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The thing with the flies is so silly that (together with the talking fox, the Giants and the black swans) I always interpreted them as hobbit folklore. I mean the Lord of the rings is supposed to be a translation of a hobbit book, the red book of the westmarch, a book that has probably been copied and edited multiple times by hobbits. We experience the whole story trough their eyes. Of course if you take this fiction to its logical conclusion you have to wonder how much of the story we can take at face value at all!
Back to Sauron: it's quite clear that Morgoth and Sauron were very interested in genetic engineering right from the start. In the third age you have the plague, clearly a biological weapon, but also the Uruks and the Olog-hai. But I guess that apart from those two races the "normal" orcs in Mordor were also "bred" and did not reproduce freely.
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