The disordered skin microbiome has been reported to contribute to the pathogenesis of acne vulgaris, for which benzoyl peroxide (BPO) has long been recommended as the first-line therapy. However, there are no data regarding the effect of BPO treatment on skin microbiota and the epidermal barrier in young adults with acne vulgaris. Thirty-three patients with acne vulgaris and 19 healthy controls were enrolled in the study. All patients received topical treatment with BPO 5% gel for 12 weeks. The epidermal barrier was analyzed at baseline and after treatment. Microbial diversity was analyzed using a high-throughput sequencing approach targeting the V3-V4 region of 16S rRNA genes. After receiving treatment with BPO, patients had significant improvement in their Global Acne Grading System (GAGS) score, porphyrin, and red areas (p < 0.05), and the presence of sebum, stratum corneum hydration (SCH), and transepidermal water loss (TEWL) increased (p < 0.05). When compared with baseline, microbial diversity was significantly reduced after treatment, as calculated by the goods coverage (p = 0.0017), Shannon (p = 0.0094), and Simpson (p = 0.0017) diversity indices. The prevalence of the genus Cutibacterium (before treatment: 5.64 [3.50, 7.78] vs. after treatment: 2.43 [1.81, 3.05], p = 0.011) was significantly reduced after treatment while Staphylococcus (before treatment: 43.80 [36.62, 50.98] vs. after treatment: 53.38 [44.88, 61.87], p = 0.075) tended to increase. The abundance of Staphylococcus was negatively associated with SCH (p = 0.008, r = −0.286). Despite its contribution to an improved GAGS score, BPO treatment for acne vulgaris may reduce microbial diversity and damage the epidermal barrier.

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