Rinsing the mouth three times with water (for example, during the course of ablution) rids it of a large number of microorganisms, which inhabit the mouth. It is estimated that the number of germs in saliva is approximately one hundred million per square millimetre. There are also a large number of microorganisms which feed on food remnants between the teeth; the growth and multiplication of these creatures produces acid and other secretions which affect the mouth and its smell, and the colour and function of the teeth. Rinsing the mouth thrice, five times a day, rids the mouth of a huge number of these organisms and their toxins.
(from Islamic Medicine: The Key to a Better Life by Yusuf Al-Hajj Ahmad, Published by Darussalam)