Well, getting poop on everything would be a problem because poop is loaded with potentially harmful stuff. Hygiene is important because I think there are certain levels of viral or bacterial load that can become more dangerous. But if you sterilize a container & put sterilized or freshly cooked materials in it it keeps very well. If you put biodegradable things in a container that hasn't been sterilized then things will grow pretty quickly. And we did bacterial tests of different surfaces in highschool. All of which seems to suggest that there are low levels of potentially harmful things everywhere. Which makes sense, there is also visible dust & pollen & bugs everywhere (you generally have to wipe off a seat that's outside every day, sometimes more than once in the same day), why would it be any different on a microscopic level? They just don't matter most of the time because our gut (and the rest of our system) is good at either putting them to work in the digestion process and/or keep them out of the body.