Samples over time of ME/CFS Spouse

This is the spouse of someone with significant ME/CFS. It is well known that bacteria is transferred between people in the same household unit.

This raises all sorts of questions — which I am not interested in exploring… “For better or worse, in sickness and in health”

My wink wink suggestion for microbiome issues has been “Snog a lot of pretty young healthy things as the best probiotic” — my wife does not agree…..

Comparison between Samples

The first step that I did was to verify that all samples used the same reference sticks. This means clicking this for each sample first.

New reference tables are uploaded once a week.

This person has processed FASTQ data thru both BiomeSight and OmbreLabs. I am using OmbreLabs data below. Using reference tables uploaded in 2023.

Criteria6/8/20228/4/20229/6/202210/26/2022
Lab Read Quality2.13.83.68.3
Bacteria Reported By Lab534774721775
Bacteria Over 99%ile10326
Bacteria Over 95%ile58272422
Bacteria Over 90%ile99534450
Bacteria Under 10%ile256848127
Bacteria Under 5%ile13281577
Bacteria Under 1%ile53116
Lab: Thryve
Rarely Seen 1%814912
Rarely Seen 5%43806073
Pathogens21343327
Outside Range from JasonH5577
Outside Range from Medivere13131717
Outside Range from Metagenomics9999
Outside Range from MyBioma7788
Outside Range from Nirvana/CosmosId23231919
Outside Range from XenoGene44444949
Outside Lab Range (+/- 1.96SD)38392622
Outside Box-Plot-Whiskers177202153118
Outside Kaltoft-Moldrup206257203292
Condition Est. Over 99%ile0000
Condition Est. Over 95%ile0000
Condition Est. Over 90%ile0000
Enzymes Over 99%ile1418523
Enzymes Over 95%ile11510559112
Enzymes Over 90%ile212192143320
Enzymes Under 10%ile6310693266
Enzymes Under 5%ile294527141
Enzymes Under 1%ile2208
Compounds Over 99%ile373631119
Compounds Over 95%ile289288275281
Compounds Over 90%ile372381361385
Compounds Under 10%ile288255235298
Compounds Under 5%ile192159136216
Compounds Under 1%ile3714431

General Impression

  • After the first sample, the next two had improvements but the last one went the wrong way.
    • Too high and Too low reduce for 2 samples and then increased
    • Too high or too low for Enzymes were the highest for the last sample
  • Most of the third party ranges were constant for the first two samples and most got worst for the last two samples.
  • Compounds are much less indicative of issues.
  • Special Studies are sensitive to lab quality,
    • 6/8/2022 4-14%, top items: ME/CFS without IBS, Poor gut motility, Cold Extremities
    • 8/4/2022 5-17%, top items: ME/CFS without IBS, Poor gut motility
    • 9/6/2022 4- 18%, top items:  ME/CFS without IBS,  Easily irritated
    • 10/26/2022 7 -22%, top items: General: Fatigue, ME/CFS without IBS

ME/CFS without IBS is a consistent top item and we see that the percentage is increasing.

Proposed Approach

Unlike many samples, we see distinct deterioration in several 3rd party criteria. For many samples, there is no change between samples. We will include those in the consensus, namely:

  • JasonH
  • Medivere
  • MyBioma
  • Xenogene

It is interesting to note that one 3rd part criteria improved: Nirvana. To this, we do our usual:

  • Lab ranges
  • Box-Plot-Whiskers
  • Kaltoft-Moldrup

The net result will be more bias to those in the 3rd party criteria cited above. Another way of stating that, we will emphasis more that which everyone agrees are most concerning.

The top suggestions (easily obtained):

The top avoids are:

The downloads are attached:

SimpleSuggestions_I-Download
I_ConsensusDownload

Food Suggestions

We mostly eat pastured meats and vegetables. No cereals and little in the way of carbs or even fruit. I used to eat linseed crackers in the USA, but here I eat buckwheat instead. Here in Spain we switched from wild Alaskan salmon, to seasonal, local, small blue fish, like mackerel, sardines, etc. Added Rabbit and can eat a lot more quality raw cured pork, if we want to. I have always enjoyed natural wine and Spain has plenty of it. Fresh made coffee and 100% cocoa. Raw goat, sheep and cow’s milk are also available and I do enjoy them with some regularity.

I used the latest sample with the Kaltoft-Moltrup Normal Ranges. The top suggestions are each because of different nutrients that appear significant with Fiber, total dietary and Magnesium, Mg being a common theme.

On the avoid list we have at the bottom:

Remember, foods are filtered to the nutrients that are above typical levels for foods containing the same nutrients. The goal is to reduce the intake of nutrients that have been identified to shift things in the wrong direction.

For most people, if you say reduce folic acid in your diet — most people will not have a clue. The purpose of the food suggestions is to translate a precise item into common foods.

Note: If a food in your diet is not in the list then we deem it as neutral. For example: there are 24 variety of rabbit in the food database, only one shows up in the suggestions from the sample, Rabbit, meat, raw, Oryctolaguscuniculus, (Nyama ya kalulu), which suggests to keep eating rabbit. Similarly for milk, the two that shows up are Milk with Cow’s blood (from Africa) of 626 entries for milk.

The video below may help understand Food Suggestions better.

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”.  I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that appears to have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

I use modelling and various mathematical technique to estimate forecasts when there is no hard data available.

The information above should always be considered/discussed with your medical professional if possible.