There are a few different ways that fermentation could have happened without the knowledge of germ theory. One way is that fermentation is a naturally occurring process, so it is possible that it just happened without anyone knowing why. Another possibility is that people knew that fermentation happened, but they did not know the reason why it happened. It is also possible that people had a general idea that fermentation happened because of microorganisms, but they did not know exactly how it worked.
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