Taxonomy and Nomenclature

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Classification of organism

Techniques that apply the principle of nucleic acid hybridization:

Fluorescent In Situ Hybridization (FISH)

Ribotyping and Ribosomal RNA Sequencing

DNA Chips

Southern Blotting

Phylogenetic Tree

Tree constructed based on molecular attribute

Evolutionary relationships among group of species

Numerical taxonomy

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

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

All characters having same degree of importance

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

Computer assisted taxonomy

Different ways to describe strains within a species

Serovars: distinctive antigenic properties

Morphovars: differ morphologically

Biovars: strains characterize by biochemical or physiological differences

Process of naming a NEW bacteria

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

Definition of Taxonomy

The science of biological classification

Definition

identification

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

nomenclature

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

classification

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

Methods use to classify and identify microorganisms after various analyses

Cladograms

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

Dichotomous Keys

METHODS OF CLASSIFYING AND IDENTIFYING MICROORGANISMS

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

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.

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)

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

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

Serology

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

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

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

Commercially available serum with specific antibody: antiserum

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

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

Biochemical Tests

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

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

Tests to verify its metabolic acJvity

Differential Staining

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

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

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

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

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

Phylogenetic/Phyletic classification

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

Inspiration of Names

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

Strain

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

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

General Rules in Nomenclature

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)

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)

Nomenclature

Genus name + specific epithet (species)

Example: Homo sapiens Homo sapiens

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

Called the binomial nomenclature

Defined by two names

classification of organism