Can antibiotics (cipro) affect bms? have been on antibiotics for about a week and the last two days my stool appears darker and has a bit of mucus

Yes- definitely: Antibiotics kill every bacteria that is susceptible-so we hope this effect extends to the bacteria causing an infection, but there can be side effects such as wiping out the GOOD bacteria in your gut. As a result, it's quite common to see changes in the bowels. Hopefully though this is just temporary. If u are concerned, call the doc who prescribed the antibiotics to begin with. They need to know.