No, acidophilus is not toxic.
It's a beneficial bacteria in most mammal and some avian digestive systems.
Many people will offer their canine companions regular servings of natural yogurt in order to help maintain this bacteria and for the other benefits, including calcium.
The only potential drawback, which may cause a bit of an upset stomach (pancreatitis) is if it's high in (dairy) fat - otherwise, you can relax.
http://www.starbreezes.com/11/foodsafe.html
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I want to talk to someone else here about this for their opinion. The bottom part of your question didn't come through with the original question. Still, the drink isn't likely the culprit and I'd lean toward agreeing with the vet that it may have been something congenital - but hang on for a few minutes and let me get back to you.
Still working on a follow up for you - thanks for being so patient. It's very difficult to come up with possibilities without seeing the puppy of course, so trying to get you the best opinions we can based on your description.
Thank you for waiting. The input I've received from a top expert and veterinarian (thank you Dr. Fiona) is the suspicion of aspiration due to megaesophagus:
"Often with congenital megaesophagus, the pup does fine while nursing but once moved to solids, it starts to show problems. This sounds like it fits. Not a good prognosis to have this problem in such a young pup...."
http://www.petplace.com/dogs/megaesophagus-in-dogs/page1.aspx
Without a necropsy (the animal version of an autopsy) it's very difficult to know for sure.
Do not press accept again on this question. This is a follow up to your original question and we are hoping we helped.
We are very, very sorry for your loss by the way. This is a tragic event and you must be heartbroken.
I hope you find some peace in knowing you didn't do anything wrong.