Unfortunately, I don't know what comment prompted you ask this question... But I'll answer as best I can given the information provided. The intestinal tracts of all animals (including humans) contain beneficial bacteria which help to break down/digest the foods that are eaten and allow us to extract nutrients. If the pup has diarrhea, the last thing you want to do is get rid of the beneficial intestinal bacteria, that will only make matters worse. There are actually products on the market to repopulate or boost the numbers of beneficial bacteria in the gut, they're a very important part of a healthy digestive system.
If your vet was the one who mentioned intestinal bacteria, and prescribe antibiotics to get rid of them, than I can only assume that there was a misunderstanding and he was referencing these beneficial forms of bacteria as a good thing your dog has in his intestinal system to help with his recovery.
Hope that helps... And hope your pups feeling better soon.. Good luck.