22.1: Learning Objectives

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Learning Objectives

After this lab you should be able to:

Perform biochemical tests used in the identification of bacteria.
Evaluate the results of the biochemical tests.
Judge which tests are appropriate for some bacteria, but not others.
Formulate how you will organize and address identifying unknown bacteria based on observations of the patterns in your results.

“Rice University scientists have invented a technology that could potentially identify hundreds of bacterial pathogens simply, quickly and at low cost using a single set of random DNA probes. Rice's "universal microbial diagnostic," or UMD, uses pieces of randomly assembled DNA and mathematical techniques that were originally pioneered for signal processors inside digital phones and cameras.”

"If a laboratory today wants to test for 200 known pathogenic species, they need 200 different tests, each with its own specific DNA probe that was designed specifically to bind with DNA from a particular pathogen," said study co-author Richard Baraniuk, the lead scientist on the new study. "Our technology is fundamentally different. With a small set of DNA probes, we can test for a large number of species."

"In many U.S. hospitals, it still takes several days to definitively identify the specific bacterium that's making someone sick," said Baraniuk, Rice's Victor E. Cameron Professor of Electrical and Computer Engineering. "The lack of rapid bacterial diagnostics can promote antibiotic resistance. Having an accurate, efficient and rapid system for identifying infectious pathogens quickly and inexpensively would help, and such a system would also be a valuable tool for public health, defense, global health and environmental science."

http://phys.org/news/2016-09-id-pathogens-dna-probes.html

Research article: http://advances.sciencemag.org/content/2/9/e1600025.full

New technologies are improving both the ability to identify organisms, especially in clinical settings, and the time needed for identification. These rapid tests are essential in improving patient outcomes. As databases of information increase, more organisms will be identified more rapidly and accurately. Traditionally, before the onset of genomic databases and technological advancements in testing procedures, bacteria were identified by phenetic means. Culture characteristics, staining characteristics, and the use of biochemical tests were the gold standard for ID. These procedures, as you are discovering, are labor intensive and take several days to complete. This has been a hurdle in improving diagnosis and treatment of infectious disease, especially in the current age of antibiotic resistance. Although these traditional procedures are being used less and less, and are often automated now, they still have value in clinical, industrial, environmental, and food testing labs. New technology is expensive, may not be widely available, and will not always ID unusual strains, new organisms, etc. Laboratory personnel are still trained to utilize and evaluate traditional tests as well as new tools.

For the microbiology student, performing these exercises not only introduces you to the types of tests traditionally done to identify bacteria, and a glimpse into the clinical lab, they teach you how bacteria grow and metabolize: use of different nutrients, molecules and enzymes they produce, respiratory abilities, etc. These exercises serve to reinforce that bacteria are living organisms capable of exhibiting a diverse array of biochemical properties. That even though they are invisible in our macro world, they are alive and well and going about the business of being extremely successful organisms, regardless of whether we are aware of them or not. It is essential that students understand them in this way, and not just as abstract “germs”.

To this end, you will learn how to run the tests and evaluate the results using your known stock cultures. You will then be able to apply your knowledge and logic to the identification of unknown bacteria later in the course. As you work through the tests and fill in the charts, it’s a good idea to produce your own master chart for the unknowns, and include cultural and stain characteristics.

The detailed tests are listed in the subsequent sections.

Contributors and Attributions

Kelly C. Burke (College of the Canyons)