Because there are different types of bacteria that are vying for domination. The "good" bacteria are fine with antibiotics because they usually only get used when there are too many "harmful" bacteria that threaten the life support system.
Penicillin did, but I think a lot of the newer ones were derived from bacteria. But doing a quick web search right now I'm mostly getting potential new antibiotics that came from bacteria, rather than proven antibiotics, so now I'm wondering about the actual bacterial contribution...