User:Jonathan Cline/Notebook/Ideal Microbe

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Please edit this page to add ideas / thoughts / corrections

  • Working in a garage-lab or skunkworks environment imposes some restrictions on choice of organisms to engineer: expensive equipment/chemicals may be unavailable, protocols may need to be simplified to reduce man-hours, etc.
  • There are many choices of host organisms for engineering, each having different strengths and weaknesses.
  • Host organisms can be genetically improved for fitness to these requirements, if a concise set of requirements are made.
    • A great example is the "eau d'e coli" project from iGEM which removed (and subsequently enhanced!) the non-desirable smelly feature of the common BioBrick host.

Requirements for The Ideal Microbe

  • "Must" means that the requirement must be met for proper acceptance.
  • "Should" means that the requirement should attempt to be met, however operation is not jeopardized by failure to meet the requirement.
  • "Hopefully" means that the requirement isn't necessary for operation, however is nice to have.
Feature Details Requirement Candidates
Genome is 100% complete Complete mapping means fewer unknowns, less trial-and-error, improved accuracy MUST ADP: Yes
Acido: Yes
Casei: Yes
Pathway description is over 50% complete Hard to quantify; though, "a lot is known" about the internals of the host. MUST
Non-pathogenic Cloning and growth is not harmful to people. MUST ADP: Yes
Acido: Yes
Casei: Yes
Transformable Accepts vectors easily, makes engineering more precise. MUST
Doubling time under 1 hr At ideal temperature, allows fast growth. MUST
BioBrick Compatibility Existing BB parts and protocols can be used MUST ADP: Yes
Acido: ?
Casei: ?
Non-regulated biosafety Host can be purchased by individuals through simple paperwork MUST
Shelf life at least 1 year at 4C Allows easy archival and low cost lab setup MUST
Simplified environmental selection for Modified clone Allows using non-transfer protocols for selecting the modified host; simplifies protocol. Add new reagent to existing environment to select only modified hosts. hopefully ADP: No
Acido: No
Casei: No
Cyano: Yes
Low mutation rate Lower mutation rate makes engineering more precise. Should
Room Temperature reproduction Allows low cost lab setup Should
Electroporation Allows modification using electroporation for low cost engineering Should
Cells can be freeze-dried Allows simple shipment method and low cost lab setup hopefully
Public perceives host as "Friendly" Hearing the name makes people smile rather than frown. Should ADP: No
Acido: Yes
Casei: Yes
Doesn't smell bad Indole production is limited or absent. hopefully ADP: ?
Acido: Yes
Casei: Yes
Looks translucent or opaque (or green?) Doesn't invoke "yuck" when seen. hopefully
Gram-((negative or positive??)) higher metabolic compatibility with existing parts, ??other?? Should ADP: Neg
Acido: Pos
Casei: Pos
((Aerobic -or- Anerobic preference??)) (?)
Host can be readily supplied today Obtaining the host is possible from ready stocks hopefully

Suggested Microbes so far

  • Acinetobacter sp. ADP1
  • Lactobacillus acidophilus
  • Lactobacillus casei


[Full Text] Acinetobacter sp. ADP1: an ideal model organism for genetic analysis and genome engineering. Nucleic Acids Research 2004 32(19):5780-5790; doi:10.1093/nar/gkh881