good find PZ - these are the kinds of things that create confusion in human understanding due to our tendency to compartmentalize things.
there are both, beneficial and harmful bacteria, there is also pleomorphism... the issue is us and what we do... what are we passing through to the bacteria; what are we feeding it?
Are we encouraging the proliferation of good bacteria or bad? Are we, through diet and environment, supporting pleomorphism towards beneficial or bad? etc. We could get Biblical here in the implications.
When we challenge our systems by using Antibiotics or eating chemical food additives , the recent splenda article here being and example;