The most common way to identify a microorganism is to place a suspect material onto the surface of a petri dish and allow it to grow. Petri dishes are special flat dishes with covers that contain a mixture of agar and sheep's blood. The agar gels in the dish and provides a firm surface for the bacterium to grow upon, and the sheep's blood gives the bacterium the protein they need to grow. After visible evidence of growth has been observed, a stylus is used to scrape some of the material up and place it on a slide. The slide is then stained and then placed under a microscope for observation and identification. This method is popular and easy to do, especially for schoolchildren.
Here is a very complex and much more difficult method. A team at Brookhaven National Laboratory recently came up with a new technique for identifying germscalled "single point genome signature tagging." As BNL.gov says . . .
"Using enzymes that recognize specific sequences in the genetic code, they chop the microbial genomes into small segments that contain identifier genes common to all microbial species, plus enough unique genetic information to tell the microbes apart."
Apparently, it's a "dice and splice" type of procedure that requires the use of an electron microscope. The spliced segments are then compared to a known database of bacterium. If an exact match of DNA material is obtained, they have identified the microbe. Sometimes, an exact match isn't found and they have identified a new strain or new species of germ! This method is quick and accurate, but expensive!
Another way of identifying bacteria is by a special litmus strip that measures the Ph balance of certain bacterium as they grow and multiply. The strip is dipped in or soaked with a culture medium. A color change takes place on the strip, each bacterium changing the strip to a certain color. By observing the bands of color and their Ph readings (+ or -), scientists can determine the presence of certain bacterium. This only works to confirm the presence of certain suspected bacterium and will not identify other types of microbes. This method is called The Oxidation-Reduction Colorometric Indicator.
These are only three of the many ways that scientists are using to identify, isolate, and study the many harmful microbes that exist in our world today. But, there are many more I haven't mentioned at this time.