Germs. If you want a list there are too many to fit in this space, but most due not cause disease.
Cause decay/bone los. Some oral bacteria are responsible for cavities and gum disease. The primary cause of cavities is called streptococcus mutans. It adheres to the enamel of teeth and if not brushed away can produce acids that cause cavities. Other bacteria that can be present in the mouth lead to periodontal disease or gum diseases like gingivitis. However, a lot of our oral bacteria are actually prevent disease.