When microbes are cultured in the lab (often yeast or bacteria), the cells grow, divide and mutate in response to their environment.

Researchers use colony picking as a means to sift through this microbial soup to identify colonies of interest based on observable characteristics (phenotype). So whether you’re trying to pinpoint the next blockbuster drug or perfect the perfect pint, colony picking is a vital tool for any microbial researcher.

How it works 

You’ve got a sample containing your strains of interest and now you’re ready to grow them into individual colonies. Where do you start?

Step 1: Grow it on agar 

The growth of pure single-strain colonies starts with a single cell inoculated onto a solid agar medium, usually in a Petri dish or SBS plate. To achieve this streak the cells onto the agar using a wire loop or alternate method to spread the solution such that individual cells no longer touch. Apply the right growth conditions depending on your organism (nutrient medium, temperature, time) and overnight you’ll have individual colonies dotted around the agar, each one originating from a single parent cell. For example, see how to grow yeast.

TOP TIP: Some microbes, such as gut bacteria, will only grow in low oxygen levels so consider whether you need an anaerobic chamber.


Step 2: Choose your favourites

Working with a few plates, picking can be done manually using an inoculation loop or simply a toothpick. Alternatively if working with many samples, to save time, and boredom and eliminate human error it is typically automated using a high-precision robot. Researchers usually identify colonies using a predetermined set of criteria based on how they look (morphology) or particular traits they exhibit (phenotype), such as antibiotic resistance, colour, ability to grow on specific substrates or fluorescent markers.


Step 3: Replicate and record

Picked colonies may be stored for future use or replicated onto multiple plate formats for further downstream testing, such as high throughput screens.

Accurate record-keeping is crucial. Being able to track the identity of picked colonies, their location on stored plates, and any relevant information about their characteristics ensures traceability, and reproducibility and supports interrelated workflows.

And that’s colony picking in a nutshell. Sorted!

PIXL set up

Key considerations

Before you get cracking, you must have your workflow optimised to achieve the goals of your experiment. You’ll need to consider:

  1. Which organisms are most appropriate?
  2. What time and resources are available?
  3. How can these be put to best use to achieve the highest impact science within the project’s scope?