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Many DNA isolation and protein expression protocols contain instructions to use a starter culture of E. coli that is then used to inoculate the main culture.

What are the advantages of using starter cultures compared to just let the bacteria grow in the same medium for a longer time? When should one use starter cultures and when can one safely skip that first culture?

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Larry's answer is correct. The other advantage with respect to DNA isolation is that it's very easy to grow up a 5 mL miniprep (ie, overnight) so that the next day you can triage your bacterial colonies (eg, check if they harbor a subcloned DNA fragment in a plasmid). Once you run your diagnostics, then it's very easy to take a small sample of your colony to innoculate a larger growth and carry on for downstream purposes. You could go directly from picking a colony from a plate to grow up 500 mL of your bacteria, but it would be rather wasteful if you aren't certain it is useful. –  leonardo Mar 28 '12 at 13:19

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Growth can be quite slow for some species under certain conditions when the concentration of cells is too low. Log-phase growth is powerful, and so one would like to keep cells in this state for the experiment at hand. Different genes are expressed then compared to a stationary phase.

In addition, you'd like your culture to out-compete a contaminant if there is one. That is more easily accomplished with a starter culture, which is then used to inoculate a larger culture for scale-up. Inoculating directing into the large-sized flask may allow your bacteria to enter a stationary phase, thus giving an opportunity for other species to out-compete your bacteria.

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I'm not sure if I'm reading into this incorrectly, but does E. coli (or monocultures in general) function commensally? e.g., if I inoculate 5 mL or 1 L with the same number of cells, will the 5 mL produce more cells (not density) faster? –  Nick T Mar 29 '12 at 14:06
    
If a culture is too dilute, it can have a reduced doubling time. –  Larry_Parnell Apr 3 '12 at 12:49

I agree that a starter culture would out-comete a contaminant (especially if there is no antibiotic in the media).

Another advantage of inoculating with starter culture is that your results concerning plasmid preps or preparing competent cells will be easily reproducible. By inoculating with a colony, the starter number of cells is different each time you do that, so you might not know how long your cells have to grow to reach a certain OD (e.g. for preparing competent cells) or you have to measure the OD before you isolate DNA to be sure that your yields are comparable with your previous ones.

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