No more than it would affect the digestive tract from properly digesting kibble or any other food. Nor anymore than it would affect the digestive tract of a human. Would it slow it up some? Yeah problably but in my case I have never noticed a difference in my digestion whether or not I'm on abx. I don't know why a dog would be any different.
ETA: When you first asked the question, I thought you might have been asking about antibiotics in the raw food.