Bacterial taxonomy

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  • 1. ‫بسم ال الرحمن الرحيم‬ BACTERIAL TAXONOMY Prof. Khalifa Sifaw Ghenghesh Dept. of Medical Microbiology, , Faculty of Medicine Tripoli University Tripoli - Libya
  • 2. (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.
  • 3. Taxonomy • The science of classification and refers to – Classification – Nomenclature and – Identification
  • 4. A Comparison of the More Notable Classification Systems of Living Organisms Haeckel (1894( Whittaker (1959( Three kingdoms Five kingdoms Woese (1977( Six kingdoms Woese (1990( Three domains -------------------------------------------------------------------------------------------------------Protista Monera Eubacteria Bacteria Plantae Protista Archaebacteria Archaea Animalia Fungi Protista Eukarya Plantae Fungi Animalia Plantae • Animalia
  • 5. The Phylogenetic Tree of Life based on Comparative ssrRNA* Sequencing. *the nucleotide sequences of the small subunit ribosomal RNA.
  • 6. Classification
  • 7. • The systematic division of organisms into related taxa (groups) based on similar characteristics
  • 8. 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
  • 9. Adansonian or Numerical. 2 Classification • Numerical taxonomy, the use of computers. • A large number of biochemical, morphological and cultural characteristics are used to determine the degree of similarity between organisms (similarity matris) and conversion to dendogram (phenogram)
  • 10. OTU = operational taxonomic unit
  • 11. Phylogenetic Classification. 3 • 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
  • 12. • 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.
  • 13. INTRASPECIES CLASSIFICATION • Biotypes – Biochemical properties. • Serotypes – Antigenic features. • Phage Types – Bacteriophage susceptibility. • Colicin Types – Production of bacteriocins.
  • 14. Nomenclature
  • 15. • Naming of microorganisms. • Governed by international rules • Rules published in the International Code of Nomenclature of Bacteria. • The International Journal of Systematic Bacteriology
  • 16. 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.
  • 17. Nomenclature • Casual or Common Name: • e.g. "typhoid bacillus" • Scientific or International Name: • • • • • • Salmonella typhi Salmonella london Staphylococcus aureus Clostridium tetani Mycobacterium bovis Borrelia burgdorferi
  • 18. Identification
  • 19. • 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.
  • 20. 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)
  • 21. TEST Organism Gram Shape Catalase Indole B. subtilis + Rod + - C. freundii - Rod + - E. faecium + Coccus - - P. vulgaris - Rod + + S. aureus + Coccus + -
  • 22. • Dichotomous Key Gram reaction + - morphology rods indole + cocci P. vulgaris B. subtilis catalase + S. aureus E. faecium C. freundii
  • 23. Enterotube
  • 24. • 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
  • 25. 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.