Ventilation or the lack of it has multiple effects. First, poor ventilation will allow microorganisms to accumulate, suspended in the air, hence increasing the number of organisms ready to be inhaled. A second very important effect of poor ventilation is to allow the buildup of ammonia. Dirty stalls with the accumulation of manure and urine are ripe with ammonia. Ammonia lingers in the first few feet above the ground and feeding the horse on the floor worsens the problem because it places the head directly into the ammonia.
Ammonia damages the ciliated cells and slows the mucociliary apparatus.
The horse's ability to resist and eliminate microorganisms is related to its general health, immunity, and the mucociliary apparatus. General health influences immunity, as does regular vaccination. This leads to the recommendation of vaccinating every 2-3 months in horses at high risk. Still, regular vaccination of high-risk horses will decrease the severity and duration of respiratory disease. Anything that damages this function enhances the chances for disease to become established.