Capsid called it.
If no bacteria could get past the stomach, nobody would ever get Salmonella or Campylobacter or Yersinia, in fact the sterile neonatal intestine would never be colonised in the first place! I've read one study where different oral loads of probiotic bacteria were administered, then the faeces cultured to see what was getting through. The highest dose did the trick. If 99% of the bugs are going to be killed in the stomach, you have to take that into account and realise that your money is on the remaining 1%.
Shoving probiotics up as an enema doesn't seem to work because you're going against the flow. A colleague of mine did a study where the vets treating 50 cats with chronic bowel problems were asked to use probiotics and then submit faecal samples to see whether the bowel flora was getting any better. Two of the 50 didn't improve. One turned out to have short bowel syndrome and should never have been in the study in the first place. The other was a cat belonging to the vet himself. Unable to understand why this one individual wasn't responding like the others, my colleague phoned the clinician/owner. He then discovered the guy had come across this idea that probiotics were ineffective by mouth and had been giving the stuff by enema. "Stuff it down its throat, dammit!" shouted my colleague. The vet did and the cat promptly got better.
Rolfe.