Identification and
Classification of
Prokaryotes
Chapter 10
Taxonomy
 The science of classification
 Provides an orderly basis for the naming of
organisms
 Places organisms into a category or taxon
(plural: taxa)
 Carolus Linnaeus: 18th century Swedish
botanist; the Father of Taxonomy
Carolus
Linnaeus
(1707-1778)
Identification and Classification
 Living organisms are divided into groups to better
understand relationships among species
 Taxonomy is the science that studies organisms to
order and arrange them
 Taxonomy can be viewed in three areas
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Identification
 Process of characterizing in order to group them
Classification
 Arranging organisms into similar or related groups
Nomenclature
 System of assigning names
Binomial Nomenclature
 The system used to name all living things
 The first name designates the genus (plural: genera)
and its first letter is capitalized
 The second name is the specific epithet, and it is not
capitalized
 Together the genus and specific epithet identify the
species
The Meaning of the Names of Some
Microorganisms
 Escherichia coli: Named after Theodore
Escherich in 1888; found in the colon
 Entamoeba histolytica: Ent, intestinal;
amoebae, shape/movement; histo, tissue; lytic,
lysing or digesting tissue
 Strain: A subgroup of a species with one or
more characteristics that distinguish it from
other members of the same species
Principles of Taxonomy
 Strategies Used to Identify Prokaryotes

Wide assortment of technologies used to
identify organisms including

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Microscopic examination
Culture characteristics
Biochemical test
Nucleic acid analysis
Principles of Taxonomy
 Strategies Used to Classify Prokaryotes

Understanding organisms phylogeny assists in
classification

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Allows for organized classification of newly
recognized organisms
Development of molecular techniques for
classification and identification make genetic
relatedness possible
Principles of Taxonomy
 Taxonomic hierarchies
 Classification categories arranged in hierarchical order
 Domain – collection similar to kingdoms
 Archaea, Prokaryotes, Eukaryotes

Kingdom – collection of similar phyla
 Monera, Protista, Fungi, Plantae, Animalia
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Phylum – collection of similar classes
Class – collection of similar orders
Order – collection of similar families
Family – collection of similar genera
Genus – group of related species
Species – group of related isolates or strains
 Most basic unit
Classification of Human Dog Wolf
and a Bacterium
Principles of Taxonomy
 Classification system


No such thing as “official” classification system
Scheme favored by most microbiologists is
three domain system

Before three domain system five kingdom system
was used
Principles of Taxonomy
 Nomenclature

Names given according to International Code
for the Nomenclature of Bacteria
Using Phenotype to
Identify Prokaryotes
 Phenotype can be used in the process
identification of bacteria
 Methods used include

Microscopic morphology
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Metabolic capabilities
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Gram -. Gram +, cocci, rod, vibro, spirillum, etc.
Anaerobic, aerobic, Produces SH, Lactose, etc
Serology- do specific antibodies attach
Using Phenotype to
Identify Prokaryotes
 Microscopic morphology
 Important initial step in identification
 Can be used to determine size, shape and staining
characteristics
 Size and shape can readily be determined
microscopically
 Gram stain differentiate Gram + from Gram –
 Narrows possible identities of organism
 Special stains
 Identifies unique characteristics of organisms
 Acid fast stain
Using Phenotype to
Identify Prokaryotes
 Metabolic capabilities

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Identification relies heavily
on analysis of metabolic
capabilities
Culture characteristics

Colony morphology can
give clues to identity
 Red pigment of Serratia
marcescens

Biochemical tests

More conclusive
identification
 Most test rely on pH
indicators

Commercial biochemical
tests allow for series of
test with single
inoculation
Using Phenotype to
Identify Prokaryotes
 Serology


Technique relying on specific interaction
between antibodies and antigens
Serological tests are available for rapid
detection of numerous organisms

Streptococcus pyogenes the causative agent of
strep throat
Using Genotype to
Identify Prokaryotes
 Nucleic acid probes can locate unique
nucleotide sequence of a particular species
 Numerous technologies discussed previously
are being used to identify organisms based
on genotype
 Advantage

Identification of organism that can’t be grown
in culture
Using Genotype to
Identify Prokaryotes
 Using PCR
Used to amplify sequences
that allow for detection of
specific sequences for
identification
 Sequencing ribosomal RNA genes
 There is little genetic variation
in rRNA

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Newer technologies are
available to sequence rDNA
 The DNA that encodes rRNA
Characterizing Stain Differences
 Biochemical typing
 Biochemical tests can be used to identify species

They can also be used to identify strains by tracing
specific biochemical characteristics called biovar or
biotype
 Serological typing
 Identification made based on differences in
serological molecules
 Serological characteristics are termed serovar or
serotype
Characterizing Stain Differences
 Phage typing

Certain strains of given species susceptible to various
bacteriophages

a.k.a phage
 Virus that infect bacteria

Phage typing identifies organism by phage that infect them

Phage type has been largely replaced by molecular
methods
Characterizing Stain Differences
 Antibiograms
 Identifies organism
based on antibiotic
susceptibility
 Disc impregnated with
antimicrobial placed on
inoculated plate
 Clear are indicates
microbial
susceptibility
 Different strain will
have different
susceptibility
patterns
Classifying Prokaryotes
 Classification historically based on phenotype
 Size, shape, staining characteristics and metabolic
capabilities
 New molecular techniques make identification more
accurate
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Allows for accurate construction of phylogenetic tree
 Trees show divergence and relationships between
organism
Molecular techniques highlighted transfer mechanism
of prokaryotic cells
 Horizontal or lateral transfer of DNA
Classifying Prokaryotes
 Sequencing methods include

16s rDNA sequence analysis

Comparison of 16s rRNA and rDNA sequences
revolutionized classification
 Lack of mutation allows identification of distant
relatedness
 DNA hybridization better tool for assessing
relatedness on species level
Classifying Prokaryotes
 DNA hybridization

Relatedness of organism can be determined
by similarity of nucleotide sequences

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Sequence homology is measured by DNA
hybridization
Extent of hybridization reflects degree of
similarity

If two strain show high percentage of DNA
hybridization they are considered related
 70% similarity is considered same species
Classifying Prokaryotes
 DNA base ratio

Comparison of genomes to determine DNA
base ratio
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Looking at relative proportion of A:T and G:C
bonding in DNA
Base ratio is expressed in G:C content
If GC ratio deviate more than a little organism
are not related

Similarity of base composition does not mean
relatedness
Using a Taxonomic Key
 Dichotomous Key: A commonly used
key to identify organisms.
 Has paired statements describing
characteristics of organisms.
Dichotomous Key for Classifying
U.S. Coins
Bacterial Identification Tree
David H. Bergey
(1860-1937)