Guts with Michael Mosley just aired on PBS April 17, 2013. Hopefully,it will air again, if you haven’t seen it.
In this fascinating documentary, Michael volunteers to undergo a number of invasive tests and also has his entire digestive tract viewed live all day in a museum setting with a capsule or submarine camera. They also explain the details of the digestive process and talk about the role of bacteria in digestion, as well as fecal transplants. I will post more info if I see another time or a video archive where this can be viewed again.