bacterial taxonomy

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.