Microbiome Comparisons

Over this weekend I deprecated my earlier comparison tool and replaced it with more comparisons. To use this tool you need at least three samples uploaded. The comparisons available ate:

  • By Bacteria
  • By End Products
  • By Enzyme production
  • By KEGG Module

Purpose or Usage

The intent is to address the following two needs (there may be more)

  • You want to see what has changed from your prior samples. Typically, to see improvement or deterioration.
  • You have an individual with challenges and have other samples from your microbiome bubble.
    • People with shared DNA are part of your bubble
    • People eating the same diet (i.e. family meals) are part of your bubble
    • Conceptually, people with the share medical conditions could by part of the bubble. My observations is that these people should have the same symptoms not just the same diagnosis.

There are four methods of comparison of one specific sample against a collection of reference samples.

  1. Values outside of the values of the reference sample
  2. Values outside of the values of the reference sample increased by one standard deviation up and down
  3. Values outside of the values of the reference sample increased by two standard deviations up and down
  4. Values outside of the values of the reference sample that are also in the extreme compared to other samples uploaded (top or bottom 3-6%)
Select the reference below the buttons, pick up the one to compare to above and then click one of the buttons


I picked several prior samples and my latest sample for comparison. Note that Reference Samples Reporting if less than all (in this case 8), it means that there were some zero values (and thus, you may wish to ignore shifts being low for those).

I tried different method and was surprise to see a long list of bacteria that have readings very different than than prior samples and also extreme values.

Note: The high and low thresholds are listed and your current values. You may need to use judgement if something is a significant change.


When I want to see just what shifted without restricting to high/low values also, we get a much bigger list.

End Products

Changes that also pushed values into top and bottom of ranges
Things that significantly changed
Items with some changes


Change with values going to extremes

When I look at changes in general, the list became massive…

Bottom Line

This tool gives information on what changed… what it means and what to do with it is a different question. At the moment, I would suggest reading and researching items that seems to be major. The microbiomeprescription.com site gives suggestions on modifying bacteria numbers.