4. Microbial Taxonomy

• Taxonomy


  The science of biological classification
• Taxon/Taxa


  A group or level of classification or hierarchy categorized at different levels
• Systematics/Phylogeny


  The study of diversity of organisms and their evolutionary relationship
• Dichotomous key

  A tool used for assigning an organism to a specific taxonomic category

  
• Taxonomic categories or hierarchy

  • An ordered group of taxonomic ranks used to classify organisms from general to specific

  
• Major taxonomical characteristics


  • Morphological
  • Physiological
  • Geographic and behavioral
  • Molecular
  • Ecological
• Phenotypic (Phenetic) classification system


  Groups do not necessarily reflect genetic similarity or evolutionary relatedness, groups are based on convenient observable characteristics

  
• Genotypic (Phylogenetic) classification system


  Considers characteristics of the genome
• Classification hierarchy


  • Family
  • Genus
  • Species
• Species

  Groups of populations that can potentially interbreed freely within and among themselves, collection of bacterial strains that share common physiologic and genetic features and differ notably from other microbial species
• Subspecies


  • Biotype
  • Serotype
  • Genotype
• Biotype


  A group of organisms having the same or nearly the same genotype
• Serotype


  A group of organisms within a species that have the same type and number of surface antigens
• Genotype


  May be given to groups below the subspecies level that share specific but relatively minor characteristics
• Clone


  A population of cells derived from a single parent cell and identical
• Strain differentiation methods


  • Immunological reactions
  • Protein profiling
  • Flow cytometry
  • Phage typing
• Nomenclature


  The branch of taxonomy concerned with the assignment of names to taxonomic groups in agreement with published rules

  
• Carolus Linnaeus introduced a formal system of classification dividing living organisms into two kingdoms— Plantae and Animalia

  
• The taxonomic classification scheme for prokaryotes is found in Bergey's Manual of Systematic Bacteriology

  
• Rules governing microbial nomenclature is limited to two taxa, genus and species known as binomial nomenclature

  
• Pointers on how to write a scientific name

  • Suffixes for order and family
  • Genus and specific epithet (species) are printed underlined or italicized
  • Genus name is always capitalized, species name is lowercase
  • Name may be abbreviated using first letter of genus and full species name

  
• Identification


  The process of determining a particular (organism) belongs to a recognized taxon. The process by which a microorganism's key features are delineated.

  
• Identification methods


  • Genotypic characteristics
  • Phenotypic characteristics

  
• Genus name


  Always capitalized in first letter and is always a noun

  
• Species name


  Lowercase in first letter and is usually an adjective

  
• Scientific name abbreviation


  First letter of genus designation followed by a period (.) and the full species name, which is never abbreviated

  
• Scientific name abbreviation

  • S. aureus
• Identification methods

  • Genotypic characteristics
  • Phenotypic characteristics

  
• Genotypic characteristics

  Relate to an organism's genetic makeup, including the nature of the organism's genes and constituent nucleic acids
• Genotypic characteristics


  • Hair color, height, eye color
• Phenotypic characteristics


  Features beyond the genetic level, including both readily observable characteristics and features that may require extensive analytic procedures to be detected

  
• Phenotypic characteristics


  • Skin color
• Identification methods in bacterial identification

  • Microscopic morphology
  • Macroscopic morphology
  • Physiological/biochemical characteristics
  • Chemical analysis
  • Phage typing
  • Serological analysis
  • Pathogenicity
  • Genetic and molecular analyses

  
• The Three Domain System divides all living organisms into Domain Archaea, Domain Bacteria, and Domain Eukarya
• Ribosomal RNA (rRNA) data suggests that Archaea & Eukarya may share a more recent common ancestor with each other than with Bacteria
• There is often great metabolic and ecological diversity among the members of a group, perhaps reflecting parallel evolution of such things as fermentation pathways, photosynthetic pathways, etc.
• Phyla in Domain Archaea

  • Crenarchaeota
  • Euryarchaeota
• Phyla in Domain Bacteria

  • Aquiflexa
  • Cyanobacteria
  • Chlorobi
  • Proteobacteria
  • Firmicutes
  • Actinobacteria
  • Chlamidiae
  • Spirochaetes
  • Bacteroidetes

  
• Phylum Aquiflexa


  • The earliest deepest branch of bacteria
  • Contains genera Aquiflex and Hydrogenobacter that can obtain energy from hydrogen via chemolithotrophic pathways
• Phylum Cyanobacteria


  • Oxygenic photosynthetic bacteria