I like it
I would watch it.
If you need any ideas of how a germ looks, you would be surprised on the many different shapes they take.
Isn't it covered it basic biology anymore? :P
If you need ideas on germs, I can remember a few things.
Here are some ideas. The shape of one germ can be a giant blob that absorbes another germ and grows larger...then divides (mitosis I believe.) This can be a "sneaky" cell since it has to absorb its prey.
Another are snake-like germs. Sometimes they are shown on television. They travel around by wiggling around in real-life, but you can make they deadly large equivalents of snakes for your flash.
Another random idea are the little germs that only survive by their superior numbers and fast division. I can not describe them, but you can use your imagination.
For a forth...hmmmm, nothing comes to mind right now. Just do some research. I am sure you can find something.
Another nice idea is that germs tend to infect certain parts of the body...maybe they have have their "territory" before they start out on their full-scale war?
A trend I saw in your flash is the tendency to make the little germs use modern weapons like guns and vehicles. I don't know if my recommendations can work with those. But you can always try. :D
All in all, I like your idea and I hope you continue with it.