoing Samples

This is a series of samples from a long time suffer from Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). In looking at the samples, we must keep in mind two factors:

  • Lab Read Quality. A low read quality reports much fewer bacteria than a high read quality.
    • 1.8 reports 300, a high read quality can triple the bacteria counts a category
    • This usually does not impact the broad stroke criteria such as Dr. Jason Hawrelak (JasonH)
  • A sickness (COVID, Flu) or even vaccination will alter the microbiome and create the appearance of lost ground. This was seen and covered in the post below

My usual practice is compare the latest with the prior only. Trying to weave a dialog covering all prior tests is contra productive with going forward. What is past, is water under the bridge.

This reader had one major question — the suggestions seem to have changed a lot. That is the focus of this post. Have there been a dramatic change, or are the changes likely connected to a few bacteria dropping off the list and a few new ones being added.

Earlier post for this person

Person’s Subjective Report: “Symptom-wise and treatment-wise, I don’t have much to report that is new or an outlier to previous years of samples and treatments.”

Review over Multiple Samples

Data from the same lab (using Ombre data, Biomesight version is also available).

Compared to the prior sample, we see:

  • Less extreme percentiles than prior sample
  • Less rarely seen bacteria
  • Less pathogens
  • Less outside of:
    • Outside Lab Range (+/- 1.96SD)
    • Outside Box-Plot-Whiskers
    • Outside Kaltoft-Moldrup
  • No change using a multitude of 3rd party criteria.
  • Less compounds at high levels, more compounds at low levels

General impression, there has been objective improvement

Lab Read Quality4.85.38.615.
Bacteria Reported By Lab638734800750312394544
Bacteria Over 99%ile414123934
Bacteria Over 95%ile36422421301012
Bacteria Over 90%ile56794649462536
Bacteria Under 10%ile2546154329162632
Bacteria Under 5%ile102154287101511
Bacteria Under 1%ile21784150
Lab: Thryve
Rarely Seen 1%101578029
Rarely Seen 5%366158702418
Outside Range from JasonH4444777
Outside Range from Medivere13131919141414
Outside Range from Metagenomics101077999
Outside Range from MyBioma13131010888
Outside Range from Nirvana/CosmosId22222222171717
Outside Range from XenoGene51514848424242
Outside Lab Range (+/- 1.96SD)18241417855
Outside Box-Plot-Whiskers67976363582845
Outside Kaltoft-Moldrup14321829040089102141
Condition Est. Over 99%ile0005210
Condition Est. Over 95%ile00224651
Condition Est. Over 90%ile073381192
Enzymes Over 99%ile134744414156
Enzymes Over 95%ile11417999727311465
Enzymes Over 90%ile46926624215254683512
Enzymes Under 10%ile13312321943070141106
Enzymes Under 5%ile5847108310478853
Enzymes Under 1%ile711646145
Compounds Over 99%ile113122312753
Compounds Over 95%ile3712267469305276
Compounds Over 90%ile1461902319338488365
Compounds Under 10%ile954809823998530617800
Compounds Under 5%ile906789788961521599787
Compounds Under 1%ile872783757892515582776

Comparing Suggestions

The reader noticed a significant change of suggestions between the samples. So I am going to document out how to verify or see the results. Also, remember that you can merge consensus from two different samples. Minor items like taking samples at different time of days, unusual food, significant dosages of herbs, probiotics or supplements within 48 hours of taking a sample can cause temporal shifts.

Step by step:

  • Do “Just Give Me Suggestions” for 1st sample
    • Click “For more technical details”
    • Click Download, save the file
  • Repeat for 2nd sample
  • Open Excel or equivalent on the .csv file downloads
    • Each sample will be in a difference instance of Excel
  • Add a new work sheet to one
    • Copy one set of data to the other
    • Rename worksheets as “Current Consensus” and “Prior Consensus”
  • Copy the Mid2 column to the first column in the Prior Consensus”
  • Insert a blank column after the Mid2 column,
  • Insert into this new blank column: =VLOOKUP(I2,’Prior Consensus’!A:J,2,FALSE)
    • This brings the net value over.
    • You can brink other values over by changing “2”

I have done a video below of the process.

Wait! This is more for your mobile phone users

Go to Multiple samples, then pick your samples as shown below

You will now see a summary at the top

In this case we have 80% agreement on suggestions between samples

Bottom Line

I have not done further analysis etc. The reader has acquired those skills already. I have address only the issue of shifting suggestions. My best advice is simple: Do an uber consensus between the present and the last sample. The logic is simple — samples has some volatility based on time of day that the sample was taken as well as substances consumed in the prior 48 hours. Remember we are dealing with a lot of fuzzy data — both in what is reported from your sample, and what changes what from the literature.

The result of an uber consensus is a continuation of the prior suggestions (with a little pruning) and incorporation of the current suggestions.