1. Classification of Microorganisms – Chapter 9
Taxonomy
The science of classifying organisms
Provides universal names for organisms
Provides a reference for identifying organisms
Phylogeny
The study of the evolutionary history of organisms

2. The Three-Domain System

3. Taxonomic Hierarchy

4. Species Definition Eukaryotic species:
A group of closely related organisms that breed among themselves and produce offspring that can produce offspring
Viral species:
Population of viruses with similar characteristics that occupies a particular ecological niche

5. Prokaryotic species:
A population of cells with similar characteristics
Based on:
morphology
biochemistry
genetics
Strain: Genetically different cells within a species

6. Domain Eukarya
Animalia: Multicellular; no cell walls; chemoheterotrophic
Plantae: Multicellular; cellulose cell walls; usually photoautotrophic
Fungi: Unicellular or multicellular; cell wall structure varies; Chemoheterotrophic
Protista: A catchall for eukaryotic organisms that do not fit other kingdoms; Predominantly unicellular

7. References • Bergey’s Manual of Determinative Bacteriology
Provides identification schemes for identifying bacteria and archaea
Morphology, differential staining, biochemical tests
• Bergey’s Manual of Systematic Bacteriology
Provides phylogenetic information on bacteria and archaea
Based on rRNA sequencing
• Approved Lists of Bacterial Names
Lists species of known prokaryotes
Based on published articles

8. Identification Methods
Morphological characteristics: More useful for identifying eukaryotes than prokaryotes
Differential staining:
Gram staining
Acid-fast staining
Special staining
Negative staining
(Endo)spore staining

9. Identification Methods
Biochemical tests:
Determines presence of specific bacterial
See Animations → Dichotomous Key (chapter 10 Microbiology Place CD or website)

10. Miniaturized Rapid Identification – “Enterotube”
Vitek 2 – a more advanced miniaturized rapid identification system

11. Serology
Combine known antiserum + unknown bacterium or bacterial antigens
Slide agglutination
ELISA
Western blot

12. Another antibody-antigen test
Rapid “Strep” throat test
Detects Group A streptococci (i.e. Streptococcus pyogenes) in minutes.

13. Flow Cytometry Can identify different cell types
Fluorescently labelled antibodies are attached to cells
Computer detects cells

14. Genetics DNA fingerprinting Electrophoresis of enzymatic digests
rRNA sequencing

15. Nucleic Acid Hybridization: DNA chip