Classification of Microorganisms
Bergey' s Manual of Determinative Bacteriology is the standard reference for laboratory identification of bacteria.
1. Morphological characteristics are useful in identifying microorganisms, especially when aided by differential staining techniques (Gram staining and acid fast stains can suggest a course of treatment before the organism is positively identified).
2. Differential staining for cell wall characteristics is also used as part of a classification scheme, so this particular method is used for both identification and classification. (See Table 10.5)
3. The presence of various enzymes, as determined by biochemical tests, is used in identifying microorganisms.
Rapid identification can be accomplished with specific sets of biochemical tests.
4. Serological tests, involving the reactions of microorganisms with specific antibodies, are useful in determining the identity of strains and species, as well as relationships among organisms. Slide agglutination (Figure 10.10), ELISA (Figure 10.11), and Western blotting (Figure 10.12) are examples of serological tests. I would argue that flow cytometry also employs serological methods, but doesn't have to.
5. Phage typing is the identification of bacterial species and strains by determining their susceptibility to various phages.
6. Fatty acid profiles can be used identify some organisms.
7. Flow cytometry measures physical and chemical characteristics of cells.
The DNA and RNA based methods (except for DNA fingerprinting) are used primarily for classification rather than identification, although PCR and nucleic acid hybridization are used for both. (See Table 10.5)
To read more about these techniques follow these links:
Restriction enzymes (needed for DNA fingerprinting by RFLP)
Colony hybridization - scroll down the page until you see it
DNA fingerprinting, Southern blotting, PCR, DNA sequencing, and DNA chip technology (microarrays) - click here
8. The percentage of GC base pairs in the nucleic acid of cells can be used in the classification of organisms.
9. The number and sizes of DNA fragments, or DNA fingerprints, produced by restriction enzymes are used to determine genetic similarities.
10. The sequence of bases in ribosomal RNA can be used in the classification of organisms.
11. The polymerase chain reaction (PCR) can be used to detect small amounts of microbial DNA in a sample.
12. Single strands of DNA and RNA, from related organisms will hydrogen-bond to form a double-stranded molecule; this bonding is called nucleic acid hybridization.
Southern blotting and DNA probes, including DNA chips, are examples of hybridization techniques. (Figure 10.16, Figure 10.17) Summary: (Figure 10.18)
Dichotomous keys are used for the identification of organisms. A dichotomous key may incorporate information from a variety of identification methods to identify organisms.
Cladograms show phylogenetic relationships among organisms. A cladogram can be constructed using data from different methods but typically uses one type of information.