TAXONOMY AND

CLASSIFICATION OF BACTERIA
Said Aboud, Department of
Microbiology and Immunology,
MUHAS
 Learning Objectives
• To describe classification/taxonomy
of bacteria
• To describe nomenclature of bacteria
• To describe identification of bacteria
 Introduction – 1
• Taxonomy (Greek word taxes=arrangement) is
the orderly classification and grouping of
organisms into taxa (categories)
• Involves three structured, interrelated categories
–Classification/Taxonomy
–Nomenclature
–Identification
• It is based on similarities and differences in
genotype and phenotype
• Taxa are categories or subsets in taxonomy
 Introduction – 2
• Nomenclature provides naming assignments
for each organism
– Micrococcaceae
– Staphylococcus
– Staphylococcus aureus
• Identification refers to obtaining data on the
properties of the organism (characterization)
and determination on species it belongs to
– This is based on direct comparison to
known taxonomic groups
 Rationale for Classification – 1
• Estimated that 40,000 species do exist
but only 5,000 are well studied and
identified
• Permits the organization of huge
amounts of information
• Allows predictions and hypotheses to be
made upon this information
 Rationale for Classification – 2
Places organisms in useful groups with
precise names that permit effective
communication between investigators
Essential for the identification of
organisms
 Taxa: Group of Organisms – 1
Examples
• Spirochetes
– Genus Borrelia, Leptospira, Treponema
• Aerobic/microaerophilic, motile,
helical/vibroid gram negative bacteria
– Geneus Camphylobacter
• Gram negative aerobic/microaerophilic rods
and cocci
– Genus Agrobacterium, Alkaligenes,
Pseudomonas
 Taxa: Group of Organisms – 2
• Facultative anaerobic gram negative rods
– Genus Enterobater, Escherichia, Klebsiella,
Serratia, Shigella, Yersinia, Eikenella
• Gram positive Cocci
– Genus lactococcus, streptococcus,
Staphylococcus
• Endospore forming gram positive rods and
cocci
– Genus bacillus, clostridium
• Regular, non-sporing gram positive rods
– Genus Lactobacillus, listeria
 Classification Systems
• Phenotypic system
• Genotypic/Phylogenetic system
• Cellular type system
– Prokaryotes
– Eukaryotes
– Archaeobacteria
 Phenotypic Classification – 1
• Natural classification system that groups
organisms together based upon mutual
similarity of their phenotypic
characteristics
• Classification which is based on the
observable characteristics of existing
organisms regardless of their ancestral
lineage.
 Phenotypic Classification – 2
Morphology
Cultural characteristics
Susceptibility to antibiotics,
Biochemical tests
Percentage of similarity is used
Also known as numerical or
taxometrics
 Phylogenetic Classification – 1

• Based solely on evolutionary

relationships
• Modern methods instead use gene
sequences (e.g. RNA genes) or their
products (proteins) to estimate
phylogenetic relationships
 Phylogenetic Classification – 2
• The total DNA of one organism can be
compared with that of another organism by
the method called nucleic acid hybridization
or DNA hybridization
• This method can be used to measure the
number of DNA sequences that 2 organisms
have in common and
• Then estimate their convergence or their
diversity
 Phylogenetic Classification – 3
• Five factors can be used to determine DNA
relatedness:-
1. Genome size
2. Guanine + cytosine content
3. DNA relatedness under conditions optimal
for DNA reassociation
4. Thermal stability of related DNA sequence
and
5. DNA relatedness under supraoptimal
conditions for DNA reassociation
 Phylogenetic Classification – 4
• Bergey`s Manual first published in 1927 by
David Bergeys and colleagues
• Groups bacteria into phenetic groups.
• It's second edition gives the most up to date
phylogenic classification of prokaryotic
organisms including eubacteria and
Archaeobacteria
• It’s now in it`s 9th edition
• It is considered by most microbiologists as the
best consensus for prokaryotic taxonomy.
 Taxonomic Ranks

Formal Rank Example

• Kingdom Prokaryotae
• Division Gracilicutes
• Class Scotobacteria
• Order Eubacteriales
• Family Enterobacteriaceae
• Genus Escherichia 
• Species coli 
 What is a Bacterial Species?
• A bacterial species is a distinct organism
with certain characteristic features, or a
group of organisms that resemble one
another closely in the most important
features of their organization.
• It is a group of similar organisms within a
genus
• Are designated by biochemical and other
phenotypic criteria and by DNA
relatedness, which group strains on the
basis of their overall genetic similarity
 What is a Strain?
• A population of microbes descended from a
single individual or pure culture
• Different strains represent genetic variability
within a species
• Biovars: Strains that differ in biochemical or
physiological differences
• Morphovars: Strains that vary in morphology
• Serovars: Stains that vary in their antigenic
properties
 Nomenclature (Naming) – 1
• Naming of an organism by international
rule according to its characteristics
• Is the means by which the
characteristics of a species are defined
and communicated among
microbiologists.
• A species' name should mean the same
to all microbiologists
 Nomenclature (Naming) – 2
• Use binomial system of nomenclature
– Genus name + species name
• Italicized or underlined
• Genus name is capitalized and may
be abbreviated
• Species name is never abbreviated
• A genus name may be used alone to
indicate a genus group
• A species name is never used alone
• E.g. Bacillus subtilis, Bacillus subtilis
 Nomenclature (Naming) – 3
• Common or descriptive names
• Names for organisms that may be in common
usage, but are not taxonomic names
• E.g. tubercle bacillus
        (Mycobacterium tuberculosis)
• meningococcus
(Neiserria meningitidis)
• Group A streptococcus
(Streptococcus pyogenes)
 Identification
• Practical use of classification scheme
• Its is done after the organism has been
classified and recognized as being
different from other organism
• Practically used to:-
-isolate and distinguish desirable
organisms from undesirable ones
-verify authenticity or the special
properties of a culture or in clinical
setting
-isolate and identify the causative
agent of disease e.g. in epidemics, in
the pathology
 .

A scheme of specimen isolation and identification

Properties Used in Identification – 1
• Colony morphology
• Cell shape and arrangement
• Cell wall structure
• Special cellular structures
• Biochemical characteristics
 Serological Test
– Solutions containing known antibodies can be
prepared-they are called antisera (antiserum =
singular)
– Samples of an unknown bacterium can be placed
on slides and mixed with several likely antisera.
– If there is a match, the bacteria will clump
together (agglutinate)
– This is a slide agglutination test
– Serological testing can even distinguish between
strains of the same species.
Advantages of Serological Test
• Highly specific
• Does not usually require the
organism to be isolated into pure
culture
• Can be used to identify organisms
that can’t be grown on medium
 Serological Test
• Combine
known
antiserum +
unknown
bacteria
– Slide
agglutination
– ELISA
– Western blot

Figure 10.10
 Nucleic Acid Hybridization – 1

• Nucleic acid hybridization assumes that if

2 organisms are closely related, their
nucleic acid sequences will be quite
similar.
• Less closely related organisms will have
less similarity.
• This is the basis for several means of
testing
 Nucleic Acid Hybridization – 2
• DNA single strands from 2 different
organisms are mixed, and the more the
strands that match up the more similar
the DNA so the more closely related the
organisms are
 Nucleic Acid Hybridization – 3
• Since RNA is transcribed from a single strand
of DNA, it will pair up with the proper section
of single-strand DNA if the 2 are mixed
• RNA from one organism can be mixed with
separated strands of DNA from another and
relatedness can be determined by observing
the amount of pairing that occurs
• The technique can be used to identify
unknown organisms by a technique called
Southern blotting
DNA/DNA Reassociation – 1
• In this example, which is a control
experiment (the radiolabeled
sample is reannealed with
unlabeled DNA from the same
strain), the degree of reassociation
is highest and treated as 100%.
• If a different strain is reannealed
with the radiolabeled DNA, it will
show a lower degree of
reannealing (compared with the
100% attributed to the control),
indicative of the similarity between
the two strains being tested.
• Strains with reannealing values of
70% or greater are considered to
be the same species.
DNA/DNA Reassociation – 2
 Nucleic Acid Sequencing

– Genes for specific enzymes

– The nucleic acid sequence for the complete
genome of several species is now available
– 5S and 16S rRNA (ribosomal RNA)
sequences
• Comparison of these sequences has been
extensively used to determine the
phylogenetic relationships of microbial
groups
 Guanosine+ Cytosine Content

• The (G + C) percentage will be very close to

the same, in closely related organisms and
differ more in organisms that are not so
closely related.
• Similar percentages are not conclusive proof
of a relationship, but they do give a good
indication of whether more tests should be
done.
Mol Percent Guanine + Cytosine (Mol% G+C)
PAGE - Polyacrylamide Gel Electrophoresis
» Polymer of acrylamide monomers with a
mixture of other buffers and solutions
» This polymer can be changed into a gel matrix
» Electricity is used to pull the protein through
the gel
» The negatively charged protein moves to the
positive poles
» Smaller sized proteins will move at a faster rate
due to their ability to maneuver through the gel
PAGE - Polyacrylamide Gel
Electrophoresis
 Bacteria Subtyping – 1
• Examining bacterial isolates for
characteristics that allow discrimination
below the species level
• Bacteria subtyping is done to distinguish
between strains of a given species or to
identify a particular species
 Bacteria Subtyping – 2
• It is commonly done in epidemic
• Use characteristics that allow
discrimination below the species level
• Must differentiate case from non case
isolates
 Bacteria subtyping – 3
• Classically accomplished by: -
-Biotyping
-Serotyping
-Antimicrobial susceptibility test
-Bacteriophage typing
-Bacteriocin typing
Example: Vibrio cholerae has more than 130
serogroups, O1 and O139 has been associated
with epidemics and pandemic cholera
 Bacteriophage Typing – 1

• This technique uses viruses which attack

bacteria (bacteriophages)
• These viruses are highly specific, even
down to specific strains of bacteria, and
they generally cause lysis (bursting) of
the bacteria that are susceptible to them
 Bacteriophage Typing – 2
• The bacteria to be identified are spread over
the surface of an agar plate and allowed to
grow
• One drop each of various phages are placed
on the bacteria
• If the bacteria are susceptible to a particular
phage, a clear area called a plaque will appear
• Determining which phage or combination of
phages the bacteria are susceptible to can be
used to test the similarity of samples taken
from different sources (Food poisoning,
surgical infections)
 Bacteriophage Typing
.

Negative phage
reaction
Positive phage
reaction
 Nucleic Acid-based Subtyping
• Plasmid profile analysis
• Restriction endonuclease analysis
• Ribotyping
• Pulsed filled gel electrophoresis
• PCR amplification and
• Nucleic acid sequence analysis-finger
printing
 Polymerase Chain Reaction
• Detection and identification of infectious
agent without need for culture
• Process includes
– DNA or RNA extraction
– Amplification of specific gene
– Digestion of amplified product with
restriction endonuclease
– Analysis of fragment by
 DNA Fingerprinting – 1
• This is a more complicated test.
• It is time-consuming and expensive.
• However, it actually determines the sequence
of bases in an organism's DNA and can give
much more conclusive proof of relatedness.
• Restriction enzymes cut a molecule of DNA
everywhere a specific base sequence occurs.
• One specific restriction enzyme would cut
DNA everywhere these sequences occur:-
– G A A T T C or C T T A A  G
 DNA Fingerprinting – 2

• DNA samples from two different

organisms are treated separately with
the same restriction enzyme.
• The resulting fragments are separated by
electrophoresis, and the number and
sizes of the fragments are compared.
• The more similar the patterns, the more
closely related the organisms.
DNA Fingerprinting – 3
Fluorescent in Situ Hybridization
(FISH)
 Cellular Type Classification
• Another method of classifying organisms is by
cell organizations
• It is now organized that organisms fall into
three distinct groups based on type of cell
organization and function: -
– Prokaryotes
– Eukaryotes
– Archaeobacteria
 Comparison of Prokaryotic and
Eukaryotic Cell Organization
Characteristic Prokaryote Eukaryote
Typical size 0.4-2 um in diameter; 0.5-5 10-100 um in diameter; >10
um in length um in length
Nucleus No nuclear membrane Membrane bound nucleus
Genome
Location In the nucleoid, at In the nucleus
mesosome
Chromosomal DNA Circular complexed with RNA Linear complexed with basic
histones
Extrachromosomal circular DNA Plasmids In mitochondria and
chloroplasts
Reproduction Asexual (binary fission) Sexual and Asexual
Membrane bound organelles Absent All
Golgi bodies Absent in all Present in some
Lysosomes Absent in all Present in some
Endoplasmic reticulum Absent in all Present in all
Mitochondria Absent in all Present in algae and plants
 Archaeobacteria
• Appears to be more closely related to
eukaryotic cells than to prokaryotic cells
• Found in microorganisms that grow
under extreme environmental conditions
• Cell wall lacks peptidoglycan, a major
reason they are placed in a domain
separate from bacteria