Crohn’s Over Three Years

This is a reader with a diagnosis of Crohn’s diseases with complications (severe histamine and mast cell issues, severe multiple chemical sensitivity). She also have had ongoing hot flashes for a few decase The Crohn’s has been stabled and does not require prescription medications; it has been treated by diet and the use of E.Coli probiotics (Symbioflor-2: SOURCES: and, and Mutaflor). When a flare starts, the E.Coli probiotics have been able to quiet things down quickly.

Using the new Food Suggestions (with consensus)

This is a new feature that is intended to supplement the first class suggestions from microbiome prescription. Almost 8000 different foods are evaluated. The intent is to allow people to fine tune diets for the most impact especially when flavonoids and sugar types are given by name, but not by what food contains them. Some foods may have both good and bad content, the intent is do a deep evaluation of the foods based on their reported nutrients. For more information, see this blog post.

Overview of Samples

The general impression of the samples is reasonable stableness. Some third party criteria improved (Metagnomics, Xenogeme) and other third party criteria (Medivere,MyBioma,Nirvana) got worst, and one with no change(JasonH). The same is seen with the statistical ranges.

Lab Read Quality34.13.8
Bacteria Reported By Lab524584721
Bacteria Over 99%ile596
Bacteria Over 95%ile304436
Bacteria Over 90%ile528284
Bacteria Under 10%ile452526
Bacteria Under 5%ile15104
Bacteria Under 1%ile000
Lab: Thryve
Rarely Seen 1%849
Rarely Seen 5%272951
Outside Range from JasonH777
Outside Range from Medivere151514
Outside Range from Metagenomics101012
Outside Range from MyBioma131312
Outside Range from Nirvana/CosmosId232314
Outside Range from XenoGene404049
Outside Lab Range (+/- 1.96SD)312218
Outside Box-Plot-Whiskers138109142
Outside Kaltoft-Moldrup184163205
Condition Est. Over 99%ile000
Condition Est. Over 95%ile121
Condition Est. Over 90%ile121
Enzymes Over 99%ile390
Enzymes Over 95%ile326423
Enzymes Over 90%ile6519471
Enzymes Under 10%ile1364568
Enzymes Under 5%ile422137
Enzymes Under 1%ile040
Compounds Over 99%ile261421
Compounds Over 95%ile1222929
Compounds Over 90%ile3503837
Compounds Under 10%ile1492422
Compounds Under 5%ile311718
Compounds Under 1%ile466

Looking at Special Studies:

  • 2020 – 7%- 21% matched, 38%ile against PubMed Criteria
  • 2021 – 5% – 18% matched, 32%ile against PubMed Criteria
  • 2022 – 5% – 16% matched, 74%ile against PubMed Criteria

The top common ones across the years are:

  • Poor gut motility
  • ME/CFS without IBS
  • Easily irritated
  • Post-exertional malaise
  • Depression

We do not have sufficient samples yet to do a special study for Crohn’s disease.

There appears to be a weak indication of worsening — this may be due to not being able to get Mutaflor (E.Coli Nissle 1917) during COVID restrictions. This was remedied shortly after the last sample.

Going Forward

Doing the usual three statistical methods (Standard Lab Ranges (+/- 2 Std Dev),  Box Plot Whisker, Kaltoft-Moltrup Normal Ranges) to get suggestions (including prescription drugs). I included prescription drugs to see if any typical Crohn’s drugs are suggested.

  • risperidone: was the top one, this is used to treat mood disorder (depression and irritability bacteria?)
  • hexestrol:  a nonsteroidal estrogen which was previously used for estrogen replacement therapy (hot flashes)
  • ethopropazine hydrochloride: a drug uses for Parkinson’s disease. A blood family member had Parkinson’s and the person has seen the occasion “shake” in her hands that has raised concerns about that condition
  • The next items were antibiotics and significantly less confidence.

This is not totally surprising that prescription items appear to match conditions. The mechanism of action of these prescription drugs may be partially thru the microbiome.

Returning to the non-prescription world, in terms of priorities:

In one sense, the reader was very pleased with these suggestions being almost entirely supplements. The histamine issues greatly restricts her food choices (she is already gluten free!)

Food Suggestions

I did a walk thru of the food suggestions for this sample. See the video below.

Experimental Food Suggestions

Presentation on What we are doing

This is a short video on the process

Sources of Data

How to Use

Go to Microbiome Prescription, log in and go to [Changing Microbiome]. At the bottom of each section you will see a check box. Make your usual selection and then check this choice and click [Get Suggestions]

You may wish to do a regular suggestion first. It seems that the more bacteria being selected, the finer the suggestions are.

The suggestions are on a subdomain to distribute the load.

Clicking on a food shows the nutrients. Nutrient that are higher than typical have a * . These are the reason for the food being selected. One or more of these nutrients should help your microbiome.

Walkthru of Updated Suggestions — with CONSENSUS

See this post for background of the sample used.

Pending Feature: Synthetic Impact

A reader asked me what is the impact on the microbiome of prunes. My response was simple — I know of no studies reporting the impact on the microbiome. Having a study is first class evidence.

I then pointed out to him that I have prunes on my web site under Foods with Flavonids,

With several listed

Clicking on it shows the contents, data is coming from these open sources:

I suggested that he looks up the main items that have studies and estimate.

Over the weekend, I reflected and realized that it would be more friendly for me to do this mathematically using some simplifying assumptions (i.e. the impact is linearly related to the component for all bacteria). The result is now added to the existing list of modifiers

These are second, perhaps even third class suggestions. We are running off inference.

You can get suggestions using these by selecting this


I am refreshing source data from US Dept of Agriculture and the EU equivalent and then need to redo the mapping of the components to appropriate proxies. This is not expected to be done before 2023. Feel free to play around with it — but the results are suspect until the data is updated and re-mapped.

Some lab ranges are Questionable!

People may transcribe data from the tests below to microbiome prescription for suggestions. I just added statistics for how many transcriptions that has been done for each, and I also provided statistics for what they report by bacteria. These latter statistics are very interesting, one lab reports 50% of people have too low lactobacillus, another lab reports 8% only.

Example of the statistics on usage.


In the video below, I show how you can verified that the ranges they are using are correct, or if the ranges are incorrect — perhaps based on some ideological theory about what makes a healthy microbiome.