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.
|Genome is 100% complete||Complete mapping means fewer unknowns, less trial-and-error, improved accuracy||MUST||ADP: 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|
|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|
|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|
|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|
|Doesn't smell bad||Indole production is limited or absent.||hopefully||ADP: ?|
|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|
|((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