Since P. acnes is the major skin commensal bacterium found in both acne and healthy skin, this strain-level analysis is important to help understand the role of P. acnes in acne pathogenesis and in skin health. We demonstrate a strong association between strains of RT4 and RT5 with acne and a strong association between strains of RT6 and healthy skin, each with unique genetic elements. Other P. acnes strains, including ribotypes 7, 8, 9 and 10, or interactions among different strains, may also contribute to the development of the disease. In addition, host factors, such as hormone level, sebum production and physical changes in the pilosebaceous unit, may also play a role in acne pathogenesis. Further studies aimed at identifying the specific functions of these strains, host factors in the development of acne, as well as the associations of microbiome characteristics with the sub-types of acne (comedonal, pustular, inflammatory, cystic, etc.) with larger cohort sizes may improve our understanding of the molecular mechanisms of the disease. These studies may also help to develop a targeted therapeutic approach to treat this extremely common and sometimes disfiguring skin disease.