Can antibiotics cause dark stools? I know some get upset stomach when taking Flagyl and/or Cipro. Taking with food may fix that. As Jan has posted - too many antibiotics and excessive doses can cause neuropathy. ( tingling and numbness ) We should be careful and look out for those side-effects.
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Cipro can cause dark stools. It is one of the more uncommon side effects.
Jan 
I ended up with ligament pain and inflamation while on Cipro...another nasty side effect.
Sharon
Years before having my colon removed I got c.diff from taking Cipro for sinus infections. I wish I could have taken it for my pouchitis.
I took a lot of flagyl for pouchitis until I it was making my peripheral neuropathy, in my feet, worse.
I was alternating augmenten and xifaxan before I had surgery diverting to a permanent ileostomy. The latter is very expensive but is specific for intestines. (There's a TV commercial out marketing it for IBS with diarrhea. It includes a pink cartoon glob of intestines.)
I'm not suggesting people don't take these. Just a warning. I had c.diff in my pouch. Many courses of flagyl eventually got rid of it.
Extreme tendinitis in every joint from Levaquin, which is in the Cipro family. Painful! Several bouts of Pancreatitis from Sulfa based meds. Also not fun.