The holes or eyes in such cheeses are actually bubbles formed as the cheese matures. These propionibacteria metabolise the lactate which is produced by the other organisms into propionate, acetate and carbon dioxide. The gas expands, forming bubbles within the protein matrix of the cheese. Presumably the bacteria are clustered together so that the gas is produced in small pockets.
Cheese is a viscoelastic material that is able to flow under quite small stresses.
The lactate production peaks about 20 days after the manufacture of the cheese. The propionibacteria are therefore active when the curd is quite plastic and deformable. The structure of the curd is thus critical in determining the quality of eye formation in the cheese. If the curd is quite smooth and cohesive, nice round bubbles will form whose size depends on the amount of carbon dioxide that is present and also the plasticity of the curd. If the curd is grainy or layered, poor quality slits will be formed instead of the holes usually seen in the finished shop product.