Microbe is a somewhat outdated way for scientists to talk about the tiny bugs that cause diseases. When you get the flu, you can blame a microbe.
In the nineteenth century, the idea that germs caused illness was brand new, and doctors referred to both germs and microbes interchangeably. The word microorganism is more scientifically precise, and in fact microbe is a shortened form of that long, Greek-rooted word. Mikro means "small," and in microbe it's combined with bios, or "life."