Skin microbiome characterization in acne vulgaris across urban and rural Egyptian populations

Abstract

Background Cutibacterium acnes is recognized as a key contributor to acne, but recent evidence suggests that shifts in skin microbial diversity, rather than simple overgrowth, are critical in disease progression. Despite the unique genetic and environmental characteristics of the Middle East and North Africa, microbiome data on acne remain scarce. Objective To characterize the skin microbiome associated with acne vulgaris in Egyptian urban and rural populations and assess the influence of acne severity and lifestyle factors on microbial diversity. Methods We recruited 45 acne patients (urban n=37, rural n=8) and 25 healthy urban controls. Skin swabs were collected and analyzed by 16S rRNA sequencing. Microbial community profiles were generated with QIIME2, while differential taxa and functional pathways were evaluated using ANCOM-BC and PICRUSt2. Results In urban patients, moderate-to-severe acne was associated with greater microbial evenness and diversity, though species richness was unchanged. Community composition differed significantly by severity. Functional analysis revealed enrichment of amino acid biosynthesis pathways. Rural patients showed greater diversity, distinct microbial structures, and functional enrichment in amino acid and lipid metabolism pathways, with reduced enrichment in energy metabolism pathways. A depletion of C. acnes ASVs in patients with more severe acne across both cohorts was observed, possibly indicating a strain-specific behavior of C. acnes . Conclusion Interventions that selectively eliminate pathogenic C. acnes strains while conserving beneficial ones may prove more efficacious for managing acne than broad-spectrum approaches. Environmental context significantly shapes the acne-associated skin microbiome. It influences both the taxonomic composition and potential function.