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.