Research Techniques Made Simple: Profiling the Skin Microbiota

Abstract

Skin is colonized by microbial communities (microbiota) that participate in immune homeostasis, development and maintenance of barrier function, and protection from pathogens. The past decade has been marked by an increased interest in the skin microbiota and its role in cutaneous health and disease, in part due to advances in next-generation sequencing platforms that enable high-throughput, culture-independent detection of bacteria, fungi, and viruses. Various approaches, including bacterial 16S ribosomal RNA gene sequencing and metagenomic shotgun sequencing, have been applied to profile microbial communities colonizing healthy skin and diseased skin including atopic dermatitis, psoriasis, and acne, among others. Here, we provide an overview of culture-dependent and -independent approaches to profiling the skin microbiota and the types of questions that may be answered by each approach. We additionally highlight important study design considerations, selection of controls, interpretation of results, and limitations and challenges.

Figure 1:. Approaches to profile the skin microbiota.

A specimen is collected and then subjected to culture-independent and/or culture-independent techniques. Typical workflows for amplicon-based sequencing and shotgun metagenomic sequencing are compared. Examples of output for each are shown as a stacked bar plot depicting relative abundance of bacteria and a heatmap illustrating enrichment of different genetic and metabolic pathways among samples.