We have very careful sampling processes to try and make sure that when we collect a sample, we just take the target species and nothing else. When @graeme and the lab team extract the DNA, they work in sterile conditions to reduce the risk of contamination.
One thing that can be quite exciting though is when the analysis teams find contaminants we weren’t expecting- such as parasites and bacteria. When that happens, we sometimes get two genetic codes for the price of one! @Marcela, @Sujai, @Lewis and others have neat methods for when this happens- they may be able to tell you more