Humans are not born with complete immune function. Children less than 10, particularly babies, are somewhat immune suppressed. The elderly too. Gradually lose immune function as natural aging process. AIDS and some other diseases of immune cells.
Chronic disease reduces immune function, ie., diabetes.
Also individual variations in immune function. When an organism can't carry out normal cell function, results in a disturbance in state of health. Not just microbes that cause these malfunctions, but when microbes are the cause, it's called infectious disease. In late 1800's this German scientist was the first to say the simple truth that microbes can cause disease. But in order to prove that a particular microbe was responsible for disease, Koch devised Koch's postulates which are criteria that must be fulfilled before you can say for sure that a microbe is responsible for a disease.