Example of how Lab Quality Can make Intrepretation Difficult + Oral Bacteria Issue

This person is a long time ME/CFSer. I should start by pointing out that the Eubiosis measure is easy to misinterpret. This person has a good 90.2% eubiosis. This indicates that things are more even (balance is likely a poor choice of word, too many meanings attached) — this is not a health measure as such. It’s a statistical measure whether the microbiome is matching the ideal pattern (not health specific).

Health Analysis is health orientated. Looking at those values we see a loss of health indicators while the evenness has improved.

  1. “Leaked” from Oral Cavity
    • By Taxa is 70%ile, was 48%ile (7/2023), 70% (09/2022)
    • By Volume 49%ile, was 19% (7/2023) , 38.5 (09/2022)
  2. Jason Criteria: 17%ile was 17%ile the same
  3. Key Symptoms bacteria went to 18 was 12

The Oral Cavity stands out as a concerning factor for this person.


We have a historic trend of 6 samples. We need to be careful of our interpretation because of differences in Lab Read Quality. The Lab Read Quality bounces around, and with that, other values may echo these shifts (i.e. up to 20% shifts for some measures). A low read quality means less bacteria are reported, for example, when it was low, the Outside Kaltoft-Moldrup has low, when it was high, the value became high.

Another way to view it is this: If 10% are out of range and 850 are reported then we have 85. If we have 500 in another report then we would expect 50. This could be misread as a 85/50 or a 70% increase in out of range bacteria. Technically, it is more complicated but that should explain the problem.

We have only one item 🙂 that is a clear improvement and one item suggesting a loss :-(.

Lab Read Quality7.94.4113.33.63
Outside Range from GanzImmun Diagostics151519191313
Outside Range from JasonH445566
Outside Range from Lab Teletest212118182727
Outside Range from Medivere161617171313
Outside Range from Metagenomics557788
Outside Range from Microba Co-Biome222222
Outside Range from MyBioma10103399
Outside Range from Nirvana/CosmosId222218182020
Outside Range from Thorne (20/80%ile)215215224224228228
Outside Range from XenoGene363635353737
Outside Lab Range (+/- 1.96SD)7142101126
Outside Box-Plot-Whiskers5549467392103
Outside Kaltoft-Moldrup114 🙁7284473886
Bacteria Reported By Lab749545838495660483
Bacteria Over 90%ile23 🙂47346669100
Bacteria Under 10%ile49282111244
Shannon Diversity Index1.9581.1721.5951.4911.970.933
Simpson Diversity Index0.0410.2340.0750.1280.0450.012
Chao1 Index165547002186146127111127513
Condition Est. Over 90%ile000000
Actual Symptoms in top 10 Forecastedn/a5n/a358

We have a good number of bacteria strongly statistically associated with symptoms

The difference between the two symptom forecast methods is shown below. The newer method (genus only) appears to predict symptoms better

Going Forward

With the revised algorithm (see Algorithm for “Just Give Me Suggestions” with symptoms we get the following. Unlike many samples, there were few antibiotics at the top of the list.  

To Take

Spices and herbs can be done as capsules, teas, oils or just putting on food, but given the Oral leakage — as teas should be considered.

raffinose(sugar beet)
lactobacillus casei (probiotics)
fructo-oligosaccharides (prebiotic)
rosmarinus officinalis,rosemary
garlic (allium sativum)
lactobacillus paracasei (probiotics)
vitamin b2,Riboflavin
Lactobacillus Johnsonii (probiotic)
peppermint (spice, oil)
bifidobacterium longum bb536 (probiotics)
trametes versicolor(Turkey tail mushroom)
lactobacillus reuteri (probiotics)
chondrus crispus,red sea weed
jerusalem artichoke (prebiotic)
lactobacillus sakei (probiotics)
lauric acid(fatty acid in coconut oil,in palm kernel oil,)
lactobacillus kefiri (NOT KEFIR)
green tea
foeniculum vulgare,fennel

Looking at probiotics, we have a good number that would allow easy rotation of probiotics. Two are usually difficult to obtain: lactobacillus kefiri and lactobacillus sakei . Most are available at my usual two preferred sources: Custom Probiotics and Indian Bulk Exporter (Maple Life Sources). See this list for sources not available there. By rotation, I mean 20-50 BCFU daily of one probiotic for 2 weeks and then change to another probiotic.

lactobacillus kefiri (NOT KEFIR)
lactobacillus casei (probiotics) [CB,MLS]
lactobacillus sakei (probiotics)
lactobacillus reuteri (probiotics) [CB,MLS]
bifidobacterium infantis,(probiotics) [CB,MLS]
bifidobacterium longum bb536 (probiotics)
lactobacillus paracasei (probiotics) [CB,MLS]
Lactobacillus Johnsonii [MLS]
Modifier To Avoid
Ferric citrate (iron)
Slippery Elm
Psyllium (Plantago Ovata Husk)
vegetarians Top of Form Bottom of Form
fibre-rich macrobiotic ma-pi 2 diet
xylan (prebiotic)

Oral Bacteria Issue

This may be a likely contributor to ongoing issues. Why? the sinus and oral cavity repopulates the gut and undo prior improvements. My best suggestions are to address this are:

  • When possible, drink teas with the any of the suggested herbs.
  • Do not take probiotics as capsules, instead as powder dissolved in warm water and hold in the mouth before swallowing. See Symbioflor® 1 – Respiratory diseases | SymbioPharm, this may help.
  • Address any dental issues

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 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.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.