Antibiotics surely can mess with your system and screw up your digestive balance.
My sister who is four years younger than me could testify to this as she has gone thru it as well. She actually had to have a "poop" transplant in order to finally get her arse and shit under control. (please excuse my French there.)
But it worked and she hasn't had any problems since then, she also now stays away from as much medicine as she can. I think the doctors termed her condition as having C-difficle and if you google it they google lady will say it comes from not washing your hands properly but her doctors said it was the antibiotics that were the cause of her condition.