I find that the stress of handling mice will usually induce fresh defecation. If you grab a fresh sample when you have the mouse out of the cage for ear tagging or other such manipulation, it should not be difficult to separate stool samples, and record which animal the sample came from.

I agree. If you pick up a mouse, hold it in your hand with the tail end pointing upwards towards your thumb you can easily squeeze out a faecal sample with the other hand.Separation of samples should therefore be easy.

Thanks for all of you.