Scraping enhances microbial DNA recovery over swabbing in sensitive facial skin: a pilot study of 10 patients

Sensitive skin is a common condition with a complex pathogenesis involving both host-related factors and microbial interactions. Emerging evidence suggests a bidirectional relationship between skin microbiome dysbiosis and sensitive skin, although whether microbial shifts are causal or consequential remains unclear. Characterizing the microbiome in this population is particularly challenging due to low microbial biomass and heightened skin reactivity, both of which may compromise sampling and data quality. While swabbing remains the most common method for skin microbiome collection, it may fail to yield sufficient DNA, especially from delicate facial areas. In this pilot study of 10 patients with sensitive facial skin, we compared swabbing to gentle scraping using a sterile No. 10 surgical blade. Swabbing consistently failed to recover detectable microbial DNA. In contrast, scraping was well-tolerated and enabled one-time sampling that yielded sufficient DNA for both bacterial and fungal sequencing. DNA concentrations ranged from 0.065 to 13.2 ng/µL for bacteria and 0.104 to 30.0 ng/µL for fungi. Genus-level classification rates exceeded 99.7% for bacteria and 97% for fungi. Shannon diversity indices ranged from 0.03 to 2.85 for bacteria and 0.106 to 2.849 for fungi. PCoA revealed substantial inter-individual variation in community composition. Dominant taxa included Staphylococcus aureus group, Cutibacterium acnes group, Malassezia restricta, and Malassezia globosa. These findings indicate that skin scraping is a feasible and reproducible method for microbiome studies of sensitive skin, providing comprehensive taxonomic and ecological profiling in a single, non-invasive session.