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.

Classification

• The systematic division of organisms

into related taxa (groups) based on

similar characteristics

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)

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.