Not all bacteria can be identified through gram staining but it is usually the first step taken. It is a fairly simple technique that labs use all of the time. Gram staining splits the bacteria into two groups which are gram negative and gram positive.
Another method used to identify bacteria is phase contrast microscopy. This method is sometimes used because individual bacteria are very hard to see, in fact they appear to be transparent. A special microscope is used and through illumination light passes through the bacteria and amplitude and contrast are used to make the bacteria visible and able to be viewed.
There are several techniques for differentiating bacteria from other bacteria. One of the methods is using a flow cytometric technique. This is often used when there is a bulk of fluid such as in wheat germ agglutinin that binds to the cell wall of bacteria. Hexidium iodide is used to bind with bacterial DNA, and in this way the bad bacteria that are the result of poor hygiene can be identified.
The other method that involves staining is called Gram staining. In this case one has Gram positive and Gram negative bacteria. The outcome is identified because of the differentiation in the cells walls.