‫بسم هللا الرحمن الرحيم‬

BACTERIAL TAXONOMY

Prof. Khalifa Sifaw Ghenghesh

Dept. 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 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
• 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:
• 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
 Adansonian or Numerical .2
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
 Phylogenetic Classification .3

• 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

+ -

morphology indole

rods cocci + -

B. subtilis P. vulgaris C. freundii

catalase

+ -
S. aureus E. faecium
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.