The skin microbiome

Abstract

The skin is the human body's largest organ, colonized by a diverse milieu of microorganisms, most of which are harmless or even beneficial to their host. Colonization is driven by the ecology of the skin surface, which is highly variable depending on topographical location, endogenous host factors and exogenous environmental factors. The cutaneous innate and adaptive immune responses can modulate the skin microbiota, but the microbiota also functions in educating the immune system. The development of molecular methods to identify microorganisms has led to an emerging view of the resident skin bacteria as highly diverse and variable. An enhanced understanding of the skin microbiome is necessary to gain insight into microbial involvement in human skin disorders and to enable novel promicrobial and antimicrobial therapeutic approaches for their treatment.

Figure 1. Schematic of skin histology viewed in cross-section with microorganisms and skin appendages

Microorganisms (viruses, bacteria and fungi) and mites cover the surface of the skin and reside deep in the hair and glands. On the skin surface, rod and round bacteria — such as Proteobacteria and Staphylococcus spp., respectively — form communities that are deeply intertwined among themselves and other microorganisms. Commensal fungi such as Malassezia spp. grow both as branching filamentous hypha and as individual cells. Virus particles live both freely and in bacterial cells. Skin mites, such as Demodex folliculorum and Demodex brevis, are some of the smallest arthropods and live in or near hair follicles. Skin appendages include hair follicles, sebaceous glands and sweat glands.

Figure 2. Factors contributing to variation in the skin microbiome

Exogenous and endogenous factors discussed in this Review that contribute to variation between individuals and over the lifetime of an individual.

Figure 3. Topographical distribution of bacteria on skin sites

The skin microbiome is highly dependent on the microenvironment of the sampled site. The family-level classification of bacteria colonizing an individual subject is shown, with the phyla in bold. The sites selected were those that show a predilection for skin bacterial infections and are grouped as sebaceous or oily (blue circles), moist (typically skin creases) (green circles) and dry, flat surfaces (red circles). The sebaceous sites are: glabella (between the eyebrows); alar crease (side of the nostril); external auditory canal (inside the ear); retroauricular crease (behind the ear); occiput (back of the scalp); manubrium (upper chest); and back. Moist sites are: nare (inside the nostril); axillary vault (armpit); antecubital fossa (inner elbow); interdigital web space (between the middle and ring fingers); inguinal crease (side of the groin); gluteal crease (topmost part of the fold between the buttocks); popliteal fossa (behind the knee); plantar heel (bottom of the heel of the foot); toe web space; and umbilicus (navel). Dry sites are: volar forearm (inside of the mid-forearm); hypothenar palm (palm of the hand proximal to the little finger); and buttock. Data from REF. 42.

Figure 4. Interpersonal variation of the skin microbiome

The microbial distribution of four sites on four healthy volunteers (HV1, HV2, HV3 and HV4) is depicted at the antecubital fold (inner elbow; part a); the back (part b); the nare (inside the nostril; part c); and the plantar heel (bottom of the heel of the foot; part d). Skin microbial variation is more dependent on the site than on the individual. Bars represent the relative abundance of bacterial taxa as determined by 16S ribosomal RNA sequencing. Data from REF. 42.