Identifying Bacteria in Petri Dishes

Identifying bacteria in Petri dishes is a phenomenon that has grown and expanded over the last couple of centuries. Scientists went from simply being fascinated with the concept of getting to see these microscopic living organisms to fully exploring their depths, shapes, edges, and functions. Thus, it is worth discussing the various ways in which we identify bacteria in petri dishes to better understand them.

Why We Examine Bacteria in Petri Dishes

First, we began examining bacteria as far back as 1676, with Antonie Van Leeuwenhoek. He noticed them under a microscope and called them “animalcules,” which means “tiny animals” in Latin. He found them while investigating pond water, and he went on to become the father of microbiology.

It would be more than one hundred years later than the Petri dish was invented.

Scientists long needed a place to hold bacteria in place while examining their structure and their activities.

Thanks to Julius Petri and Fanny Hess in the late 1800s, Petri dishes and agar plates gave scientists an opportunity to place bacteria on a firm medium and cover the dish with a nesting lid. The dish could then be flipped upside down and the bacteria could be observed growing through the clear thin medium.

These two inventions offered scientists a solid medium as well as an airtight container, which meant they could be relatively certain the bacteria would not be contaminated and that it could be either fed a nutrient through the agar or experimented on with various antibiotics. It was a major breakthrough in science and microbiology specifically.

How Do You Identify Bacteria in Petri Dishes?

Today, students of microbiology learn to examine and identify bacteria in Petri dishes in multiple ways.

First, you’ll likely need to dilute the bacterial sample to ensure you can actually examine it. Most bacterial cultures are so rich with colonies that the colonies will crowd the Petri dish and you won’t be able to differentiate among them.

You can dilute your bacterial culture by adding a 10:1 ratio of filtered water to bacteria. Shake the dilution well, and then dilute it in the same way at least one more time.

Next, you’ll need to ensure you adequately culture your medium with bacteria. This first essential step means making sure you have the right medium. Some bacteria can be examined on plain agar. Other bacteria might require blood agar or another nutrient.

Then, you’ll need to make sure you use gloves and swab the bacteria thoroughly with a cotton swab.

Finally, swipe the cotton swab in tight lines across the agar from edge to edge. Turn the plate and swipe again to fully cover the surface of the agar.

You can now close the lid of the Petri dish and later examine the bacteria under a microscope. You should be able to see separate colonies forming and mark them with a sharpie on the underside of the Petri dish. Decide how long you want to wait to observe the growth of these colony forming units, or CFUs.

For more on this, check out our complete Free Guide (19 pages) on How to Count Colonies on Agar Plates!

Colony Identifying Bacteria on Agar Plates

CFUs can come in many forms, and we can use different terminology to discuss what we observe.

When examining bacteria on Petri dishes, you can note the form, elevation, and margins of the bacteria.


Form can be circular, irregular, filamentous, or rhizoid.


Elevation refers to whether the bacteria appear to be raised, convex, flat, umbonate, or crateriform.


And the margins are what you will see if you look at the side view of the colony. You can use the terms entire, undulate, filiform, curled, or lobate to describe this view.

Counting CFUs

Of course, you also want to note whether the number of CFUs increases or decreases, depending on your experiment.

Summing It All Up

Fortunately, science has come a long way from those early days of wondering what we were observing and how we could possibly identify what we were seeing.

Today, scientists have many options for examining bacteria in Petri dishes and many ways to describe what they see.

All you need is a Petri dish with an agar plate, a sanitary environment, some gloves and Pasteur pipettes, glass vials, and a microscope, and you can begin your own scientific observations in the field of microbiology.

And thanks to artificial intelligence, automated colony counting is quickly coming onto the scene to help identify various bacteria for you, taking the guesswork and the room for human error entirely out of the equation.

Are you an agar plate manufacturer / distributor? Enhance your product offering by providing your customers with an automated analysis for pre-poured agar plates, which eliminates the need for laborious manual counting! The Automated Counter developed by Oculyze can count colonies with high accuracy and speed, using only an uploaded image of a Petri dish.

Test our Colony Counter! Completely free of charge and with no commitment to purchase. Just please note that the recognition provided here is solely for demonstration purposes and may not accurately represent the performance of our product. Our customers receive customized recognitions tailored to their specific needs, which ensures high levels of accuracy for their plates.

Let artificial intelligence do the hard work for your customers. Want to know more? Contact us and we’ll be happy to help!




  • Publications

    What Is Bioethanol Made From?

    Have you been wondering, “What Is Bioethanol Made From?” This article explains the history of bioethanol and describes the resources used and the process.

    Read more
  • Publications

    Best Pattern Recognition Software

    A review of the best pattern recognition software for those interested in the various applications, including colony counts, bacteria identification, and more.

    Read more
  • Publications

    Petri Dish Bacteria Identification Chart: Why Use One

    This article is dedicated to those in the lab wondering whether a comprehensive petri dish bacteria identification chart could make their job easier.

    Read more
  • 0
      Your Cart
      Your cart is empty