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just lost a master culture myself due to lack of ventilation. Looks like a nucular disaster. Dead bugs covering the surface. I sealed them because of a fungus gnatt problem. I think you should be just fine with the fruit flys though. I dont think there is enough food for them to continualy breed in the cultures. I am pretty sure there is no fear of them crashing the culture either. You could try hot glueing coffee filters over the holes. I think that is next for me since my cultures are still sealed.
 
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