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Microbiology module overview

What is GIDEON’s Microbiology module?

GIDEON’s Microbiology module is designed to help users identify all bacteria and yeasts associated with humans. The database includes known or estimated incidence/prevalence rates for over 2,000 taxa, as well as the phenotypic characteristics used in their laboratory testing. Data are entered into a Bayesian matrix, which then lists all likely taxa in descending order of probability. Laboratory profiles of individual species can then be compared and analyzed.

Data are derived from all standard texts and journals through individual and electronic search. These data are upgraded on a continual basis, and phenotypic characteristics, new taxa, and classification are automatically refined in successive updates.

Identification limitations

The major problem in any identification program is the reliability of user input.

In some instances, phenotypic characteristics may represent a mixed culture, laboratory error, or the presence of a contaminant.

The Microbiology module is designed to identify and characterize Bacteria, Mycobacteria, and Yeasts.  The speciation of Parasites, Viruses, and Molds is based on a more complex array of tests that are beyond the scope of most clinical laboratories.

Virtually all human pathogens and commensals are listed. Phenotypic and biochemical tests were selected to reflect those generally available in routine clinical laboratories.

In some cases, the laboratory test profile entered by the user is not compatible with the organisms included in GIDEON.

This may reflect:

  • Inaccurate laboratory data
  • A mixed culture; or
  • A contaminant (e.g., fungus)

Altering output

While running the app, users may alter their listing of laboratory data. The flexible nature of data entry allows the user to consider, for example, “What if the organism in question were found to express pigment or ferment salicin?”


Microbiological data change continuously. New taxa, tests, and nomenclature are constantly updated in GIDEON. Check out the latest updates.