Classification of organism

Defined by two names

Called the binomial nomenclature

Common rules for both names
- Both printed underlined or italicized
- Genus name is always capitalized
- Species name is lowercase

Example:
Homo sapiens
Homo sapiens

Genus name + specific epithet (species)

1. Genus name always capitalized
(e.g. Escherichia)
2. Species name is never capitalised
(e.g. coli)
3. Species name is never used
without the genus name (e.g. coli
standing alone)
4. Genus name may be used without
species name (e.g. Escherichia)
5. Genus and species are always
italicized (or underlined)

6. First time à spell out (Escherichia
coli), thereafter à abbreviated (E.
coli)
7. Species name à never
abbreviated
8. Less simple genus abbreviation if
different genus start with same
alphabet.
e.g. Enterococcus faecalis (En. faecalis)
Escherichia coli (Es. coli)

subgroup of species with one or
more characteristics that distinguish
it from other subgroups of the same
species

identify by
a. A name or
b. Number or
c. Letter follows by specific epithet
E.g. E. coli strain O157:H7

a. Shape
b. Where it is/was found
c. Nutrient it uses
d. Who discovered it?
e. What disease it causes?

• Natural system
• Based on evolutionary relationships
• Direct comparison of genetic material and
gene products

Differential Staining

Gram Stain
• Classifies into Gram posiJve (purple/blue) or negative
(pink/red)

Acid-fast Stain
• Only stain bacteria with waxy material in their cell walls
e.g Mycobacterium

Negative staining for capsules
• Use india ink to provide a contrasJng background, then
stain with simple stain (safranin)
• Capsules to not accept simple stain, thus appear as halos
surrounding bacterial cell

Endospore staining
• Schaeffer-Fulton endospore stain
• Endospore appear green within pink cells

Flagella staining
• Flagella are too thin
• Use a mordant and stain carbolfuchsin to coat the flagella
unJl they are thick enough to be seen

Biochemical Tests

Tests to verify its metabolic acJvity

Some of the common biochemical tests
- Phenol Red broth
- GelaJn Test
- Lipase Test
- Starch hydrolysis
- MoJlity test
- Catalase test

Rapid Biochemical Test
a. StandardizaJon
b. Speed
c. Reproducibility
d. Miniaturization
e. Mechanization

Serology

Is the science that studies serum and immune responses that
are evident in serum

Background: Bacteria (antigen) enter a host, antibody will be
produced by the host. The antibody will combine with the
antigen (bacteria) and this precipitates the antigen

Commercially available serum with specific antibody:
antiserum

Slide agglutination test:
- Unknown bacteria placed on several slides
- A different known anJserum is placed on each sample
- Agglutination – positive reaction

Serological techniques
a. Enzyme-linked immunosorbent assay (ELISA)
- Fast and utilised a computer scanner to read result
- ELISA performed in microtiter plate

b. Western blotting
Serology
- Proteins from an unknown bacterium or virus are
separated by electrophoresis (proteins separated
according to molecular weights)
- Proteins are then transferred to a nitrocellulose filter by
blotting
- The filter is exposed to known antibodies, and washed
(if there is matching antigen and antibody, the antibody
will be retained)
- A second antibody which will bind to all antibodies, with
enzyme linked, is exposed to the filter, and washed
- Enzyme reaction occurred and signal can be observed

Phage typing

• Determine which phage a bacterium is susceptible to
• Bacteriophages cause lysis of bacteria that they infect
• Bacteriophages infect only particular species or even
strains

Fatty Acid Profiles

• Bacteria synthesize a wide variety of fatty acids
• These fatty acids are constant for a particular species
• Compare with fatty acid profiles of known organisms for
classification and identification of unknown

DNA Base Composition

• The base composition of a single species is a fixed property.
Thus can be used to reveal the degree of species relatedness.
• Expressed as the % of guanine plus cytosine (G+C)
• In DNA, G pair with C; A pair with T
• Two organisms that are closely related would have many
identical or similar genes will have similar amounts of various
bases in their DNA
• General guideline: Difference of more than 10% in their %GC,
the microorganism are probably not related (e.g. Bac. A 40% GC
and Bac. B 60% GC)

DNA Fingerprinting

• Use of restriction enzyme to produce banding pattern
• RE cuts specific base sequence
• The more similar the DNA fingerprints, the more closely related
the organisms are.

Nucleic Acid Hybridization

• Principle:
- When dsDNA is heated, complementary strands will separate
as the H bonds between bases break
- If ssDNA are cooled, complementary strands will reunite
• This technique can be used to determine extent of similarity
based on degree of reunion
• Nucleic acid hybridization = measures the ability of DNA
strands from one organism to hybridize with another

Dichotomous Keys

Cladograms

• Show evolutionary relationships among
organisms
• Constructed based on rRNA sequences with
the aid of software

classification

arrangement of organisms into groups or
based on mutual similarity or evolutionary relatedness.

nomenclature

the branch of taxonomy concerned
with the assignment of names to taxonomic groups
according to the published rules.

identification

the practical side of taxonomy, the
process of determining that a particular isolate belongs
to a recognized taxon.

The science of biological classification

1. Run extensive scienJfic tests to
verify the bacteria
2. New bacteria – give a name
3. DescripJon is published in
Interna.onal Journal of
Systema.c Bacteriology
4. Bacteria deposited in culture
collecJon bank
5. DescripJon of bacteria is
incorporated into a reference
called Bergey’s Manual

Biovars: strains characterize by
biochemical or physiological differences

Morphovars: differ morphologically

Serovars: distinctive antigenic properties

Computer assisted taxonomy

Organisms sorted into groups of mutual similarity
based on large number of observable properties

All characters having same degree of importance

Final result expressed in simple matching
coefficient (SSM) or Jaccard coefficient (SJ)

Based on association coefficient
0.0 (no matches)
1.0 (100% match)
80% similarity – same species
65% similarity – same genus

Evolutionary relationships among
group of species

Tree constructed based on molecular
attribute

Southern Blotting

DNA Chips

Ribotyping and Ribosomal RNA Sequencing

Fluorescent In Situ Hybridization (FISH)