Identification and Classification of Prokaryotes

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Identification and Classification of Prokaryotes

• Chapter 10

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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
• Identification
• Process of characterizing in order to group them
• Classification
• Arranging organisms into similar or related
  groups
• Nomenclature
• System of assigning names

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Principles of Taxonomy

• Strategies Used to Identify Prokaryotes
• Wide assortment of technologies used to identify
  organisms including
• Microscopic examination
• Culture characteristics
• Biochemical test
• Nucleic acid analysis

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Principles of Taxonomy

• Strategies Used to Classify Prokaryotes
• Understanding organisms phylogeny assists in
  classification
• Allows for organized classification of newly
  recognized organisms
• Development of molecular techniques for
  classification and identification make genetic
  relatedness possible

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Principles of Taxonomy

• Taxonomic hierarchies
• Classification categories arranged in
  hierarchical order
• Species group of related isolates or strains
• Most basic unit
• Genus group of related species
• Family collection of similar genera
• Order collection of similar families
• Class collection of similar orders
• Phylum collection of similar classes
• Kingdom collection of similar phyla
• Domain collection similar to kingdoms
• New taxonomic category

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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

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Principles of Taxonomy

• Nomenclature
• Names given according to International Code for
  the Nomenclature of Bacteria

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Using Phenotype to Identify Prokaryotes

• Phenotype can be used in the process
  identification of bacteria
• Methods used include
• Microscopic morphology
• Metabolic capabilities
• Serology

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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

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Using Phenotype to Identify Prokaryotes

• Metabolic capabilities
• 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

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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

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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 cant be grown in
  culture

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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
• Newer technologies are available to sequence rDNA
• The DNA that encodes rRNA

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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

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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

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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

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Classifying Prokaryotes

• Classification historically based on phenotype
• Size, shape, staining characteristics and
  metabolic capabilities
• New molecular techniques make identification more
  accurate
• 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

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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
  related ness on species level

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Classifying Prokaryotes

• DNA hybridization
• Relatedness of organism can be determined by
  similarity of nucleotide sequences
• 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

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Classifying Prokaryotes

• DNA base ratio
• Comparison of genomes to determine DNA base ratio
• Looking at relative proportion of AT and GC
  bonding in DNA
• Base ratio is expressed in GC content
• If GC ratio deviate more than a little organism
  are not related
• Similarity of base composition does not mean
  relatedness