This has been discussed before. If I remember correctly, what little DNA comes the subject is sloughed off the intestine walls. That DNA breaks down rapidly. Unless it is collected "steaming hot," there is little usable DNA in a scat sample. The DNA that is left is from what the host ate.
Sometimes species can be determined by the parasites found in feces. This could get you back into the same loop. A unknown parasite just leads to an undetermined species.