Our long national nightmare is over. Researchers have determined an enzyme is responsible for making our urine yellow.

From the article:

Gut microbes encode the enzyme bilirubin reductase that converts bilirubin into a colorless byproduct called urobilinogen," explained Hall, who has a joint appointment in the University of Maryland Institute for Advanced Computer Studies. "Urobilinogen then spontaneously degrades into a molecule called urobilin, which is responsible for the yellow color we are all familiar with.

Source: Phys.org