بسم الله الرحمن الرحيم BACTERIAL TAXONOMY Prof. Khalifa Sifaw Ghenghesh Dept. of Medical Microbiology, Faculty of Medicine, Tripoli University Tripoli - Libya

Carolus Linnaeus (1707–1778) Swedish botanist credited with founding the science of taxonomy. He introduced the binomial system of nomenclature Linnaeus also established a hierarchy of taxonomic ranks: species, genus, family, order, class, phylum or division, and kingdom. At the highest level, Linnaeus divided all living things into two kingdoms—plant and animal. In his taxonomic hierarchy each organism is assigned a species name, and species of very similar organisms are grouped into a genus and so on.

Taxonomy The science of classification and refers to Classification Nomenclature and Identification

A Comparison of the More Notable Classification Systems of Living Organisms Haeckel (1894) Whittaker (1959) Woese (1977) Woese (1990) Three kingdoms Five kingdoms Six kingdoms Three domains --------------------------------------------------------------------------------------------------------- Protista Monera Eubacteria Bacteria Plantae Protista Archaebacteria Archaea Animalia Fungi Protista Eukarya Plantae Fungi Animalia Plantae Animalia

The Phylogenetic Tree of Life based on Comparative ssrRNA* Sequencing. *the nucleotide sequences of the small subunit ribosomal RNA.

Classification

The systematic division of organisms into related taxa (groups) based on similar characteristics

1. Conventional Classification Major characteristics used in conventional classification: Feature: Cell shape Cell size Colonial morphology Ultrastructural characteristics Staining behaviour Mechanism of motility Cellular inclusions Carbon & nitrogen sources Cell wall constituents Energy sources Fermentation products Growth temperature optimum & range Osmotic tolerance Oxygen relationships pH optimum & growth range Sensitivity to metabolic inhibitors & antibiotics

2. Adansonian or Numerical Classification Numerical taxonomy, the use of computers. A large number of biochemical, morphological and cultural chara-cteristics are used to determine the degree of similarity between organisms (similarity matris) and conversion to dendogram (phenogram)

OTU = operational taxonomic unit

3. Phylogenetic Classification An evolutionary arrangement of species. Sharing a recent ancestor as in plants and animals (fossil records) In bacteria? Possible by Molecular Methods Genetic Homology: Base composition (GC ratio) Nucleic acid hybridisation. Ribosomal RNA (rRNA) sequence analysis Protein profiles and amino acid sequences

PURE CULTURE: Populations of individuals all derived from the same single organism. STRAIN: A Group of Pure Cultures Derived from a Common Source and Thought to be the Same. SPECIES: A Group of Closely Similar Strains.

INTRASPECIES CLASSIFICATION Biotypes Biochemical properties. Serotypes Antigenic features. Phage Types Bacteriophage susceptibility. Colicin Types Production of bacteriocins.

Nomenclature

Naming of microorganisms. Governed by international rules Rules published in the International Code of Nomenclature of Bacteria. The International Journal of Systematic Bacteriology

Rules for the Nomenclature of Microorganisms There is only one correct name for an organism. Names that cause error or confusion should be rejected. All names in Latin or are latinized. The first word (genus) is always capitalized. The second word (species or specific epithet) is not capitalized. Both genus and species name, together referred to as species, are either underlined or italicized when appearing in print. The correct name of a species or higher taxonomic designations is determined by valid publication, legitimacy of the name with regard to the rules of nomenclature, and priority of publication.

Nomenclature Casual or Common Name: Scientific or International Name: e.g. "typhoid bacillus" Scientific or International Name: Salmonella typhi Salmonella london Staphylococcus aureus Clostridium tetani Mycobacterium bovis Borrelia burgdorferi

Identification

Biologists often use a taxonomic key to identify organisms according to their characteristics. Dichotomous key most commonly used in identification. has paired statements describing characteristics of organisms.

Methods used for Identification of Bacteria Cellular morphology Staining characteristics Motility Growth characteristics Biochemical characteristics Serological tests Analysis of metabolic end products or structural components of organisms by different methods (e.g. GLC) Genetic analysis using nucleic acid probes and other molecular techniques (e.g. PCR)

Dichotomous Key Gram reaction + - indole morphology rods cocci B. subtilis catalase S. aureus E. faecium P. vulgaris C. freundii

Enterotube

Bergey's Manual Methods for distinguishing and identifying bacteria are assembled into Bergey's Manual of Determinative Bacteriology Bergey's Manual of Systematic Bacteriology Provides description of physical & chemical characteristics and system of identification of medically important members of selected sections of bacteria

Polyphasic Bacterial Taxonomy More data will become available, more bacteria will be identified, there will be more information, and software development will need to address the combination and linking of the different databases. A polyphasic approach to bacterial classification includes: Methods to phylogenetically allocate bacteria Methods to compare and group large numbers of strains into clusters of similar bacteria DNA-DNA hybridization to determine the relationships between represnetativies withing and between each of those clusters And descriptive methods which will provide further genotypic and phenotypic information.