The skin is the human body’s largest organ, colonized by a diverse array of microorganisms, most of which are harmless or even beneficial to the host. Because of its constant exposure to and contact with the environment, the skin is particularly apt to contain transient microorganisms. Nevertheless, there is a constant and well-defined resident flora, modified in different anatomic areas by secretions, habitual wearing of clothing, or proximity to mucous membranes (mouth, nose, and perineal areas) (Figure1).

Fig1. 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 the 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), 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 the volar forearm (inside of the midforearm), hypothenar palm (palm of the hand proximal to the little finger), and buttock. (Reprinted by permission from Macmillan Publishers Ltd: Grice EA, Segre JA, The skin microbiome. Nature Rev Microbiol 2011;9:244−253. Copyright © 2011.)

The predominant resident microorganisms of the skin are aerobic and anaerobic diphtheroid bacilli (eg, Corynebacterium, Propionibacterium); nonhemolytic aerobic and anaerobic staphylococci (Staphylococcus epidermidis and other coagulase negative staphylococci, occasionally Staphylococcus aureus, and Peptostreptococcus species); Gram-positive, aerobic, spore forming bacilli that are ubiquitous in air, water, and soil; α-hemolytic streptococci (viridans streptococci) and enterococci (Enterococcus species); and Gram-negative coliform bacilli and Acinetobacter. Fungi and yeasts are often present in skin folds; acid-fast, nonpathogenic mycobacteria occur in areas rich in sebaceous secretions (genitalia, external ear).

Based on 16S rRNA gene copies, recent studies have shown that Archaea comprised up to 4.2% of the prokaryotic skin microbiome. Most of the gene signatures analyzed belonged to the Thaumarchaeota, a recently proposed phylum that includes ammonia oxidizing Archaea. It is noteworthy that the human skin is constantly emanating low amounts of ammonia, which may, in turn, provide a suitable environment for these Archaea.

Among the factors that may be important in eliminating nonresident microorganisms from the skin are the low pH, the fatty acids in sebaceous secretions, and the presence of lysozyme. Neither profuse sweating nor washing and bathing can eliminate or significantly modify the normal resident flora. The number of superficial microorganisms may be diminished by vigorous daily scrubbing with soap containing hexachlorophene or other disinfectants, but the flora is rapidly replenished from sebaceous and sweat glands even when contact with other skin areas or with the environment is completely excluded. Placement of an occlusive dressing on the skin tends to result in a large increase in the total microbial population and may also produce qualitative alterations in the flora.

Anaerobes and aerobic bacteria often join to form synergistic infections (gangrene, necrotizing fasciitis, and cellulitis) of skin and soft tissues. The bacteria are frequently part of the normal microbial flora. It is usually difficult to pinpoint one specific organism as being responsible for the progressive lesion because mixtures of organisms are usually involved.

In addition to being a physical barrier, the skin is an immunologic barrier. Keratinocytes continuously sample the microbiota colonizing the skin surface through pattern recognition receptors (eg, Toll-like receptors, mannose receptors, NOD-like receptors). The activation of keratinocyte pattern recognition receptors by pathogen-associated molecular patterns initiates the innate immune response, resulting in the secretion of antimicrobial peptides, cytokines, and chemokines. Despite being constantly exposed to large numbers of microorganisms, the skin can distinguish between harmless commensals and harmful pathogenic microorganisms. The mechanism for this selectivity is unclear. For an excellent discussion of the immunological anatomy of skin, readers are referred to a review by Kabashima and colleagues (2019).

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