Swiss cheese has holes because of carbon dioxide gas bubbles produced by bacteria during the cheese fermentation process. The bacteria, specifically Propionibacteria, metabolize lactic acid and release carbon dioxide gas, which forms bubbles inside the cheese. These bubbles create the characteristic holes, also called "eyes" in the cheese. The holes are carefully controlled during cheese production to maintain the cheese's texture and flavor, which is nutty and distinctive. However, research from Swiss agricultural scientists also shows that tiny particles, such as flecks of hay or dust that get into the milk during traditional milking processes, act as nucleation sites where the gas bubbles form. This explains why modern cleaner milk production methods result in Swiss cheese with fewer or smaller holes. So, the holes form from a combination of bacterial gas production and the presence of microscopic particulate matter that helps bubbles to develop. In summary, the holes in Swiss cheese are formed by carbon dioxide gas bubbles made by bacteria during aging, and these bubbles cluster around small particles like hay dust in the cheese curd.