Another thought

I also have noticed that pups left with the mother do not seem to become symptomatic and have problems. The bottle fed pups seem to be the ones experiencing difficulty.

Do you think this might have something to do with the enzymes? of the mothers milk killing off the bacteria or keeping it in check?

I've raised two litters, both were raised inside and left on the mother. Weaning started at around 2-3 weeks and by 4 weeks they were totally on food, not mothers milk. Not one of my pups has ever had bacterial problems, now worms that's a different story. We had a terrible time with hooks last year.