Phenotype to genotype and the use of 16S rRNA

Cards (21)

  • It has been proposed that a prokaryote whose 16S ribosomal RNA sequence differs by more than 3% from that of all other organisms (that is, the sequence is less than 97% identical to any other sequence in the databases), should be considered a new species.
  • Genome – total set of genes that make up genetic apparatus of the cell. (chromosome and extrachromosomal elements [plasmid])
  • Genotype – complete genetic potential of the cell, all of which may or may not be expressed under given conditions.
  • What is a genotype?
    The precise genetic composition of an organism.
  • FAME (an example of chemotaxonomy)
    •Fatty Acid Methyl Ester analysis
  • MIDI Sherlock™
    •A microbial identification system that consists of extracting  the fatty acids of the organism followed by gas  chromatograph (GC).
  • MIDI Sherlock™
    •Capable of identifying Gram positives, Gram negatives and  yeasts by analysis of fatty acids methyl esters (FAME)
    •Automated system
  • Which is the major macromolecule, by %, within the bacterial cell?
    Protein
  • Which of the following is not a descriptor for the margin of a microbial colony?
    Umbonate
  • Staphylococcus species give the following result in the Coagulase Test?
    Both negative and positive
  • Which of the following is a major limitation when using phenotype methods in bacterial identification?
    Variability due to growth conditions
  • How many protein coding genes in Helicobacter pylori?
    < 2000
  • What was the cost, per base pair, of sequencing in the early 1970's?
    $10,000
  • Thermoplasma is a genus within which Domain?
    Archaea
  • Which of the following is not a reason to choose rRNA as an evolutionary chronometer?
    Rapid sequence evolution
  • 16S rRNA is a component of which ribosomal subunit?
    30S
  • Based on 16S rRNA sequences, what is the threshold of difference required for designation of a new species?
    3%
  • Advantages of Phenotypic Methods
    • ease of use
    • Low cost
    • Established technologies with long history of use
    • Accurate
    • Provide meaningful information
  • Limitations of Phenotypic Methods
    • Results influenced by culture conditions
    • Variability due to factors such as isolates not exhibiting their typical biochemical characteristics.
    • Small library of known organisms
    • High re-test rate when compared to genotypic methods
  • Useful Biochemical Screening Techniques
    • Oxidase Test
    • Catalase Test
    • Coagulate Test
    • Indole Test
    • Methyl Red Test
  • Examples of Commercial Phenotypic Methods
    • API Strips
    • BBL Crystal
    • Vitek 2
    • Biolog
    • MIDI Sherlock
    • MALDI TOF