The bacteria in the sorts of microbiomics discussed in this article are (usually) totally symbiotic. They aren't going to harm you, they are going to help you. They are going to be a secondary immune system and provide you a layer of protection. Removing them is actually more dangerous for you than encouraging them. In removing them, you create a vacuum that is easier for harmful and parasitic organisms to invade.
Edit: I haven't actually seen the research (and it might not have been done yet) on the specific species mentioned in the article. So I edited to speak more generally.
The idea many of us have been indoctrinated with that all microorganisms are potentially harmful invaders is not only completely false, that belief has lead us as a society to take action that was potentially very harmful to us. There's an entire ecosystem down there, and much of it evolved in symbiosis with us. We provide them a home, and in return they protect and clean us. They don't want to destroy their home, they would die, too.
We could learn a thing or two from them in that regard.