As a place to start this discussion we should say, to some degree, the fewer total number of bacteria that are present in a person's mouth (i.e., the less plaque that is present) then the less likely it is that there are enough harmful bacteria on hand to cause dental problems. Individual free-floating bacteria in a person's mouth are typically of little concern and individually can do little to cause dental problems. Alternatively, a build up of dental plaque (that white film which forms on your teeth) can provide a home for millions of bacteria and therefore create an environment where the harmful effects of individual bacteria, as a collective unit, can cause dental disease.
The solution isn't to try to sterilize your mouth. It can't be done, and even if it could it wouldn't be a "good thing." There will always be bacteria present in each of our mouths. What you need to realize is that it's not the presence of oral bacteria which is bad, it's the presence of certain types of bacteria, in numbers, which causes dental disease. And reducing the number of bacteria that are present in a person's mouth is one of the goals of tooth brushing. Another important point to understand about dental plaque and its ability to cause dental disease (especially gum disease) is related to the age of the plaque itself. As a glob of dental plaque lies undisturbed (such as that plaque often found along the gum line of back teeth where a person's daily brushing easily misses) the types of bacteria that live in the dental plaque changes. There is a shift in the bacterial population living in the plaque and, in general, the change is one from a colony of bacteria composed of strains which are relatively less likely to cause dental problems to ones that have a greater ability to do so (this is especially true in the case of gum disease).
This means that an important goal of tooth brushing is to break up and disturb dental plaque on a regular basis. This way after each brushing even though many of the dislodged bacteria still remain in a person's mouth the bacteria which are present have to start all over, from square one, rebuilding and repopulating their dental plaque colony. The net effect is that the age of the plaque is kept comparatively "young" and therefore inhabited primarily by less harmful oral bacteria rather than the more pathogenic types.
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