Sometimes vets have biases. I once went to a vet who told me that my Corgi was a member of the most vicious breed of dog that he had ever encountered and spent the entire time trying to tell me to reconsider keeping him. This is the same vet who has an excellent reputation working with strong dogs such as GSDs, Pitts, Rotts, etc. I found out later he had an encounter with a particularly nasty Corgi once and it ruined the whole breed for him.
As if by magic, this previously sweet and hyper-friendly Corgi growled at him! I had never seen him do that before, and have never seen it again...he's the most loving softy there is. The vet said, "See?!?! You can't really trust them!"
My conclusion is now that the dog sensed his dislike and responded accordingly to someone who was radiating a negative vibe and also poking him with needles. The Corgi never went back to that vet and he's never had a problem at the vet's, or anywhere for that matter, since.
It's possible that your vet has preconceived notions about GSDs, or strong dogs in general. He wouldn't be the first and he won't be the last...they're only human. I don't think that your dog reacted all that oddly to two strangers restraining him physically and sticking a fecal wand up his butt (remind me not to tick off THAT fairy! ).
But if your dog isn't aggressive any other time, make sure you don't let your vet bias you against your own dog. You know him better than anyone.
Anyway, telling you to take your dog to training and get him neutered based on that incident alone is pretty reactionary and kind of insulting, IMO. MY reaction would be to say thanks for your time and get a different vet. It would make me doubt his/her judgement on other advice concerning that dog.
Because now your dog might now have new fears about the vet, I wouldn't hesitate to get him used to the muzzle while at the vet's. Then YOU can hold him with confidence, and the people helping will have confidence as well, and won't be sending some nervousness to the dog. And certainly, try to get the stool sample with more non-invasive means whenever possible!
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