In my years of practice I have seen many cases where antibiotics have resulted in long-lasting changes in the health of individuals by altering the bacteria living in the gut.
Les Dethlefsen and David Relman of Stanford University looked at over 50 stool samples from just three people over a 10 month period that included two courses of Cipro. They found that each person had a unique set of microbial flora which fluctuated with the use of the antibiotic. In most cases the natural flora rebounded after use of the Cipro. But in a few , bacterial species present before treatment were replaced by another specie. One person completely lost a common genus of bacteria, which did not return for the duration of the study.
So when we take antibiotics we are rolling the dice as to whether of not we will have any long term effects. Thus, antibiotics should be used only when absolutely necessary.