Actually, the gut is the home to a great deal of beneficial bacteria, and recently a lot of science has been pointing to the kind of bacteria you have there as being really important for your health.
You definitely don't want to kill this beneficial bacteria because if you did, you wouldn't be able to digest your food, food would just sit there and likely poison you.
Probiotics like yogurt are made from milk, etc, by seeding the milk with some of this bacteria and warming it to approximately body temperature for a period of time until it turns gelatinous. That makes many nutrients more bioavailable.
So, all this is a good reason to stay away from things that could kill them. Babies pick up their beneficial bacteria from their mother and their environment and a good helping of beneficial bacteria gives them a good start on having a healthy life.
Antibiotics can kill off the bacteria and that can cause major problems for people. They may actually end up someday reseeding their guts with bacteria from somebody else.