A search on swiss cheese holes revealed that gassy bacteria are behind all that holey cheese. In order to make cheese, you need the help of bacteria. Starter cultures containing bacteria are added to milk, where they create lactic acid, essential for producing cheese. Various types of bacteria can be used to make cheese, and some cheeses require several different bacteria to give them a particular flavor.

Propionibacter shermani is one of the three types of bacteria used to make Swiss cheese, and it's responsible for the cheese's distinctive holes. Once P. shermani is added to the cheese mixture and warmed, bubbles of carbon dioxide form. These bubbles become holes in the final product. Cheesemakers can control the size of the holes by changing the acidity, temperature, and curing time of the mixture. Incidentally, those holes are technically called eyes, and the proper Swiss name for the cheese is Emmentaler (also spelled Emmental or Emmenthaler).