Like all cheese, milk is cultivated with bacteria and turns into cheese. But unlike all cheese, they don’t tend to have holes in them. It was initially thought that these bacteria create these air holes. The bacteria give off enough carbon dioxide and form these bubble in the cheese, once fermented, these holes would stay as part of the hole of the Swiss cheese.
The new theory, however, comes from tiny specks of hay that was accidentally collected while milking a cow. These hay particles weaken the cheese structure and allow air to accumulate into it. With the modern milking method, less flecks of hay is found in the milk that later made into the cheese, and these cheese end up with less holes. So there is a correlation of higher numbers of little hay particles to a higher number of holes in Swiss cheese, or “eyes” as the cheese farmers call it. It could also be the combination of both bacteria and the hays theory. Whatever the case is, they still taste delicious!