Majority of the microbes do not cause the disease. The disease
causing microbes also, probably, keeps your species healthy and
your immune system tuned.
Not all microbes are harmful. Some are quite helpful. As humans,
we actually have microbes in our bodies and on our skin that work
to keep us from getting certain diseases.
Microbes cause many diseases, to make this even broader microbes
encompass a whole range of microscopic organisms that can cause
diseases. But since you asked for any old common one: the Influenza
virus causes common colds and flu.