How did the advent of the microscope most likely affect the foul-air theory?

The answer for this question is: It allowed scientists to see small organisms in sick individuals and change the theory.

A lot of biological process/mechanism that happened around us could only be explained if we observe it on a smaller scale.

The advent of microscope allows scientists to observe a lot of things, such as the activity of virus, the movement of cells, the pores, etc.