Antagonist

Would it be a good idea to use animals/creatures as antagonists rather than a villain character?

Of course! I've seen people do it lots of time before! It might even be better than using a humanoid villain if written right. It will be hard to get their point through if they can't talk though.

Thanks. (I've been using the idea of experiments so the motive will be clear.)

Also, with a collective, there can't be any one, well-written, beloved antagonist.

Antagonists don’t have to be people. It can be AI, or a disease, or some kind of impending doom.

Make the animal villain a predator who needs to kill unless the animals in that universe are anthropomorphic.