A reader wrote me saying:
I have 5 Biomesight samples uploaded to my MP.com account, of which 3 are mine and 2 are my kids.
When I choose a different sample from the dropdown list, the ‘Suggestions’ change as I would expect them to, however, the commercially available Probiotic recommendations do not change. So the Priobiotic ‘weighting’ is the same on all 5 samples, which I included a screenshot of.
Any idea why this is happening and how I can get accurate commercial Probiotic suggestions for each different sample?
Thanks much,
Step #1 Reproduce the issue
First item was checking that there was not duplicate uploads – there were not. I then got suggestions from each sample and list them below: I also included the top suggestion to verify that different suggestions were made.
There were duplicate suggestions between some samples:
- Two the same (2024-12-17, 2024-03-10)
- Three the same ( 2023-12-15, 2024-01-08, 2023-12-15)
One item was on all of the recommendation: L.Gasseri.
I also did Experimental Probiotics Suggestions using Taxa R2 Site. I find that I trust R2 suggestions more than the default suggestions. The differences are:
- Default is based on available studies — most have not been duplicated and have small sample size. Small sample size means only things that really stand out are reported. Most are done with 16s testing which is much less accurate than shotgun. We have 4,625 data points.
- R2 is based on 1000 shotgun samples and based on statistical associations ween between probiotic species and other species. There are no clinical studies showing that they work. We have 2,446,755 data points.
So the decision is trusting limited clinical studies, or trusting statistics with 529x more data points. My personal experience is that I have noticed more benefit from R2 suggestions than the default suggestions.
Sample 2025-06-29
Top amoxicillin [CFS] 1444
R2 Suggestions for Available:
Step #2 2024-12-17
Top Item: metronidazole [CFS] 1434
R2 Suggestions for Available:
- Bifidobacterium longum 399
- Bifidobacterium longum subsp. infantis 298
- Bifidobacterium catenulatum 268
Step #3 2024-03-10
Top Item: metronidazole [CFS] 584.5
R2 Suggestions for Available:
Step #4 2023-12-15
Top Ferrum {Iron Supplements} 1013
R2 Suggestions for Available:
Step #5 2024-01-08
Top imipenemL 932
R2 Suggestions for Available:
Step #6 2023-12-15
Top Cichorium intybus {Chicory} 839
R2 Suggestions for Available:
Bottom Line
The reader did report correctly that the same suggestions were being made. The default probiotics were likely correct based on the sparse data from clinical studies available. I would suggest that this user try the top 3 probiotics suggested by the novel R2 algorithm; I suspect they will have a greater and more targeted impact.
I am not surprised that given the limited palette of probiotics from clinical studies that we have convergence because the microbiomes have convergenes.
Key findings from published studies include:
- Overall Microbiome Similarity in Households: Multiple studies found that members of the same household, especially couples, have more similar gut, skin, and oral microbiota than individuals from different households. The effect is strongest for the skin microbiome, likely due to frequent direct contact and shared environment. The trend also extends to pets, with household dogs sharing microbiota with both adults and other dogs in the home.
- Cohabitation and Person-to-Person Strain Sharing: A large-scale study using over 9,700 human metagenomes reported substantial strain sharing among cohabiting individuals. Cohabitants shared a median of 12% of gut microbiome strains and 32% of oral microbiome strains. Time spent living together correlated with increased microbiome similarity, and this sharing was driven more by social interactions and environment than by genetics.
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