BACTERIAL TAXONOMY

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• BACTERIAL TAXONOMY
• Prof. Khalifa Sifaw Ghenghesh
• Dept. of Medical Microbiology, Faculty of
  Medicine,
• Tripoli University
• Tripoli - Libya

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Carolus Linnaeus (17071778)

• 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 kingdomsplant and animal.
• In his taxonomic hierarchy each organism is
  assigned a species name, and species of very
  similar organisms are grouped into agenus and so
  on.

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Taxonomy

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

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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
• -------------------------------------------------
  --------------------------------------------------
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• Protista Monera Eubacteria Bacteria
• Plantae Protista Archaebacteria Archaea
• Animalia Fungi Protista Eukarya Plantae
  Fungi
• Animalia Plantae
• Animalia

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The Phylogenetic Tree of Life based on
Comparative ssrRNA Sequencing.
the nucleotide sequences of the small subunit
ribosomal RNA.
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Classification
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• The systematic division of organisms into related
  taxa (groups) based on similar characteristics

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1. Conventional ClassificationMajor
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

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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)

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OTU operational taxonomic unit
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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

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• 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.

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INTRASPECIES CLASSIFICATION

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

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

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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.

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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

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Identification
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• 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.

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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)

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• Dichotomous Key

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Enterotube
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• 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

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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.