The eyes are bubbles of carbon dioxide gas.
The gas is produced by various species of bacteria in the cheese.
[2] In Swiss-type cheeses, the eyes form as a result of the activity of propionic acid bacteria (propionibacteria), notably Propionibacterium freudenreichii subsp.
[3][4] These bacteria transform lactic acid into propionic acid and carbon dioxide, according to the formula: The CO2 so produced accumulates at weak points in the curd, where it forms the bubbles that become the cheese's eyes.
[1] In Dutch-type cheeses, the CO2 that forms the eyes results from the metabolisation of citrate by citrate-positive ("Cit+") strains of lactococci.