Because bacteria use the Cori cycle for anaerobic metabolism, discovered by Carl and Gerty Cori, in which lactic acid is produced as a byproduct. Fungi (well, specifically yeast) use a different metabolic pathway which produces carbon dioxide and ethanol as a byproduct. Cheese fermented using bacteria is unpalatably sour, while the ethanol produced by the fungus can be evaporated away in the cheesemaking process. And the carbon dioxide makes the holes.
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