Cheese is what you get when you take milk, and let it curdle and be fermented by microbes.

First, either raw milk or pasteurized is used. Raw milk contains a large variety of natural microorganisms, while the process of pasteurization eliminates pretty much anything alive.

The milk is curdled, either giving the bacteria that convert the lactose in lactic acid time to do the job, or by adding rennet, which is made from the enzymes of a calf's stomach. The curdled milk clumps together, due to the protein casein.

After the milk has curdled, the clumps are removed from the remaining liquid. The curds are cut open, and the whey is drained. The curds are then taken, pressed together, and pressed into molds.

The cheese is then ripened, which is letting it age while various molds do their work. The ripening may also be called affinage, when done by an expert cheese maker. This is where the type of cheese gets selected. The molds digest various ingredients in the curd, and release enzymes which can color and flavor the cheese. The more molds involved, the more complex the flavor. This is one reason that cheese made with raw milk is usually considered tastier, as there is more to the flavor. Cheese made with pasteurized milk has only a few strains of mold introduced to create the desired type, but may lack the variety of microfauna.

There is some controversy about making cheese with raw milk, due to worries about natural contaminants that may be present, such as E. Coli 0157:H7. However, some argue that the natural variety of organisms keeps such harmful ones from growing to large enough proportions to be harmful. In fact, in the United States, the FDA has required all fresh and soft cheeses to be made from pasteurized milk. Only hard cheeses which are ripened for at least 60 days may use raw milk.

Discover Magazine, November 2001, "Ripe for Controversy"
More to come...