Investigation of the skin microbiome: swabs vs. biopsies

Abstract

Summary 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. Objectives As the pathogenesis of many skin conditions is dermal, we wanted to compare the microbiota obtained in swabs (surface) and biopsies (dermis). Methods Using 16S rRNA gene sequencing we established the microbial profiles of skin swabs and skin biopsies in 16 patients. Results 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. Most published research on cutaneous microbiota has been based on skin swabs, which represent the surface of the skin. Conclusions Our study demonstrated a clear difference between the microbiome observed from skin swabs and skin biopsies. These findings may be highly relevant in disorders such as psoriasis where pathogenesis arises in the dermis. What's already known about this topic? 16S RNA gene sequencing has facilitated study of the skin microbiome. Several studies have sequenced the microbiome sampled by skin swabs. What does this study add? The microbiome data obtained using swabs and biopsies were different. Diseases that are predominantly dermal should be studied using both swabs and biopsies.

Combined culture and metagenomic analyses reveal significant shifts in the composition of the cutaneous microbiome in psoriasis

“…The complex relationship between the cutaneous microbiota and the host immune system is slowly being unravelled. Commensal bacteria are present not only on the epidermal surface, but also throughout the skin and pilosebaceous unit . The composition of the host skin microbiome is likely regulated by genetic factors, including polymorphisms in filaggrin expression, hormonal factors and variations in skin barrier function.…”

“…However, more recently Prast‐Nielsen et al . have reported significant differences in the diversity and composition of the cutaneous microbiome when comparing swabs and biopsies from the same individuals.…”

“…Nevertheless, it should be borne in mind that the patients who were biopsied in the study of Prast‐Nielsen et al . ranged in age from 21 to 85 years, and almost half were treated for skin cancer.…”

“…Concordance between swabbing and tape stripping has also been confirmed in several studies. 48,59 However, more recently Prast-Nielsen et al 60 have reported significant differences in the diversity and composition of the cutaneous microbiome when comparing swabs and biopsies from the same individuals. Several taxa, including Clostridiales and Bacteroidetes, were increased in skin biopsies, while S. aureus was more abundant in swabs.…”

“…Commensal bacteria are present not only on the epidermal surface, but also throughout the skin and pilosebaceous unit. 9,25,34,59,60 The composition of the host skin microbiome is likely regulated by genetic factors, including polymorphisms in filaggrin expression, 63 hormonal factors and variations in skin barrier function. This may facilitate early colonization with pathogenic bacteria (Staphylococcus aureus), 8,64 favouring T helper (Th)2/Th17 as is postulated in atopic dermatitis.…”