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Question:

Does the aging process for raw milk cheeses kill the good bacteria as well as the bad?

Answer:

Aging cheese develops lactic acid through the life cycles of lactobacilli. This acidity creates an environment inhospitable to bacteria associated with food poisoning. Eventually the acidity reaches a point where the "good" lactobacilli die off as well.

Fermentation Q&A

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What cheeses are fermented?  I need to know because I like cheese, but can't eat fermented ones.
In general the blander cheeses, often called "fresh," are not fermented, or very mildly. Any with a sharp flavor (like cheddar) is fermented, as well as any runny cheeses and blue cheeses.