Release Notes — 2023


  • Dec 31,2023 — Added Emoji to Suggestions Taxon to improve clarity on the list (See above)
  • Dec 27-31,2023 — Fixed some sign reversals for impact on parent and child bacteria. The logic used could produce the wrong sign (i.e. minor increases when minor decrease was intended)
    • This impacts some suggestions, in some cases major impacts.
    • The adding Emoji above exposed the issue.
  • Dec 1,2023 — Update the Taxonomy Hierarchy and Names to the latest NCBI Standards.
    • This may cause some suggestions to move up or down
  • Nov 1,2023 — started to purge stale and unused tables and code. Minor breakages are expected.
  • Oct, 2023 — Updated Processing of Kaltoft-Moldrup ranges with tuning.
  • April 11th, Updated Modifiers inferred from Bacteria Association
  • April 9th, Updated Bacteria Association data (3 hours of computations)
  • April 7th, added impact of modifiers on PubMed Medical conditions, Video
  • April 5th, add percentage vs percentile to Multiple Samples compare Video
  • April 3rd, added detection of likely bacteria causing microbiome dysfunction Video.
  • April 1st, added finding antibiotics for treating multiple bacteria issues with ability to see which would have the best side effects. Video
  • March 30, added “Just give me the suggestions” – a dumb down fast way to get suggestions. The items listed are partially based on the amount of information we have on each substance.
    • There has also been de-duplication of some items that are apparent contradictions. The one with more information was usually selected. Video
  • March 20, fixed bug entering symptoms when symptoms were entered for a prior sample.
  • March 19, Automatic removal of specific probiotic species suggested when the sample has a percentile over 70%ile.
  • March 4, Cleaned Citations removing duplicate facts, restructured to prevent future duplications
  • March 2, Add Food button to Bacteria Look Up
  • Feb 19, Added new filter buttons to Modifier Page.
Where the new page is – this uses the symptoms entered with the sample’s enzymes computations
  • April 22, Added Probiotics for Symptoms based on KEGG Enzymes (not sample specific – generic), see this post
  • Apr 4-21 Implemented Categoric Logistic Regression to Symptoms for:
    • Bacteria (Taxonomy)
    • Compounds estimated from KEGG
    • Enzymes estimated from KEGG
The page show the odds for increasing or decreasing by over 1690 different significant factors
  • April 3, Refactor KEGG Probiotic Suggestions, see post.
  • April 2, Added/Update Bacteria Healthy ranges on per bacteria basis. The computed ranges are linked to pages explaining the method
Example from
  • April 1, Implement periodic update from NCBI on new bacteria (on 21st of each month). Today, there was 2,419,768 different bacteria classified and assigned NCBI numbers
  • Mar 27,investigate odd Kaltoft-Moldrup ranges. Discovered typo in formula, running tests and recalculations.
  • Mar 26, Change all distribution charts to real time (Taxon broke for a short while — now fixed)
  • Mar 25, added MicrobiomePrescription : KEGG NET Compounds Produced by aor / probiotic-3
  • Mar 18, added MicrobiomePrescription : Using OATS test to pick probiotics
  • Mar 20, revised the Components Menu.
  • Mar 16, Comparing Probiotics using KEGG Data
  • Mar 12, Some Downloads Available in “Nerd” mode
  • Mar 8, What Probiotics Produced and Consumed (with amount)
  • Feb 12, implemented Display Levels to allow people to better handle information overload.
  • February — rework the KEGG data to estimate species from existing strain information
  • Jan 19, Added links to Bacteria Details from Researched Probiotics Page
  • Jan 17, added Kegg Detail pages (for bacteria in KEGG)
  • Jan 15, Fixed bacteria selection bug on GMRepro page
  • January – onwards. Move periodic updates to a dedicated machine (16 GB memory, SSD Drive, 8 processors) and proceeding to replace old adhoc code with consistent new code. as well as improve performance. (The first complete update run of the old code was over 72 hrs, this has been greatly reduced). Work is still ongoing (mainly catching issues)