1. بسم الله 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) 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

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

7. Classification

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

9. 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

10. 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)

11. OTU = operational taxonomic unit

12. 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

13. 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.

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

15. Nomenclature

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

17. 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.

18. 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

19. Identification

20. 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.

21. 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)

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

24. Enterotube

25. 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

26. 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.