BACTERIAL TAXONOMY
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 agenus 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
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Protista Monera Eubacteria Bacteria
Plantae Protista Archaebacteria Archaea
Animalia Fungi Protista EukaryaPlantae Fungi
Animalia Plantae
• Animalia
The Phylogenetic Tree of Life based on
Comparative ssrRNA* Sequencing.
*the nucleotide sequences of the small subunit ribosomal RNA.
1. Conventional Classification
Major characteristics used in conventional classification:
• 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
Feature:
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)
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.
• 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:• e.g. "typhoid bacillus"
• Scientific or International Name:• Salmonella typhi
• Salmonella london
• Staphylococcus aureus
• Clostridium tetani
• Mycobacterium bovis
• Borrelia burgdorferi
• 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)
TEST
Organism Gram Shape Catalase Indole
B. subtilis + Rod + -
C. freundii - Rod + -
E. faecium + Coccus - -
P. vulgaris - Rod + +
S. aureus + Coccus + -
• Dichotomous Key
Gram reaction
+ -
indole
+ -
morphology
rods cocci
B. subtilis
catalase
+ -
S. aureus E. faecium
P. vulgaris C. freundii
• 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.