The sefer hachinnuch writes in mitzvah 163: "the prohibition against eating minute insects engendered in grains and fruits", as follows:

It is in effect in every place and time, for both man and woman. If someone violated it and willfully ate an entirely whole creature that was unclean (non-kosher), whether it was alive or dead, even if smaller than a mustard seed, even if it was putrid, whether it was engendered through a male and a female creature, or from any decaying matter in the world, and it had swarmed on the ground--if someone ate it entirely, he would be punished with whiplashes. But if it was missing even one leg, he would not be whipped until he ate an olive's amount of it.

Read about the regular flies here

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