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Tutorial: Microbiology

Now that we’ve seen the drug, let’s look at the bug. As you remember, the cause of the Mongolian Mystery illness was identified as a facultative, gram negative bacillus. Let’s see how GIDEON can help us identify the organism.

In the Microbiology module, select the Identify tab next to Bacteria (upper left). Enter the following data by clicking yes or no. As you do this, note that GIDEON knows enough to ‘neutralize’ irrelevant tests using a yellow sign. The organism in question was:

  • Gram negative +
  • Coccus –
  • Bacillus +
  • Facultative +
  • MacConkey agar +
  • Oxidase –
  • Catalase +
  • Glucose fermenter +
  • Motile –
  • Indole –
  • ONPG +
  • Voges Proskauer –
  • Citrate –
  • Hydrogen sulfide –

… now enter a negative ( – ) for all tests from Nitrate to Nitrite, Nitrite to gas, DNA’se, Esculin … through Phenylalanine deaminase. In the Fermentation or Acidification list, check Adonitol negative, Alpha methyl glucoside negative, L-Arabinose positive, Mannitol positive, Sucrose negative.

The resulting screen should look something like this:

A list of probable organisms is displayed in the Identification List box on the right.

At this point, the Mongolian mystery bug appears to be Yersinia pestis !

This icon indicates that no information has been published regarding some of the tests we entered and the organisms in the list. Thus a positive/negative test cannot ‘rule out’ the relevant organism in these cases. The tests in question and other details are displayed when you click on the organism name.


As in the other modules, further information can be obtained for individual taxa or for the entire list using the buttons at the bottom. For example, we can ‘ask’ GIDEON, “What is the best additional test to perform at this point?” Tests which are most likely to shorten and focus the list are listed in the upper left, Suggestions box. You may also study the value of individual tests in differentiating among the listed taxa by generating a comparison chart. To do this, select all taxa by clicking top checkbox, and then press Compare .

As in the Diagnosis module, GIDEON lists additional tests to perform (best listed first), with additional hints in the lower box.

The and tabs allow you to access information on any specific organism; or compare a group of organisms. For example, I’ve asked GIDEON to contrast four well known species of Clostridium. Such charts are ideal for preparing student handouts, slides, etc.

Similar functions are used in the and modules.