1 SFX: JURRRZ! {time machine appears}
2 Isaac Newton: Anton van Leeuwenhoek, you're needed on a journey through time to save the universe!
3 Anton van Leeuwenhoek: But... I've just discovered tiny invisible creatures with my micro-scope! I need to learn more about them.
4 Isaac Newton: They cause disease. Bread mould can kill them, but they mutate and grow stronger.
4 Anton van Leeuwenhoek: Eeeeuuuw!! Get me out of this barbaric time!

Isaac and Edmond hardly needed to bother with a time trip to pick up van Leeuwenhoek, since he lived contemporaneously with them. Van Leeuwenhoek was only 11 years older than Newton, and died a mere 4 years before him. It's certain that Newton would have known of van Leeuwenhoek and his work, since he published his observations in the Philosophical Transactions of the Royal Society beginning from 1673, just a year after Newton presented the Society with his reflecting telescope design. Newton became President of the Royal Society in 1703, and van Leeuwenhoek kept up a steady stream of publications and correspondence with the Society up until his death in 1723.

It's also a virtual certainty that van Leeuwenhoek would have known of Newton's work, as he was clearly the greatest scientist of his time, recognised as such during his own lifetime. If I'd spent more than about 15 minutes Googling I probably could have found some direct references indicating they knew each other or met at some point, but alas I didn't.

EDIT: In fact, I've found the following, an extract from the diary of the prominent Dutch scientist Christiaan Huygens, written on 12 June, 1689, while on a visit to London, describing his attendance at a meeting of the Royal Society:

Meeting at Gresham College in a small room, a small cabinet of curiosities, over-full but well kept. Hoskins President, Henshaw Vice-President, Halley Secretary. Van Leeuwenhoek's letter was read. Newton and Fatio were there too.