Contrary to what you may have been told when you were a kid, the holes in Swiss cheese are not made by mice nibbling away at a big wheel of Swiss. As sweet (or gross) as that image may be, the reason for holes in Swiss cheese (known as "eyes" in the cheese world) is a bit more scientific and a little less "cute."
Swiss cheese, properly known as Emmentaler, gets its hole-y appearance and distinctive flavor thanks to the bacteria that turns milk into cheese. All cheeses contain bacteria (they're responsible for producing lactic acid) which help them develop into a final edible product, yet not all those bacteria are the same.
To make Swiss cheese, the cultures of the bacteria S. thermophilus, Lactobacillus and P. shermani are mixed with cow’s milk. The bacteria helps produce curds, which are pressed and soaked in brine inside of cheese molds. The cheese is then stored at 72 to 80 degrees Fahrenheit and left to ripen. It's at this point when the bacteria really does its work. While it's working, it releases lactic acid and one of those bacteria, a gassy one, consumes it.
That bacteria, more specifically P. shermani, releases carbon dioxide when it consumes the lactic acid and forms bubbles. The bubbles don't just disappear, they form little air pockets, resulting in the holes of the Swiss cheese. The size of the holes can be controlled by cheese makers through the acidity, temperature and maturing time, which is why it's possible to have a baby Swiss and regular Swiss option.
An interesting tidbit: The holes in Swiss cheese have created trouble in the past for commercial cheese slicers. In 2000, the FDA regulated the holes in Swiss cheese to be between 3/8 and 13/16 of an inch in diameter.
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