With microorganisms it’s particularly interesting because the time and space scales are so different there’s no coherent narrative between humans and bacteria - it’d be like a species of sentient space nebulas seeding a promising planet with proto-humans so we’d eventually plant fruit trees there or something. In one sense, yes, if you were one of the eventual resulting humans, you’re the result of an alien species enslaving humans to do their bidding, but you’re living your entire life just generally doing what you’d do as a human totally unaware of your apparent enslavement and with no apparent restrictions on your movement or decision-space. I’m not an ethicist - anything that doesn’t involve the full consent of all parties gives me pause, but I’m not quite sure what the conversation there looks like.