Taxonomy

• Taxon = arrangement

• Classification,

• Nomenclature,

• Identification

Classification

•the arrangement of organisms into taxonomic groups (taxon / taxa) on the basis of similarities or relationships.•Biochemical

•Physiologic•Genetic•morphologic

Nomenclature

• Naming an organism by international rules.

• International Committee on Systematic Bacteriology

• Bergey’s Manual of systematic Bacteriology

Identification

• The practical use of a classification scheme

• Taxonomic Ranks• Kingdom Prokaryotae

• Division Gracilicutes• Class Scotobacteria• Order Eubacteriales• Family Enterobacteriaceae • Genus Escherichia• Species Escherichia coli• Subtype Escherichia coli O157:H7

• Species

Sp.

Spp.

• Escherichia

• Escherichia coli

• E. coli

Classification• Species

• group of individual isolates or strains sharing a high degree of similarity in many independent features

Criteria for Classification • cell shape• Specialized structures (spore, flagella)• Staining ( Gram)• Characteristic pigments• Extracellular enzymes ( hemolysis )

• Characteristic metabolic functions (biochemical tests)

• Sensitivity to antibiotics• Molecular biology (comparing genes or genomes)

Numerical Taxonomy• Computer taxonomy

• Phenetics

• Taxometrics

Phylogenetic Classification• Common ancestor

• Close phylogenetic relatedness : recent ancestor

• No fossil record exist for bacteria

• There is considerable genetic diversity among bacteria

• G + C content

• DNA-DNA hybridization

• DNA sequencing

• Highly conserved genes

• Ribosome

• Ribosomal RNA

• Ribosomal proteins

• 16S rRNA

• Cells:

• Eukaryotes

• Prokaryotes

• Based on molecular phylogeny, prokaryotes fall into two major groups.

• the Eubacteria

• the Archaebacteria,

• 3 Domains

• Bacteria

• Archaea

• Eucarya

• Eubacteria:

• Gram-negative eubacteria

• Gram-positive eubacteria

• Eubacteria lacking cell walls

• Progeny

• Clone

• Colony

• Epidemiology

• Outbreaks

• Clonality

• Practical purposes (genetically identical)

• Biotyping

• Serotyping

• Morphotyping

• Bacteriophage typing

• Bacteriocin typing

• Antimicrobial susceptibility testing

Subtyping

• Nonculturable pathogens

• Molecular analysis