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So I should eat skinny people’s poop?

I would recommend against that.

There has been some success in treating severe cases of C. Diff (Clostridium Difficile) with fecal transplant from healthy family members. So, as disgusting as it sounds, you're close, just at the wrong end of things. In through the out door, more or less.

So I should eat skinny people’s poop?

Aptly put.

Any such condition that prevents certain (skinny) people from absorbing every available calorie would be a terrible genetic disadvantage, and would have been bred out of the population by all the periods of deprivation and famine.

I suppose maybe in addition to your hypothetical answer to the intelligent question: “So where do the calories go?” is that perhaps they are consumed by the bacteria (converted into heat energy?), whose waste products are non-caloric.

My observation (including myself most of all) is that caloric input, and energy output are the prime determinants (but for minuscule other factors) of obesity or the lack thereof.

Most of the secondary factors are have to do with conditions that cause people to want to eat more, or exercise less. Moreover, there are calories that are easier to eat, or easier to store, as compared to some formed of nutrients and dietary patters that presumably store poorly (leading to the “nutritious poop”) such as the Atkins/Ketosis effect.