A disease is a condition in which the life of an organism does not proceed easily; Encyclopedia Britannica defines it as "a harmful deviation from the normal structural or functional state of an organism". Modern medicine recognizes many, but not all, diseases as infections by bacteria, other microbes, or viruses. A more holistic approach blames disease on stress, since germs are everywhere (like radiation and toxins). This has some factual basis, though, as stress can weaken the immune system.
Germ theory is the scientific theory that many diseases are caused by germs, a catchall . Many forms of alternative medicine pre-suppose a different cause of illness and don't bother to verify whether those suppositions hold true. Vaccination is a great way to prevent many of the most deadly and debilitating diseases caused by viruses and bacteria.