Classification of Organisms

Taxonomy
1. Greek
  1. Taxis=Arrangement
  2. Nonos=Laws
  3. Nemein=To Distribute
2. 3 parts:
  1. classification
    1. arrangement organisms into groups or taxon (Plural: taxa)
      1. based on mutual similarity or evolutionary related
  2. Nomenclature
    1. assignment of names to taxonomic group
      1. with agreement published rules
    2. Deﬁned by 2 name
      1. Other name : binomial nomenclature
      2. Genus + speciﬁc epithet (aka species)
      3. rules for both names
        must be underlined or italicized
        Genus name = capitalized
        Genus name may be used without species name
        Less simple genus abbreviation if different genus start with same alphabet.
        Ex: Enterococcus faecalis (En. faecalis) , Escherichia coli (Es. coli)
        Species name = lowercase
        Species name is never capitalised
        Species name never used without the genus name
        Species name: never abbreviated
        spell out (Escherichia coli)
        then can used abbreviated (E. coli)
    3. Name based on:
    4. Process (Ex. Bacteria):
      1. 1. Run extensive scientiﬁc tests to verify microbe, Bacteria
        2. New bacteria – give a name
        3. Description is published in International Journal of SystematicBacteriology
        4. Deposit bacteria in culture collection bank
        5. Description of bacteria is incorporated into a reference (AKA Bergey’s Manual)
    5. Strain
      1. Small permanent genetic difference
      2. Defined as: subgroup of species with one or more characteristics
        distinguish it from other subgroups of the same species
      3. identified:
        name
        Shape
        place was found
        Nutrient uses
        Who discovered
        disease it causes
        Number
        Letter follows by specific epithet
        Ex: E. coli strain O157:H7
      4. Describe strain:
        Biovars: strains characterize by biochemical or physiological differences
        Morphovars: differ morphologically
        Serovars: distinctive antigenic properties
      5. New Species:
        Published : International Journal of Systematic and Evolutionary Microbiology
        Deposited in Culture Collection Banks
  3. identification
    1. Process determining isolate or trait belongs to recognized taxon .
3. Numerical taxonomy:
  1. Computer assisted taxonomy
    1. Final result expressed:
      1. Based on association coefficient : 0.0 (no matches) 1.0 (100% match) •  80% similarity – same species •  65% similarity – same genus J )
        Jaccard coefficient
        simple matching coefficient (S SM )
  2. Organisms sorted into groups of mutual similarity
    1. based on large number of observable properties
  3. characters: same degree of importance
  4. Phylogenetic/Phyletic classification:
    1. Natural system
    2. Based on evolutionary relationships
    3. Direct comparison of genetic material and gene products
    4. What makes it possible?
      1. Highly conserved genetic sequence
      2. Advancement in sequencing technique
    5. Phylogenetic Tree:
      1. Evolutionary relationships among group (species)
      2. Tree constructed based on molecular attribute
4. METHODS OF CLASSIFYING AND IDENTIFYING
  1. Morphological Characteristics
    1. Easy study and analysed
    2. Characteristics studied
      1. cell type (prokaryote or eukaryote)
      2. shape
      3. size
      4. cellular grouping (chain, clump)
      5. external structures (ﬂagella, moJlity)
      6. internal structures (inclusion granules, endospores, contracJle vacuole, chloroplast)
      7. Differential Staining
        Gram Stain
        Classiﬁes: Gram positive (purple/blue) or negative (pink/red)
        Acid-fast Stain
        Only stain bacteria with waxy material in their cell walls
        Ex: Mycobacterium
        Negative staining for capsules
        Use india ink to provide a contrasting background
        then stain with simple stain (safranin)
        Capsules to not accept simple stain
        appear as halos surrounding bacterial cell
        Endospore staining
        Schaeﬀer-Fulton endospore stain
        Endospore appear green within pink cells
        Flagella staining
        Flagella: too thin
        Use a mordant and stain carbolfuchsin
        coat the ﬂagella until they are thick enough to be seen
  2. Biochemical Tests
    1. Tests to verify its metabolic activity
      1. Rapid Biochemical Test
        Standardization
        Speed
        Reproducibility
        Miniaturization
        Mechanization
    2. proper classiﬁcation and identiﬁcation,
      1. at least 50 attributes should be tested
        Tedious and time consuming
    3. Common Test
      1. Phenol Red broth
      2. Gelatin Test
      3. Lipase Test
      4. Starch hydrolysis
      5. Motility test
      6. Catalase test
    4. Serology
      1. studies serum and immune responses that are evident in serum
        Ex
        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
      2. Slide agglutination test
        Unknown bacteria placed on several slides
        diﬀerent known antiserum is placed on each sample
        Agglutination
        positive reaction
      3. Serological techniques
        Enzyme-linked immunosorbent assay (ELISA)
        Fast and utilised a computer scanner to read result
        ELISA performed in microtiter plate
        Western blotting
        Proteins from an unknown bacterium or virus
        separated by electrophoresis (proteins separated according to molecular weights)
        Proteins
        transferred to a nitrocellulose filter by blotting
        The filter is exposed to known antibodies (Washed)
        if there is matching antigen and antibody, the antibody will be retained
        second antibody which will bind to all antibodies, with enzyme linked, is exposed to the filter (washed)
        Enzyme reaction occurred and signal can be observed
    5. Phage typing
      1. Determine which phage a bacterium is susceptible to
      2. Bacteriophages
        cause lysis of bacteria that they infect
        particular species or even strains
      3. How
        1. Prepare a lawn of bacteria
        2. Drop different spots of known phage
        3. Lysis indicate matching phage and bacteria
    6. Fatty Acid Profiles
      1. Bacteria synthesize wide variety of fatty acids
      2. fatty acids are constant for a particular species
        Compare with fatty acid profiles of known organisms
        classification and identification of unknown
    7. DNA Base Composition
      1. base composition of a single species is a fixed property
        reveal the degree of species relatedness.
      2. Expressed as the % of guanine plus cytosine (G+C)
      3. DNA, G pair with C; A pair with T
        General guideline: Difference of more than 10% in their %GC,
        microorganism are probably not related
        Two organisms that have the same % GC
        not necessarily closely related
    8. DNA Fingerprinting
      1. restriction enzyme to produce banding pattern
      2. RE cuts specific base sequence
      3. more similar the DNA fingerprints,
        more closely related the organisms are.
    9. Nucleic Acid Hybridization
      1. Principle
        heated dsDNA
        complementary strands will separate
        as the H bonds between bases break
        cooled ssDNA
        complementary strands will reunite
        technique
        determine extent of similarity based on degree of reunion
        Example
        Southern Blotting
        DNA probes used hybridization process
        DNA probe
        short specific unique DNA sequence
        DNA Chips
        Composed of various DNA probes for specific gene/bacteria
        DNA
        unknown organism is labelled
        with a fluorescent dye, added to the chip
        Hybridization of the probe and unknown DNA
        detected by fluorescence
        Ribotyping and Ribosomal RNA Sequencing
        Targets on rRNA
        present in all cells and is conserved
        Signature sequence
        rRNA gene sequence: by PCR of the DNA coding for rRNA
        PCR products : digested with RE
        analysed by electrophoresis for pattern/ profile/ typing
        Fluorescent In Situ Hybridization (FISH)
        DNA or RNA
        labeled with fluorescent dye
        used to specifically stain microorganisms in situ
        in cell
        Probe enter treated cell to react with target
        Very sensitive
        do not require high number of cells
        determine identity, abundance and relative activity oF microorganisms in environment
      2. measures the ability of DNA strands from one organism to hybridize with another
    10. after various analyses
      1. Dichotomous Keys
        Widely used: identification
        Identification
        based on : successive questions, and each question has two possible answers
        Very little to do with phylogenetic relationships
      2. Cladograms
        evolutionary relationships among organisms
        Constructed based on rRNA sequences with the aid of software
        Process
        1.Agarose gel electrophoresis set
        2.Excision of DNA fragments from agarose gel on a UV transilluminator.
        3. PCR product separated on an agarose gel.

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Classification of Organisms

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	Created by Maziatul Husna Khairuzaman over 8 years ago