If all the things you eat smell good, why does poop smell bad?

Except it isn't, because most of your feces is actually dead cells, mostly red blood cells. That's what gives it its color.

Feces smells because it contains volatile chemical compounds. When you defecate, these compounds come into contact with the air (however briefly) and "outgas," as it were. We're talking here about things like thiols, which are similar to alcohols but contain sulfur. These compounds give healthy feces its distinct, unpleasant smell.

Thing is, these compounds are not present in your food. (At least, not in high concentrations. Low-molecular-weight thiols like methyl mercaptan are found in very low concentrations in some cheeses, for example.) So where do the stinky things come from?

The answer is gut flora. In your intestines there live a truly vast number of symbiotic bacteria that help you digest your food. Some of these bacteria break down large molecules which our bodies can't do anything useful with into much smaller molecules we can use, but in the process they produce these thiols — and lots of other byproducts as well, but right now we're interested in the thiols. The body has no use for these thiols, so they remain in the gut and pass through our bodies as waste, giving the distinctive smell to both feces and flatus.

As to why it is that we think "bad" when we smell thiols, that's a mystery for the ages. What is known is that the human sense of smell is highly context-dependent. Depending on context, a person will either associate the smell of butyric acid with human vomit or with parmesan cheese. It's the exact same compound producing the exact same smell, but that smell is either stimulating or revolting depending on context.

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