The Outer Frontier: The Human Skin Microbiome

This post was written by Annie Kuan, a Senior in the Department of Biological Engineering at MIT



Our skin is often forgotten, even though it is our largest organ. Regarding the human microbiome, it is also easy to forget that there are microbes living on us in addition to those living inside us. So it should come as no surprise that the human skin microbiome has been neglected in research, in comparison to the ever-popular gut microbiome. Each adult can have about 2 square meters (or up to 22 square feet) of skin, home to millions of pores housing various bacterial species. These numerous pores offer many opportunities for investigation, being very accessible and non-invasive to study. Additionally, the skin barrier, and perhaps our little friends that reside there, are our external boundary from the environment and the first line of defense against attacks from pathogens. Despite the ease of sampling, simplicity of perturbing, and prospective impacts of studying the skin microbiome, there is currently a lack of knowledge in this area that makes it difficult to make any concrete conclusions.


One general topic currently being explored is the relation of microbial communities to skin disorders. One of the most commonly studied conditions is acne vulgaris. A single skin species, Propionibacerium acnes has been named – literally for and in – the pathogenesis of acne. It feeds off the waxy sebum produced by our sebaceous glands to lubricate and waterproof the skin, making our pores its ideal home. However, P. acnes is a dominant player in the skin microbiome in both healthy and acne-stricken patients, making its role in these persistent bumpy lesions still unclear.


Though it has been demonstrated to be associated with acne, there is not enough supporting evidence to officially implicate P. acnes in the skin disorder. In one interesting study, only single species like P. acnes was found in individual healthy pores and follicles, while a mix of P. acnes with other commensal bacteria, such as Staphylococcus epidermis, were found in the pores of patients with acne (Bek-Thomsen, Lomholt, and Kilian, 2008). These findings suggest competition amongst skin colonizers as a source of acne.


Another group of Aarhus University in Denmark took a closer look at dysbiosis, or microbial imbalance, between P. acnes and S. epidermis, potentially causing acne via antagonistic activity (Christensen et al., 2016). They tested several strains of each species since some of have been found to be more associated with acne and some more with healthy skin (Fitz-Gibbon et al., 2013). Each strain of P. acnes was screened against an indicator strain of S. epidermis. They used a simultaneous antagonism assay where the indicator strain is grown across an entire agar plate, and each of the tester strains are point-inoculated systematically across the plate. After letting the plates incubate, they measured the diameters of the inhibitory zones around each point-inoculated strain to quantify antimicrobial activity. Anatagonsim-Assay-v1The same process was repeated with S. epidermis and indicator strains of P. acnes. They found plenty of antimicrobial responses in both species, but each species’ level of susceptibility to the rival’s attack did not vary between healthy and acne-affected samples. Based on these findings, they concluded that differences in levels of sensitivity might not play a big role in inducing acne as previously thought. However, perhaps “differences” should be the key word, as the presence of any such competitive “warfare” could potentially have an indirect effect on causing acne. One possibility is the antimicrobial activity could’ve stimulated the host inflammation response, which could cause the demise of one species while the other survives, and also induce the little red bumps we all hate.


Still, these predictions are educated guesses with yet more studies needed to determine the causes of acne and other skin disorders and what role the skin microbiome plays in the pathogenesis. Most of the studies, like the one from Denmark described earlier, are conducted in vitro in cultures that do not accurately reflect in vivo conditions in the slightest. But currently, few animal models are used or even found suitable for studying skin conditions. This is especially true for acne because it is a uniquely human problem (Avci et al., 2013), though a recently tested mouse model may be promising (Jang et al., 2015). Proper evaluation of acne pathogenesis will require more thorough in vivo studies to investigate the dynamics between the skin microbiome and the host before any definite claims can be made.


Perhaps after more research has been done in the future, we can use the knowledge to create crazy things. For example, strains commonly found on our skin could be engineered to fend against troublesome bacteria, keeping skin infections and disorders, like acne, at bay. But before that day arrives, we have much more territory to cover.


Annie Kuan is a Senior in the Department of Biological Engineering at MIT. When not performing research on the human skin microbiome in the Alm Lab, she likes to dance and practice watercolor calligraphy.