What are some common genera of pathogenic bacteria that have no species found in the human body naturally? borrelia? brucella? yersinia? mycoplasma?

The Microbiome... : Great thought question. However, you are assuming we know all the community of species of bacteria in the body (aka. The microbiome). Recently, we have discovered thousands of genera in our body through molecular techniques (most don't even have a name yet). Though it's tempting to generalize, the question you pose can't be answered with any reliability with what we know today.