It sound like the sort of thing Particular/particle illusion could do. I don’t have Particular so can’t say for definite, and I’m not sure if PI can do this.
Failing that, if you can get stock footage of bacterial growth then use it as a matte?
Or make a pre-comp of one bacteria splitting into two, then use Particle Playground or expressions to multiply it up. Or you could simply manually build dozens of pre-comps into the correct shape.
I don’t have CS3 (yet – although finally persuaded the higher ups to order it on Friday – yay!) so can’t say for certain there’s not something there you can use.
Graham