Post on 27-Mar-2015
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الرحيم الرحمن الله بسمBACTERIAL TAXONOMY
Prof. Khalifa Sifaw GhengheshDept. of Medical Microbiology,
Faculty of Medicine, Al-Fateh 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 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 --------------------------------------------------------------------------------------------------------- Protista Monera Eubacteria Bacteria Plantae Protista Archaebacteria Archaea Animalia Fungi Protista Eukarya
Plantae FungiAnimalia Plantae
• 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 ClassificationMajor 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: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)
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:
• 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.
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:• 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
• 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
Enterotube
• 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.