I hate to be the one to tell you, but microscopic organisms have already been made into plush toys.
Here is the link to the site that sells them:
http://www.thinkgeek.com/geektoys/plush/6708/It reminds me of the episode of Northern Exposure when Chris in the morning decides that he wants to fling a cow from a cataput (or would that be a cowapult?), but has second thoughts when he finds out that Monty Python did the same thing years earlier and since he wants to be original, he decides to fling a stand-up piano (which ended up being a really cool)
Two things to mention. First, ThinkGeek does not sell any "bacteriophage" plushies, so in that detail, you are orginial. Second, any good fabric store will have patterns and instructions on how to make a plush doll. (And most do not have good websites...so you'll have to hoof it)
Hope that helps,
Rosie
p.s. to the editors: this was not MEANT to be an ad for the above website...it was completely necessary to answer StanSquidPirate's post...so if I broke any rules, I apologize and won't do it again.