Methods for the analysis of skin microbiomes: a comparison of sampling processes and 16S rRNA hypervariable regions.

Background: The skin microbiome is increasingly recognised as a critical component of the innate skin immune response and is central to the pathogenesis of many inflammatory skin disorders including atopic dermatitis. Previous studies have not looked in detail at the impact of changing both sampling methodology and hypervariable region sequencing for skin microbiome analysis. Objectives: We set out to undertake a detailed analysis comparing microbe population diversity and resolution at the single species level by swab, tape, scrape and scrape then swab sampling assayed by hypervariable region sequencing. Methods: In triplicate samples from the antecubital fossa were taken from healthy volunteers for 16s RNA analysis by primer amplification for hypervariable regions 1-3, and 3-4. Results: Alpha (phylogenetic) diversity was the greatest with tape sampling and V1-3 analysis, whereas for V3-4, tape and swab were equivalent. Scrape sampling showed lower alpha diversity at both V1-3 and V3-4. All measures of beta diversity showed the scrape methodology yielded a lesser diversity than the others. Phyla composition was similar across all sampling methodologies. Minor differences in composition were noted between V1-3 and V3-4 sequencing, but V1-3 was optimal for identification of firmicutes (including staphylococci). Conclusions: In the methodological planning of skin microbiome analysis skin scientists need to consider the microbes of interest to choose the optimal hypervariable region to sequence, and harmonisation of methodological approaches would be beneficial to the field. For detection of staphylococci on flexural skin, we would recommend tape sampling with analysis of V1-3.