Investigation of the Skin Microbiome: Swabs vs Biopsies

Abstract

Background

Human skin is populated by diverse bacteria and there is increasing evidence that resident bacteria play a key role initiating immune responses in cutaneous diseases such as atopic dermatitis, psoriasis and hidradenitis suppurativa. Bacteria are present at all layers of the skin but many studies have relied on swabs to profile the skin microbiota. As the pathogenesis of many skin conditions is dermal, we wished to compare the microbiota obtained in swabs (surface) and biopsies (dermis).

Using 16S rRNA gene sequencing we established the microbial profiles of skin swabs and skin biopsies in sixteen subjects. We found differences in both diversity and taxonomic composition of the microbiome obtained from swabs and biopsies of the same individual. Several taxa were found to be more abundant in the swabs, which displayed significantly higher community richness, but Clostridiales and Bacteroidetes were significantly enriched in the biopsies.

The majority of published research on cutaneous microbiota has been based on skin swabs, which represent the surface of the skin. Our study demonstrated a clear difference between the microbiome observed in skin swabs and skin biopsies. These findings may be highly relevant in disorders such as psoriasis where pathogenesis arises in the dermis.

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