Analysis Divergence: Biomesight x Microbiome Prescription

In general, I avoid comparing opinions/suggestions from different microbiome resources. Like my earlier The taxonomy nightmare before Christmas… post; some resources may be sufficient/adequate for some people; for others it is not. My criteria for both tends to be simple:

  • More data, and more complete data, tends to better results
    • For the Microbiome it means that Shotgun Analysis where the data is uploadable, complete (often 5000+ items) and has percentile ranking is my preference
    • For the Analysis it means how many substances are considered (MP: 2065), are all interactions considered (MP: 2.5 million), how many different ways of doing analysis are offered (MP: lots).

Whatever you are using may be sufficient. If it is not, then read on.

This person asked for my help on Facebook explicitly and to properly answer, I need to do some comparison of analysis, interpretations and suggestions.

ME/CFS for 9 years. LC from vax injury 2.5 years.

I’ve been following the biomesight recommendations for 18 months and my gut has improved massively. I’ve just completed my third biomesight test and results are in. I have been experimenting with nicotine patches for 6 months now and my fatigue and pem symptoms have improved massively.

However, my most recent results are back and they have never been worse! Do you think Nicotine has a really negative impact on our guts? I can’t explain why everything is soo much worse.

Ken Lassesen / Troy Roach this could be one that you guys could help on.

For info: my gut doesn’t actually feel worse, but the results are terrible 😂.

From a facebook User


The reader is relying on BiomeSight evaluation. IMHO there is no single magical number or formula but many features that needs to be examined. Below is a table of the three test results meta-information. Remember that I am use the same measurement of bacteria data as Biomesight.

My general impressions is improvement is continuing despite Biomesight indicating not. Why?

  • Shannon, Simpson and Chao1 Diversity Percentile all moved towards 50%ile from extremes, a good sign.
    • Biomesight Diversity score started at 100% (ideal) and went downwards; completely opposite read to mine.
  • Outside Kaltoft-Moldrup are the ranges that I have the most confidence in, and they continued to drop
Lab Read Quality4.47.310.3
Lab Quality Adjustment Percentage79.789.7100
Outside Range from JasonH677
Outside Range from Medivere131717
Outside Range from Metagenomics799
Outside Range from MyBioma444
Outside Range from Nirvana/CosmosId231717
Outside Range from XenoGene414040
Outside Lab Range (+/- 1.96SD)231624
Outside Box-Plot-Whiskers7961120
Outside Kaltoft-Moldrup53115120
Bacteria Reported By Lab677709866
Bacteria Over 90%ile513286
Bacteria Under 10%ile56263244
Shannon Diversity Index1.7231.9591.914
Simpson Diversity Index0.0680.0460.026
Chao1 Index134681491220849
Shannon Diversity Percentile64.491.887.9
Simpson Diversity Percentile64.643.418.2
Chao1 Percentile72.580.493.8
Lab: BiomeSight
Condition Est. Over 90%ile014
  • Biomesight (BS) and Microbiome Prescription (MP) appear to be using different list of pathobionts
    • 7 Dec 2023: MP reported 37, BS cites 49%
    • 24 Feb 2023: MP reported 31, BS cites 72%
    • 7 Jun 2022: MP reported 37, BS cites 36%

The Percentage of Percentiles

The charts are below — we see in the older samples that the 0-9%ile spike that is typical of ME/CFS has disappeared in the latest sample. My preferred single measure of gut health, Chi2 has moved from 60 to 49 to 45. Significant improvement.

Conclusion: Biomesight simple evaluation of overall health may be misleading because it is too simple an algorithm.

Health Analysis

Nicotine Patches Question

Nicotine is one of the modifiers consider by Microbiome Prescription Expert systems.

  • 2022-06-07: Nicotine patch was a low positive
  • 2023-02-24: Nicotine patch was a positive, 5x higher than above
  • 2023-12-07: Nicotine patch was a positive, less than above but 3x the first value.

Suggestions Comparisons

Biomesight just gives suggestions without any attempt to prioritize them. Looking at the suggestions from the latest sample(reader sent the PDF); we list them below. The highest Priority from Microbiome Prescription was 927 and lowest was -906.

Below are Biomesight suggestions followed by how Microbiome Prescription ranks them.

  • Prebiotics
    • Arabinogalactan: Massive Avoid: -906 (based on 331 interactions)
    • Galactooligosaccharides: Avoid -233
    • Guar gum: Avoid -106
    • Gum arabic: Avoid -107
    • Lactose (not in lactose intolerant)
    • Lactulose: Minor take: 81
    • Milk oligosaccharides: Major avoid -233
    • Pectin: Major Avoid: -570
    • Raffinose: Minor avoid: -65
    • Resistant starch: Minor avoid: -26
    • Resveratrol: Avoid -230
    • Stachyose: Avoid – 422
    • Xylooligosaccharides: Avoid: -390
    • Chitooligosaccharides: Minor avoid: -22
    • Yeast beta-glucan: Minor take: 38
    • Psyllium: Minor take: 65
    • Colostrum: Minor Avoid -95
    • Quercetin: Minor take: 39
  • Herbs and Spices
    • Triphala: Minor take: 43
    • Cinnamon: Minor take: 53
    • Ginger: Take: 108
    • Oregano: Take 138
    • Turmeric: Take: 218
    • Thyme: Take: 434
    • Curcumin: Take 180
    • Garlic: Take 200
    • Lauric acid: Take 200
    • Niacin: Major take 732
    • Cranberries: Avoid -22 / -685 (for flour)
    • Olive leaf: Take 179
    • Slippery elm: Major avoid: -803
    • Codonopsis pilosula: Avoid -113
    • Shen Ling Bai Zhu San: Minor take 26
    • high fiber diet: Avoid -99
  • Probiotics
    • Bifidobacterium longum: Avoid -120
    • Lactobacillus rhamnosus: Avoid -471
    • Bacillus coagulans: Avoid -289

So we have a few agreements but a lot of disagreements. It may be just “the change of microbiome environment shock” with either sets of suggestions is causing improvement.

Microbiome Prescription does a holistic approach for suggestions. It looks at the known impact on every bacteria being targeted for a modifier and makes the full details available to review (Click on the 📚). People have been double checking these citations. The decision on Arabinogalactan was based on considering 311 interactions, a few are shown below.

Another difference is that the bacteria selected is based on using 4 different algorithms to select what is of concern and then we do a Monte Carlo simulation on the suggestions.

My impression is that Biomesight considers one bacteria at a time and does not use that many studies to base a recommendation on. I do not know what extent BS consider the complexities of interactions. Biomesight would be the source of information to get better clarity on this.

So what are Microbiome Prescription Top Suggestions

I have placed a 🎯 besides those that are common suggestions

This person has ME/CFS and it is extremely well documented that B-Vitamins moderates those symptoms. Microbiome Prescription shouts out that they should be taken. Biomesight only cites one B-Vitamin (with no indication of importance). Some ME/CFS studies on the top suggested B-Vitamin ( Vitamin B1, thiamine ) suggested by Microbiome Prescription are shown below.

Your Choice as to Path

IMHO, there is no right answer. Go with Biomesight, Go with what a medical practitioner suggests. Go with whatever you see next in an influencer YouTube.

My best answer is above, it uses a massive amount of data to compute suggestions with a complete evidence trail for people to openly challenge. I have worked professionally as an information auditor and made sure auditability was build into the expert system. I have tuned the expert system to produce good results by doing cross-validation – i.e. 80-90% of suggestions for tested conditions are known to improve that condition from independent clinical studies. In this case, the top suggestions are in agreement with what has been known to help with his specific condition: ME/CFS. MP suggestions are not random shots in the dark but heavily data driven.

It is your choice — just don’t “mix and match” suggestions from different sources.

REMEMBER: Going Biomesight and transferring data to MicrobiomePrescription gives two analysis that you can compare and potentially ask the provider for the basis of their suggestions.

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 can compute items to take, those computations do not provide information on rotations etc.

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.

Leave a Reply

Your email address will not be published. Required fields are marked *