1. Strain
1.1. Identify by
1.1.1. Name
1.1.2. Number
1.1.3. Letters follows by specific epithet
1.2. Different ways to describe strain within a species
1.2.1. Biovars : strains characterize by biochemical or physiological differences
1.2.2. Morphovars : differ morphologically
1.2.3. Serovars : distinctive antigenic properties
2. Nomenclature
2.1. The meaning of the names of some microorganisms
2.1.1. Escherichia coli
2.1.1.1. Named after Theodor Escherich (1988) , found in colon
2.1.2. Saccharomyces cerevisiae
2.1.2.1. Saccharo , sugar ; myco , mold ; cerevisiae , beer
2.1.3. Lactococcus lactis
2.1.3.1. Lacto , milk ; kokkus , berry
2.2. Rules
2.2.1. For protozoa and parasitic worms
2.2.1.1. International Code of Zoological Nomenclature
2.2.2. For bacteria
2.2.2.1. International Code for Nomenclature of Bacteria
2.2.3. For fungi and algae
2.2.3.1. International Code of Botanical Nomenclature
2.3. General rules in Nomenclature
2.3.1. Genus name always capitalized
2.3.2. Species name is never capitalized
2.3.3. Species name is never used without the genus name
2.3.4. Genus name may be used without species name
2.3.5. Genus and species are always italicized
2.3.6. Species name is never abbreviated
2.3.7. Less simple genus abbreviation if different genus start with the same alphabet
2.3.7.1. e.g. Enterococcus faecalis (En. faecalis)
2.3.7.2. e.g. Escherichia coli (Es.coli)
2.3.8. First time , have to spell out , thereafter the genus is abbreviated .
2.4. Inspiration of names
2.4.1. Shape
2.4.2. Where it is/was found
2.4.3. Nutrient it uses
2.4.4. Who discovered it
2.4.5. What diseases it causes
3. Numerical taxonomy
3.1. Computer-assisted taxonomy
3.2. Organisms sorted into groups of mutual similarity based on large number of observable properties
3.3. All characters having same degree of importance
3.4. Final result expressed in simple matching coefficient OR Jarcard coefficient
3.5. Based on association coefficient
3.5.1. 80% similarity-same species
3.5.2. 65% similarity-same genus
3.5.3. 0.0 (no matches) , 1.0 (100% match)
4. Fatty Acid Profiles
5. DNA Base Composition
6. DNA Fingerprinting
7. Nucleic Acid Hybridization
8. Phylogenetic or Phyletic classification
8.1. Natural system
8.2. Based on evolutionary relationships
8.3. Direct comparison of genetic material and gene products
8.4. What makes phylogenetic classification possible
8.4.1. Highly conserved genetic sequence
8.4.2. Advancement in sequencing technique
9. Morphological Characteristics
9.1. Easy to study and analysed
9.2. Characteristics studied
9.2.1. Cell type
9.2.2. Shape and size
9.2.3. Cellular grouping
9.2.4. External structures
9.2.5. Internal structures
10. Differential Staining
10.1. Gram Stain
10.1.1. Gram positive
10.1.1.1. Purple or blue
10.1.2. Gram negative
10.1.2.1. Pink or red
10.2. Acid-fast Stain
10.2.1. Stain bacteria with waxy material in their cell walls
10.2.1.1. e.g Mycobacterium
10.3. Negative staining for capsules
10.3.1. Use India ink to provide contrasting background , then stain with simple stain (safranin)
10.3.2. Capsules to not accept simple stain , appears as halos surrounding bacterial cell
10.4. Endospores staining
10.4.1. Schaeffer-Fulton endospore stain
10.4.2. Endospore appear green within pink cells
10.5. Flagella
10.5.1. Flagella are so thin
10.5.2. Use a mordant and stain carbolfuchsin to coat flagella until they are thick enough to be seen
11. Biochemical test
11.1. Phenol Red Broth
11.2. Gelatin Test
11.3. Lipase Test
11.4. Starch Hydrolysis
11.5. Motility Test
11.6. Catalase Test
12. Serology
12.1. Serological techniques
12.1.1. ELISA
12.1.2. Western blotting