User:Jonathan Cline/Notebook/Ideal Microbe

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

References

[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