2-1

• Microbes


  Microscopic organisms, including bacteria, viruses, fungi, and protozoa
• Classification


  The sorting of life-forms into categories based on genetic relatedness and traits of the organisms
• Nomenclature


  The naming of categories, including species
• Taxonomy


  The classification and naming of organisms
• Why classify?


  • To understand the relationships between living organisms
  • To understand ancestry and evolution
  • To classify and catalogue recognised species
  • To describe and appreciate diversity
  • To identify pathogens and outbreaks of disease
• Bacillus cereus


  Always start with capital for Genus and small letter for species name, always underline when italics are not available (e.g. hand writing), B. cereus, Bacillus sp., Bacillus spp. (abbreviation for unknown species plural)
• Classification and Identification methods

  • Morphology or physical characteristics
  • Biochemical tests
  • Serological tests
  • Phage typing
  • Molecular tests
• Genetic relatedness is the standard for classifying and naming organisms. However in microbiology we also use non genetic systems including: Phenotypic characterisations, Ecological categories, Disease categories
• Bacterial Morphology or physical characteristics

  • Macroscopic: colony colour, texture, shape, smell
  • Microscopic: Gram stain, shape (rods, cocci or spirals), motility, presence of endospores, presence of other morphological features
• Bacterial Biochemical Tests


  • Utilisation of substrates such as amino acids, starch, citrate and gelatin
  • Presence of certain enzymes such as catalase
  • Fermentation of carbohydrates
  • Use of different carbon and nitrogen sources
  • Production of waste products such as H2S
  • Differences in fatty acid composition
• Dichotomous key


  A common strategy of practical identification that looks at a series of yes/no decisions to successively narrow down the possible categories of species
• Oxidase Test


  Add N,N,N',N'-tetramethyl-p-phenylenediamine dihydrochloride to bacteria, bacteria that possess both cytochrome oxidase and cytochrome c will turn purple
• Catalase Test


  Add hydrogen peroxide (H2O2) to bacteria, if bacteria produce catalase then the catalase converts 2H2O2 → 2H2O + O2 and bubbling from the oxygen is seen
• Serological Tests


  • Agglutination tests using antibody-coated latex beads
  • Other types of immunological test
• Phage typing


  Bacteriophage are a type of virus that infect bacteria, infection produces plaques (clearing) in bacterial cultures due to cell lysis, used in epidemiology for strain identification
• Molecular techniques


  • GC ratio
  • DNA homology
  • 16S RNA sequencing
  • Next generation sequencing
• MALDI-TOF MS


  Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry, produces a characteristic spectrum for different species, or even strains
• Bacterial genome can be sequenced in less than 24 hours using MinION
• Classification and Identification are useful in biomedical science to identify the causative organism of infection, for epidemiology, virulence factors, and antibiotic resistance