Does brushing our teeth also lower the number of 'healthy' bacteria in our mouths?

Good/Bad bacteria: Brushing your teeth does reduce both good/bad bacteria. The benefits of reducing the bad outweigh the risks of reducing some of the good bacteria. Brushing regularly after meals will keep the bacteria in check and allow a normal flora in the mouth.

Possible: Brushing your teeth will always help lower the bacterial count in your mouth but they reproduce very rapidly and that is why we must brush mulitple times in a day. So don't worry about them.