Transcript بسم الله الرحمن الرحيم

‫بسم هللا 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
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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:
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Cell shape
Cell size
Colonial morphology
Ultrastructural
characteristics
Staining behaviour
Mechanism of motility
Cellular inclusions
Carbon & nitrogen
sources
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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 characteristics 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:
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Base composition (GC ratio)
Nucleic acid hybridisation.
Ribosomal RNA (rRNA) sequence analysis
Protein profiles and amino acid sequences
• PURE CULTURE:
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Populations of individuals all derived
from the same single organism.
• STRAIN:
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A Group of Pure Cultures Derived from a
Common Source and Thought to be the
Same.
• SPECIES:
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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:
• e.g. "typhoid bacillus"
• Scientific or International Name:
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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
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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
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Rod
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C. freundii
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Rod
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E. faecium
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Coccus
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P. vulgaris
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Rod
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+
S. aureus
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Coccus
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• Dichotomous Key
Gram reaction
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morphology
rods
indole
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cocci
P. vulgaris
B. subtilis
catalase
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S. aureus
E. faecium
C. freundii
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
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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.