Yes, they do occur in shit, because they are quite smelly and so function well as scent markers. They also are used in perfumes; something that smells horrible en masse can smell good in tiny amounts. Higher plants use indoles for the perfume of their flowers, but indoles are also concentrated in rotting flesh. They were discovered by a scientist working with indigo, Indigofera tinctoria, a plant dye and a very stinky one. Tryptophane is an indole derivative. Indoles are very reactive, according to what I've read. I have wondered if a person could buy natural indigo dye (which is expensive, but certainly no one would suspect why you were buying it) in order to obtain indoles. No doubt there are easier ways to get it, though. My knowledge of this group of chems comes mostly from dyes.