A bit of both :) your respiratory tract is lined with cilliated cells - they have little finger-like projections that help move mucus and debris from your lungs to your mouth. When you wake up in the morning with crap in your throat - that's why. Some respiratory viruses and bacteria can damage those cells, and affect how well they move stuff up, so the lining is more like flattered cells for a few days. While that continues to heal, bacteria have a better chance of growing there, but eventually either your immune system clears it and the cells heal, or it gets worse and you die ;)