How were the taxon sets collected?

MicrobiomeAnalyst supports three kinds of taxon sets based on the taxonomic resolution of the organisms or microbes present:

  • Strain-level taxa sets: These sets mostly consist of phenotypes, ecological niches and disease associated traits for 2270 microbial reference genomes derived from the HMP (Human Microbiome Project). It has been collected from comprehensive databases such as GOLD (Genomes Online Database) and PATRIC (Pathosystems Resource Integration Center).
  • Species-level taxa sets: These sets are manually collected from over 60 literature publications, organized based on their associations with various host physiological (age, weight, etc.) and biochemical measures (granulocytes, leucocytes, insulin, etc.), or disease states (heart attack, crohn’s disease, etc.), or life style factors (fruits, vegetables, alcohol, etc.).
  • Higher-level taxa sets: These sets includes disease associated traits derived from the MicroPattern.

All those taxon sets can be downloaded from the MicrobiomeAnalyst Resources Page.