I took doxycycline for several months when I had small intestinal bacterial overgrowth (SIBO). It worked well, and seemed to be an effective replacement for the Cipro I was usually on. It did give me some abdominal pain, so I haven’t gone back to it.
As CT says, I’ve had good success with high-dose probiotics (VSL #3 in my case). They are very expensive, though, unless your insurance will cover them.