Lecture 9+ 10

• What is a bacteriophage?

  A bacteriophage is a virus that infects bacteria.
• What should students be able to explain by the end of the lectures on bacteriophages?

  Students should be able to explain the difference between phage lifecycles.
• What potential do bacteriophages have regarding microbiomes?

  Bacteriophages have the potential to modulate microbiomes.
• What topics will be addressed to achieve the aims of the lectures?

  The topics include the difference between phage lifecycles and types of bacteriophages.
• What is the first postulate of Koch's postulates?

  The organism must be observed in all disease cases and absent in all healthy cases.
• What does the second postulate of Koch's postulates state?

  The organism must be isolated from disease cases producing pure cultures.
• What is the third postulate of Koch's postulates?

  The organism must cause disease when inoculated into a healthy host.
• What does the fourth postulate of Koch's postulates state?

  The organism re-isolated from the experimental host must be identical to the original isolate.
• To what conditions do Koch's postulates not apply?

  Koch's postulates do not apply to polymicrobial conditions.
• What is a holobiont?

  • A collection of different organisms
  • Includes the host and various microorganisms such as bacteria, viruses, and fungi
  • Lives within and on the host organism
• What is indicated by the over-representation of phages in phage/bacteria interactions?

  It indicates that phages infect the most abundant bacteria.
• What are bacteriophages?

  Bacteriophages are viruses of bacteria that can be lytic or temperate.
• How many families and species of bacteriophages does the ICTV define?

  ICTV defines 67 families and 4817 species of bacteriophages.
• What is the range of genome sizes for bacteriophages as defined by ICTV?

  The genome size ranges from approximately 3.2 kb to 287 kb.
• What are the size differences of bacteriophages as defined by ICTV?

  Size differences range from approximately 25 nm to 2500 nm.
• What does headful packaging in bacteriophages refer to?

  Headful packaging refers to filling the capsid until full with variable genome lengths.
• What is the significance of isolating and sequencing a larger number of phages?

  It helps to fully understand phage diversity, especially temperate phages.
• What does the Gut Virome Database identify?

  The Gut Virome Database predicts viral presence in gut metagenome studies.
• What does COPSAC identify in relation to bacteriophage diversity?

  COPSAC predicts viral presence in 674 Danish children and identifies family clusters.
• What are the three types of phage life cycles mentioned?

  The three types are lysis, lysogeny, and chronic.
• What is the term for a bacteriophage that infects bacteria?

  A bacteriophage is also referred to as a phage.
• What is the role of cI and cro in the lytic switch of temperate phages?

  cI promotes lysogeny while cro promotes lysis in temperate phages.
• What promotes the SOS-response pathway in bacteria during the lytic switch?

  DNA damage and the bacterial effector RecA promote the SOS-response pathway.
• What are some bacterial defense systems against bacteriophages?

  Bacterial defense systems include adsorption blocking, injection blocking, and CRISPR-Cas.
• What is required for successful binding in adsorption blocking?

  Successful binding requires complementary ligands.
• What happens during injection blocking in gram-negative bacteria?

  Injection blocking occurs when the bacteriophage binds but cannot pass through the inner membrane to the cytoplasm.
• What is the role of cI in temperate phages?

  cI represses lysis in temperate phages.
• What is the function of cro in bacteriophage life cycles?

  cro represses lysogeny by binding to ORF (iii).
• What are some bacterial defense systems against phages?

  Adsorption blocking, injection blocking, restriction modification, CRISPR-Cas, and abortive infection.
• What is adsorption blocking in bacterial defense systems?

  • Prevents successful binding of phages
  • Involves uncomplementary ligands
  • Utilizes external barriers
• What occurs during injection blocking in gram-negative bacteria?

  Bacteriophage binds, nucleic acids are ejected, but do not pass through the inner membrane to the cytoplasm.
• What is the role of methyltransferase in restriction modification systems?

  Methyltransferase adds methyl groups to predefined regions of the bacterial genome.
• How does the presence of methyl groups affect phage binding in restriction modification systems?

  Phage binding occurs, but the phage genome is not methylated, allowing endonuclease to cut it.
• What is the CRISPR array in naive bacteria?

  The CRISPR array contains sequences that help the bacteria recognize and defend against phage DNA.
• What is the function of Cas protein in the CRISPR-Cas system?

  Cas protein degrades phage DNA after the host bacteria recognizes it.
• What are the steps involved in abortive infection in bacteria?

  • Phage binding occurs
  • Nucleic acid reaches the cytoplasm
  • Host bacteria recognizes the phage
  • Host bacteria commits suicide
• What are the main bacterial defense mechanisms against phages?

  Adsorption blocking, injection blocking, restriction modification, CRISPR-Cas, and abortive infection.
• What should students know about bacteriophages by the end of the course?

  Students should know what a bacteriophage is, explain the difference between phage lifecycles, and be aware of bacteriophage defense systems.
• What methods will be addressed to achieve the aims of the course?

  • Traditional culture
  • Metagenomic sequencing
  • Potential of bacteriophages to modulate microbiomes
• What is the first step in traditional bacterial culture methods?

  Isolate bacteria from a sample.