The context for "good bacteria" is the digestive tract, primarily the stomach and intestines (small and large).
As I understand it, there are no "good bacteria" in the stomach, which is where H. Pylori does its nasty work in causing ulcers. The stomach's acidity also does nasty things to RECCE, so while it is able to do its work in killing H. Pylori, it does not survive long enough for it to reach the intestines to harm the "good bacteria".
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