I took cipro because I had salmonella for 7 months! Salmonella when the infection stays is not pleasant, although the worst of it was over.
However salmonella was probably a cause of my liver/gastro problems in general, so I needed to have it gone.
But it was seemingly guaranteed to work- it just caused a major setback in positive bacteria.
It was also VERY strenuous to take. The first 3 days I was basically bed ridden having to sleep all the time. I basically had no side effects from flagyl, so for you to take both would probably be a struggle for you and crippling to your positive bacteria.