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Gram staining is useful in separating bacteria into two groups: Gram positive or Gram negative. They are separated into these groups based on their cell wall structure. Gram positive bacteria contain a thick layer of peptidoglycan in their cell walls, while Gram negative bacteria contain a very small layer of peptidoglycan (15% or less of what Gram positive cell walls contain). A primary stain is added, such as Crystal Violet, that will stain all of the bacteria. Then, a mordant (such as iodine and potassium iodide) is added to form a complex between the peptidoglycan and the stain, which will make the cell more resistant to decolorization. Then, a decolorizing agent is added, which will remove the primary stain from Gram negative bacteria, but will cause the cell walls in Gram positive bacteria to dehydrate, and therefore, they will retain the primary stain. Finally, a counterstain (typically safranin) is added to distinguish Gram positive from Gram negative. Gram positive cells will be purple, and Gram negative cells will be red if Crystal Violet and Safranin are used.

Acid-fast staining is entirely different. Is is used to detect species of bacteria in the genera Mycobacteria and Nocardia. These bacteria are resistant to typical staining procedures, such as Gram staining, due to a thick, waxy lipid layer in the cell wall composed of mycolic acid. Heating of the bacteria with a very strong stain such as carbol-fuchsin is necessary to "melt" this lipid layer, and force the stain through the cell wall. Once the bacteria has cooled, they will be incredibly resistant to decolorization. Non-acid fast bacteria do not contain this mycolic acid layer, and therefore, they will decolorize much easier, and are then stained with a counterstain to distinguish Acid-Fast bacteria from Non-Acid-Fast bacteria.

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