Three Parts of Taxonomy:

1. Classification - the theory and process of ordering organisms
2. Nomenclature - giving names of appropriate taxonomic rank to the classified organisms
3. Characterization and Identification - obtaining data on the properties of organisms

Interrelationship between characterization, classification, and nomenclature in the taxonomy of prokaryotes:

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Based on Linnaeus

Domain

Kingdom

Phylum (ignored in bacteria)

Class (ignored in bacteria; however there are subclasses: α, β, γ, δ, and ε)

Order

Family

Genus

Species

Subspecies

Type Strain - one strain of a species is designated as the type strain. Serves as the permanent reference specimen for the species.

Phylotype - cluster of clone sequences that differ from known species by ca 30 bases (2%) or more and are at least 99% similar to members of their cluster → different species, but cannot classify it taxonomically until more is known

Conventions when using binomial nomenclature include:

• genus comes before species (Streptococcus mutans)
• genus name is always capitalized (Streptococcus)
• species name is never capitalized (mutans)
• both names are always either italicized or underlined (Streptococcus mutans or Streptococcus mutans)
• the genus name may be used alone, but not the species name

Mutans streptococci ≠ Streptococcus mutans

Streptococcus mutans was originally isolate in 1924.

8 serotypes , a-h, were identified based on the serological specificity of carbohydrate antigens in the cell wall.

Today, these 8 serotypes have been divided into several distinct species.

Morphology (micro- and macroscopic) and cellular structures (phenotypic properties)

• Cell Shape
• Colony Morphology (texture, color, odor, size, shape)
• Spore Formation and Spore Location
• Gram-stain (Cell Wall Structure)
• Motility

Physiology/Biochemistry (phenotypic properties)

• Aerobiosis
• Photosynthetic Ability
• Growth Temperature
• pH Tolerance
• Ability to use various carbon and nitrogen sources
• Metabolic Product Formation
• Special Nutritional Requirements (e.g. vitamins)

Chemical Composition

• Components of the Cell Wall
• Components of the Outer Membrane
• Components in the Respiratory Chain
• Protein Profiling
• Mol % G+C in the Genome

Serotyping

The ability of antibodies to bind to and/or inactivate microorganisms can be employed to determine evolutionary relationships.

Phage Typing

Similar strains of organisms with similar/identical surface receptors will support the growth of identical types of phages.  The phage type (or typing) pattern thus may be employed to distinguish strains.

Genetic Characteristics (Molecular tests) --usually used in intra-species comparisons

1. DNA Fingerprint (RFLP--whole genomes are analyzed; RFLP in combination with Southern hybridization; PCR--use of random primers)
2. DNA-DNA hybridization (microarray--total genomic DNA; specific genes such as 16SrRNA; limited to the characterization of closely related strains, species and genera; checkerboard hybridization analysis--tests many unknown species together) -- interpretation of results: 100% hybridization = same organism, >70% = same species, >20-30% = same genus, <10% = "unrelated"
3. DNA Sequencing

• The gene must be present in all organisms of interest; e.g. genes involved in replication, transcription, or translation
• The gene cannot be subject to transfer between species (late transfer)
• The gene must display an appropriate level of sequence conservation
• The gen must be sufficiently large to contain a record of the historical information