Bacteria share many common features. However, there are differences between them that can used to classify and identify them. Some of the differences are due to their shapes, cell wall structure (and subsequent Gram stain) and their oxygen requirements. In 1923 David Hendricks Bergey published a manual used to classify bacteria into species, families and orders, based on their structural and functional characteristics. Bergeys’s Manual of Systematic Bacteriology, initially a set of four books, is still in use and has been amended regularly, to include evolutionary relationships between the bacteria as they have been discovered. There are currently five volumes of the manual.

Gram staining is a microbiological laboratory technique that is almost always used as the first step in preliminary identification of a bacterial species. Having carried out Gram staining, further tests are needed to identify the species. These include examining their shapes and finding their oxygen requirements. Biochemical tests are also used to see which enzymes are present.In 1884, the Danish bacteriologist Hans Christian Gram developed a staining method to make bacteria in infected lung tissue appear more visible. He found that some bacteria, for example, Rickettisia bacteria that cause typhus fever, did not retain a stain, called crystal violet, at all (Figure 3). Gram staining differentiates bacteria according to their cell wall structure.

Gram-positive bacteria retain the purple crystal violet stain because they have thick walls made of peptidoglycan. Gram-negative bacteria have thinner peptidoglycan walls and an inner and outer membrane; this means they lose the purple dye and appear pink, due to a counterstain, which is usually safranin. Most species are Gram-positive or Gram-negative, but some are Gram-variable or Gram-indeterminate. The bacteria that causes tuberculosis (TB) do not stain readily with Gram staining and re described as acid-fast.