I tried to make the bacteria look simple and cute, but still make it nasty using 'ill' colours. Not all combinations are successfull, but I think the best and probably main colour would be muddy green, which makes everything kind of look dirty and not very pleasant.
I wanted to show the difference between the bacteria and antibiotics with making a shift in the design and colours. Since antibiotics are created by humans in laboratories, for some reason I imagine them a bit robotic. I really like #8 but I think it shifts too much from the whole concept and as main character it looks a bit scary. I personally think that the main characters have to be more appealing than everything else regardless if it's a movie or a game, so I think I might go with #4, because it fits more the style and it's kind of cute.