Are you worried about public bathrooms and disease/sickness?
I think common sense should rule. Obviously "stuff" on the seat is going to be dirty. Urine is usually sterile. Fecal matter however is not. If you are worried put loads of tp around seat. Although I can't see that paper makes things anymore safe. If someone was bleeding I wouldn't wrap TP around my hands before touching to protect myself.
I think I read in several places that the first stall is usually the cleanest. I always flush with my foot. Then washing your hands will be of utmost importance.