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All fruit fly cultures made or sold to hobbyists have some level of mites in them. The whole goal is to manage the mites as you can't prevent them unless you are working in conditions that allow you to inspect each fly for mites before you put them in the culture. This is really only practical in a lab situation (and it unpractical in the terms if man hours). The simplest method of managing them is to discard cultures around 30 days as that is the average time for the mite life cycle and to keep newer cultures far away from older cultures (or keep them on mite paper which is routinely changed).
 
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