Surprisingly, it is not entirely known why Accutane, or Isotreninoin, works so well with acne. We do see a decrease in the bacteria count near the hair follicle. There is less congregation of Proprionibacteria, or p-acne (the bacteria that causes acne), which also reduces the risk of infection.
The second way Isotreninoin may work to get rid of acne is through the hair follicles. It changes the way hair follicles epithelialize (or the way skin sloughs off the inner portion of the hair follicle). With Isotreninoin, the skin sloughs off easier and the dead skin does not get caught in the hair follicle. Because of this, there is not any anaerobic environment for bacteria to thrive. In summary, Accutane decreases bacteria count.