After reading this article by Gina Kolata and this post from the Knoepfler Blog, it seems there’s some confusion about how the Human Microbiome Project (‘HMP’) was designed to look at “normal” people. Having been involved in the project pretty early on, that’s actually not quite correct.
The goal was to look at people who were not diseased or really abnormal outliers*. People in the project often used the shorcut of ‘normal’ or ‘healthy’ because, if you added all of the necessary qualifying clauses when discussing science, you would never reach the end of your sentence. Unfortunately, this habit appears to have trickled out into the public discussion.
That’s why many subjects received dental treatment: the HMP didn’t want to study people with periodontal disease–there are plenty of such studies already**. There was also a practical issue that many people have some sort of oral disease, and if that had been a disqualification, finding enough subjects would have been impossible.
Regarding the oral sites, I’m still surprised nobody has asked why 9/15 sites in men and 9/18 sites in women (cuz women have vaginas, except perhaps in Michigan) are oral sites.
*By ‘abnormal’, I simply mean way out of the ends of the phenotypic distribution (e.g., BMI <18). I'm not making a value judgement about people's bodies.
**This is general problem in microbiology. For example, most strains of human-associated bacteria (e.g., E. coli, Staphylococcus, etc.) are from sick patients, not ‘healthy’ people.