It may well be natural, BUT I have to disagree - YOU need to be in control of her herding instincts. It may seem funny her rounding up a guinea pig - although I pity the poor guinea pig - it wouldn't be so 'funny' if she then decided to round up small children or cars or bikes would it? As your collie has a strong herding instinct is there any way you can work with her constructively - sheep trialling for instance?
I don't know what area you live in or if it is an option but have you heard of Trieball. It would be a fun way for you and your dog to meet that herding instinct in a more controlled way. She may be a champion!
stephanie, she doesn't have any desire to herd children, she only does it with small animals. She is terrified of sheep, that is why she was re-homed, she was a useless sheepdog. The guinea pig is not timid, she may be small but she has a big attitude and she tells Meg off if she bothers her.
PetParent, thanks for the info, I have never heard of Trieball, but I will find out more.