Noah decided he wanted to try to swim out of the birth canal, but seeing as how he didn't know how, he took in a whole bunch of his own amniotic fluid. This fluid caused two problems.
The first, his lungs filled with some of the fluid and caused him to have some difficulty breathing. It was hard enough that he wasn't able to produce enough oxygen for his own body. The doctors took care of this by supplementing his breathing with some pure oxygen.
The second and slightly disgusting problem, was the fact that his fluid happened to be the same place where he pooped. This means that it's possible that some of the gunk made it into his system. As a result, he has to be put on antibiotics for two days.
All this makes for a pretty wired up baby.