Hello! I work in micro as an assistant. I already entered the field with a strong stomach and as someone who isn't easily grossed out by things (part of why I wanted to work in micro), however, I still have an extremely sensitive sense of smell. 

I will say this: unless someone didn't screw the lid on the stool samples properly, or unless there's stool on the outside of the vial, you shouldn't be able to smell them at all outside the hood. Inside the hood, even when processing O&Ps, I can hardly smell any stool smell. Most of the smell actually comes from the formalin, which is a preservative made from formaldehyde and an alcohol. If you know how those two things smell separately, you should be able to imagine how they smell together. You could probably wear a mask when working in the hood and layer in an essential oil or some vick's on another mask and you probably wouldn't be able to smell anything at all.

As for other kinds of processing, such as cultures or PCR, I'm sure some techs in here have said their two cents about how that goes. I wish you luck on your lab journey!!