Microbial Stains

Stains—or dyes—are used to add color and differentially emphasize structures in specimens. Staining is especially useful since many biological structures and components lack contrast or color and cannot be discriminated when visualized under a microscope. Different stains take advantage of different properties of chemicals and how they interact with parts of the microbe in order to provide information about the microbe. A stain may colorize an entire microbe or a specific component of a cell. A simple stain uses a single dye color and typically stains all microbes in a sample. A differential stain uses multiple dye colors—typically two—and can stain microbes in the same sample differently depending on certain properties, such as the composition of the bacterial cell wall or the way the microbe processes the chemicals used in the stain. The color of the specimen after being stained reveals properties of the microbe that would not be visualized without staining.

One simple stain is the negative stain, in which a dark stain is used to cover the background of the slide while the microbes on the slide remain clear. The stains used for negative staining do not permeabilize the microbes and instead are used to create a dark background in contrast with the unstained microbes. The images produced from a negative stain look like a black-and-white photograph. This technique can be used with light microscopes or electron microscopes.

One very common differential stain is Gram stain, a method of staining used to differentiate types of bacteria based on the thickness of the primary cell wall material peptidoglycan. After the sample has been stained, the bacteria will appear either red (gram-negative) or purple (gram-positive).

First, bacteria are fixed onto a glass slide using a smear where the sample is wiped on the slide and allowing it to dry. Crystal violet (purple dye) is added, and this stains all the bacteria on the slide. Next, iodine is added. Iodine binds to the crystal violet inside the bacteria, making a large complex. The slide is then decolorized, or washed with alcohol that removes the crystal violet complex from some (but not all) bacteria. The crystal violet plus iodine complex is too big to be washed out of bacteria with thick peptidoglycan cell walls, and these bacteria remain purple. However, it is able to be washed out of other bacteria. Finally, safranin (the counterstain) is added. The bacteria that were decolorized in the previous step are instead stained by safranin now, and they appear red. Looking under a microscope, the purple and red colors can be distinguished. The purple bacteria are gram-positive, while the red bacteria are gram-negative. Gram-positive bacteria have a strong, thick cell wall, while gram-negative bacteria have a thin cell wall that is dissolved during the staining process. The component that differs between the cell wall of gram-positive and gram-negative bacteria is called peptidoglycan. Gram-positive bacteria have a cell wall that is made up of 90 percent peptidoglycan, which is organized into a thick layer. Because of this, the crystal violet and iodine complex remains inside the cells during the decolorization step. Gram-negative bacteria have a cell wall that is made up of only 10 percent peptidoglycan, arranged into a thin layer. The rest of the cell wall is made up of lipids, or fat molecules. During the decolorization step, the cell wall of a gram-negative bacteria dissolves, and the crystal violet can escape. These bacteria can be counterstained with safranin, turning them red so they can be seen under the microscope.

Gram staining is frequently used in a hospital setting to differentiate between different kinds of bacteria that cause infections. Gram-positive and gram-negative bacteria respond differently to medical treatment. Some kinds of gram-positive bacteria are Staphylococcus and Streptococcus. Staphylococcus can cause skin infections, and in clinical settings methicillin-resistant Staphylococcus aureus (MRSA) is a potential threat to patients. Certain strains of Streptococcus can cause strep throat. Some other types of organisms also stain gram-positive, including the infectious algae Prototheca wickerhamii. Some gram-negative bacteria include Salmonella and Yersinia enterocolitica, which can cause food poisoning, and Vibrio, which can cause cholera.

The difference in the composition of the cell wall between gram-positive and gram-negative bacteria means that the bacteria respond differently to antibiotic treatment. Gram-negative bacteria are more likely to become resistant to antibiotics—that is, unable to be killed by them. This is because many antibiotics target peptidoglycans. Gram-positive bacteria can be killed by antibiotics because their cell wall is composed of 90 percent peptidoglycans. In gram-positive bacteria, the thin peptidoglycan layer is coated with lipids, protecting these bacteria from the effects of antibiotics.