Biota Terroir: The Human Skin Microbiome

Species Interdependence 

It’s good that interdependence is an apparent, albeit complex, biological mechanism of our survival. Without respect to this principle, we would be limited by notions of our isolation from nature’s network, which awards success to relationships, not individuals.

Colony Composition 

Dry, acidic, and ever-exfoliating, the relatively inhospitable body surface sustains microbial colonies through distributions in moisture, contour, oils, follicle density, and thickness, most abundantly in the axillaries. Stable colonies live in the deeper, dermal skin layers, whereas those in the upper strata are more transient and influenced by environmental factors. Age, ethnicity, and gender are intrinsic factors largely responsible for variations in microbial composition in the human family. 

Rich in oils, the head, face, neck, and upper torso favor sebaceous-loving Propionibacterium, S. epidermis, and Corynebacterium the latter of which is obligated to human lipids since it does not independently produce these essential fats. 

The feet and hands are particularly suitable

for at least 9 types of fungi predominantly Malassezia, Aspergillus, and Trichophyton. Fungal colonization shifts with urban living, favoring candida and aspergillus and disfavoring colonies associated with rural settings.   The urban lifestyle is associated with decreased microbiome diversity, which may inadvertently contribute to pathogenesis due to a loss of commensal species.  Additionally, reduced exposure in early life may fail to properly educate the immune system causing disproportionate immune responses in subsequent exposures.

Staphylococcus and Corynebacterium are most prevalent in moist areas like the armpits and groin. The relatively dry areas of the forearms and thighs support Proteobacteria, Bacteroidetes, and Actinobacteria. 

The viral kingdom represents roughly five percent of the colony. Unlike bacterial and fungal communities, viruses are not adapted to a specific niche. It is more accurate to describe the viral genome as host-specific with variations between individuals. Papillomavirus and Polyomavirus are common. Viruses that are transferred within the bacterial kingdom, called phages, are included in this group. 

Talking Amongst Ourselves: Regulatory Mechanisms 

Microbial colonies depend on nutrient sources, namely lipids, glycerol, and triglycerides secreted by glands via sweat and sebum. The interplay between the molecular products of the host and those originating from microbial colonies is perhaps the most profound mechanism of symbiosis. Immune and hormonal function is intricately related to the microbiome of the gut and skin. Researchers have begun to conceptualize these mutual relationships as bi-directional systems, as with the gut-brain axis. The gut-skin axis emerges as a relatively new focus.

The skin is equipped with the ability to

regulate and respond to microbial activity. Skin cells produce antimicrobial peptides, and the primary immune system surveils and counters potential microbial aggressors via phagocytes and lymphoid cells. Like cellular antennae, dendritic cells detect microbial signals and activate cellular repair and immune memory. Exfoliation of the skin, which renews the stratum corneum every 4 days, also has a regulatory effect by shedding a portion of the microbiome. Additionally, sweat inhibits population overgrowth through acidification and yields a nutritional source in the form of electrolytes.

In turn, bacterial colonies aid in overall skin health by eliciting proper barrier function and controlling potentially virulent strains through chemical and structural defenses via collective resilience known as colonization resistance. Importantly, within a species, certain strains may be benign while others become virulent, most notoriously S. epidermis and S. aureus. To appreciate the complexity of bacterial interactions, it is noteworthy that certain species may switch off potentially virulent behaviors in problematic strains. Remarkably, bacteria commonly associated with pathology remained susceptible to the antimicrobial actions of commensal strains, demonstrating a sustained inter-species mechanism of control benefitting the host. (Byrd et al., 2018).

Skin Dysbiosis

Abnormal skin conditions, such as ectopic dermatitis, psoriasis, acne, and alopecia correlate with microbiome changes marked by the proliferation of certain bacteria and the decimation of others.  Implications for infection control are imminently relevant to public health. The prospect of bacterial transplantation, or culturing and administering commensals known to restore homeostasis through inhibition of pathogenic strains shows a hopeful remedy to the proliferation of antibiotic-resistant bacteria.

Though the sequence

of dysregulation is unclear, inflammation of the gut, associated with breaches of the cellular barrier (permeability), correlates with systemic immune responses that can show up on the skin as the immune system copes with allergenic and pathologic perturbations.

Developmental Matters

A child’s microbiome is established while in the womb, during birth, and in the first few years of life with exposure to the familial microbial profile, foremost that of the mother. While colonies gradually assume a profile commensurate with other people by adulthood, delivery (vaginal or cesarean) will shape the microbiome throughout youth with vaginal delivery creating greater diversity. Microbial diversity is tantamount to immunological priming, which enables the immune system to launch appropriate responses (i.e., less prone to overactivity) toward future pathological processes.  Moreover, the native microbial colony of the infant is actively protected by the immune system throughout the lifespan (Eisenstein, 2020.)  

In adulthood, the commensal bacterial communities will continue to shift and re-organize based on physiologic and environmental factors. The loss of antimicrobial peptides may be a significant factor in age-related vulnerability to infection as the microbiome becomes less stable. 


Living in a rich biological world means

we participate with, and even contend with forces great, small, and invisible.  The skin microbiome is a frontier that promises to reveal intricate relationships affecting human health and vitality.  Most of all, interdependence represents ecological intelligence, which can be instructive in cultivating our bond with nature.  

Written By: Thomas Forlano


Byrd, A. L., Belkaid, Y., & Segre, J. A. (2018). The human skin microbiome. Nature Reviews Microbiology, 16(3), Article 3.

De Pessemier, B., Grine, L., Debaere, M., Maes, A., Paetzold, B., & Callewaert, C. (2021). Gut–Skin Axis: Current Knowledge of the Interrelationship between Microbial Dysbiosis and Skin Conditions. Microorganisms, 9(2), 353.

Eisenstein, M. (2020). The skin microbiome. Nature, 588(7838), S209–S209.

Skowron, K., Bauza-Kaszewska, J., Kraszewska, Z., Wiktorczyk-Kapischke, N., Grudlewska-Buda, K., Kwiecińska-Piróg, J., Wałecka-Zacharska, E., Radtke, L., & Gospodarek-Komkowska, E. (2021). Human Skin Microbiome: Impact of Intrinsic and Extrinsic Factors on Skin Microbiota. Microorganisms, 9(3), 543.