524 Evaluation of different skin collection methods for assessment of the skin microbiome

Abstract

Background and Objective: The sampling and sequencing of human skin microbiome represents a tremendous opportunity to understand how resident microbes impact common dermatological conditions and skin health. Understanding the differences and limitations in commonly used sample collection methods is paramount to exploiting this up and coming area of research. The objective of this study is to compare the performance of two swab-based collection (SBC) kits (from Genotek and Norgen) and an adhesive patch-based collection (APC) system (from DermTech). Methods and Materials: Following manufacturers’ instructions, samples were collected from 3 forehead skin locations from 15 subjects using all 3 collection kits. Nucleic acids from each sample were extracted, and the V1V3 hypervariable region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. Post-sequencing analysis compared the alpha diversity (AD), beta diversity (BD) and taxonomic composition (TC) among sample sites and collection kits. Results: 11 males and 4 females had samples collected from 3 forehead locations. Ten of the subjects refrained from face washing and using any topical products on the day of collection. All sample collection methods, regardless of skin location, had adequate yields for microbiome analysis. Analyses indicated the SBC method yielded similar results overall in terms of AD, BD and TC. The Dermtech APC method resulted in improved richness but similar overall diversity. The APC method also tended to cluster differentially from the SBC methods by Principle Coordinates Analysis using both the weighted and unweighted UniFrac metrics. As the APC enriched more Pelomonas, Bradyrhizobium and Sphingomonas at the genus level compared to SBC. Conclusions: All sampling methods were able to collect sufficient material for microbiome analysis. However, elevated levels of operational taxonomic unit (OTU) richness and differences between the APC and SBC methods suggest that APC method may sample the skin more completely than swab-based methods.