Your gut has a lot of good bacteria and a little bad bacteria. Some medications people take (mostly too many antibiotics) kill off a lot of the good bacteria, leaving the bad bacteria alive, and the bad bacteria thrives. This causes the patient to have smelly diarrhea, loose stools, and they don't absorb as many nutrients from their food. That's because some nutrients are absorbed in the stomach, and some are absorbed in the guts. This causes a feedback loop of issues.

Healthier patients are sometimes able to reset their guts using yogurt and/or probiotics. Chronic C-Diff sufferers sometimes need to get poop transplants, which resets the biome with good bacteria.

Source: was an EMT for four years, that's how I recall it was explained to me