Week 1

• What is the aim of the lecture on taxonomy and phylogeny?


  To differentiate between Linnaean models and modern phylogenetic methods
• What is taxonomy?


  Classification based on shared characteristics
• What does phylogeny measure?


  The evolutionary relationships between organisms
• What are the steps in the taxonomic classification of microbes?


  1. Classification: Ordering organisms into groups based on shared properties
  2. Nomenclature: Naming the classified organisms
  3. Identification: Determining species based on comparison to known groups
• Who is considered the founder of modern taxonomy?


  Carl Linnaeus
• What traditional properties are used in classification?

  Microscopy, morphology, response to oxygen, and biochemical tests
• What are the molecular and genetic methods for classifying bacteria?


  1. Choose appropriate molecular markers for a gene family
  2. Amplify and sequence
  3. Create evolutionary model
  4. Phylogenetic tree analysis and construction
• What is the basis of phylogeny?


  All living things have genes that mutate randomly at low frequency
• How do organisms differing by a few DNA base changes relate to evolutionary time?


  They have diverged more recently in evolutionary time
• What are the differences and similarities between Archaea and Bacteria?


  Similarities:

  • Share shape, size, and microscopic appearance
  • Multiply by binary fission

  
  

  Differences:

  • Archaea do not have peptidoglycan
  • Archaea genes are more similar to eukaryotes
• What is the classification system for Shigella?


  It includes biovar, morphovar, and serovar classifications
• What are the phenotypic and chemotaxonomic methods for classifying a previously unrecorded microbe?


  Physical, structural, or metabolic features and biochemical composition
• What is the role of the urease test in bacterial classification?


  It detects the presence of urease enzyme by a color change
• What is the significance of the universal phylogenetic tree based on 16S sRNA analysis?


  It illustrates the three domains of life
• What are the four classifications of bacteria based on their response to oxygen?

  Aerobes, microaerophiles, anaerobes, and facultative anaerobes
• Why might Woese have faced resistance to his proposal for reclassification of Archaea?


  Due to the similarities and differences between Archaea and Bacteria
• What is the significance of GC content in bacterial classification?


  It indicates the percentage of guanine and cytosine in DNA or RNA
• What is the focus of the study on Pseudomonadaceae and related opportunistic pathogens?


  To introduce the bacterial group, focusing on Pseudomonas aeruginosa and Burkholderia genus
• What are the characteristics of methanogens?


  They are anaerobic CH4 producers
• What is the clinical significance of Pseudomonadaceae?


  It includes opportunistic pathogens that can cause infections in immunocompromised individuals
• What is the role of microscopy in bacterial classification?


  It helps in observing morphology and size
• How do phenotypic and genotypic classification systems differ?


  Phenotypic focuses on physical features, while genotypic focuses on genetic similarities
• What are the learning outcomes of the study on Pseudomonadaceae?


  Familiarity with phylogeny, diverse roles, and understanding P. aeruginosa as an opportunistic pathogen
• What is the importance of biochemical and enzymatic tests in classification?


  They help identify specific metabolic capabilities of microbes
• Who is the author of the study material?

  Dr Jenny Ritchie
• What is the classification of bacteria based on their morphology?


  Rods, cocci, spirals, and coiled shapes
• What is the faecal carriage rate of Pseudomonas aeruginosa?


  Between 15% and 25%, higher in vegetarians
• What is the email address of Dr Jenny Ritchie?

  1. [e-mail]
• What is the significance of the analytical profile index?


  It involves multiple biochemical and enzymatic tests for classification
• What is the main focus of the module described in the study material?


  To describe the structural, physiological, biochemical and genetic characteristics of bacteria and animal viruses
• How does the classification of Archaea differ from that of Bacteria?


  Archaea lack peptidoglycan and have different cell wall structures
• What are the taxonomic classifications of Pseudomonas aeruginosa?


  • Domain: Bacteria
  • Phylum: Proteobacteria
  • Class: Gamma
  • Order: Pseudomonadales
  • Family: Pseudomonadaceae
  • Genus: Pseudomonas
  • Species: P. aeruginosa
• What are the diseases caused by bacteria and protozoa that the module aims to describe?


  Diarrhoea, sepsis, urinary tract infections, CNS infections
• What are the characteristics of hyperthermophiles?


  They thrive at temperatures between 113 – 200°C
• What are the characteristics of Pseudomonadaceae bacteria?


  They are Gram-negative bacilli, polar flagella, aerobic, and non-fermentative
• What role do bacteria and protozoa play in the environment according to the module aims?


  They have significant effects on ecological processes
• What are psychrophiles?


  Microbes that thrive at low temperatures, around -15°C
• What is the attendance code for the module?

  BR-YM-AH
• What are some genera included in the Pseudomonadaceae family?


  • Pseudomonas
  • Burkholderia
  • Xanthomonas
  • Ralstonia
  • Zymomonas
  • Sphingomonas
  • Stenotrophomonas
• What is the order that includes the family Enterobacteriaceae?


  Enterobacterales