Eye floaters are usually small flecks of collagen floating inside of your eye (the same substance that is present in the extra-cellular matrix) and as you age they can clump together and cast shadows on your retina.
They may look like microbes to you because the clumping gives the appearance of a thread-like or rod shape, commonly associated with microbes. The light falling on the eye will enhance this by making them look transparent and somewhat like microbes. But rest assured they aren't, because if they are, then you certainly have superhuman eyes!