If you smell your breath first thing in the morning it stinks. This is a sign of bacterial overgrowth. During the day, the biggest barrier to this is natural saliva production and agitation through movement of the mouth. These things are drastically reduced while you sleep and thus leads to a build up of bacteria. This is why it is advised that you brush your teeth after waking.

Technically, it is also advised that you brush your teeth after each meal but that is not practical for most.