Ecosystems have niches for aggressive behavior against participants that reduce diversity. It's why you find higher concentrations of Lyme disease in new housing developments than you do in the deep woods: it's the activation of a defense mechanism (in the Lyme disease case it has to do with there being a higher proportion of competent hosts for the pathogen: mice, but in general evolution has myriad ways if implementing this pattern).

If it's just you and one species of bacteria, you're closer to a circumstance that would call for the activation of such behavior than if diversity is high.

So it's not that the bacteria are intrinsically good or bad, but that the different circumstances call for calm or aggressive behavior, and all your friends going missing cues aggressiveness in species who have evolved by filling that niche in the past.