How Differences in Skin Bacteria May Affect Skin Health

Brian Stanton

Your skin is more alive than you know. It teems with bacteria, fungi, viruses, and other organisms with evolutionary histories far longer than ours. Now these ancient creatures colonize your skin in a vast ecology called the skin microbiome.

Your skin microbiome is, in many ways, distinct from my skin microbiome. But this microbial variation doesn’t just exist between individuals — it exists within individuals. In other words, different body parts possess unique microbial ecologies. The forehead, surprisingly enough, harbors more fungi than the toenail.

These differences may influence a range of skin conditions. Many disorders, such as atopic dermatitis, are often present in specific areas of the body with specific microbial profiles. Skin disorders also vary from person to person, which makes understanding the corresponding microbial variations potentially salient to the future study of skin health.

Sampling the Skin

The study of microbial differences on the skin has, in fact, already begun. In 2014, a group of researchers led by Julia Oh of the National Human Genome Research Institute published a paper in Nature called “Biogeography and individuality shape function in the human skin metagenome.” Their ambition? To catalogue skin microbes and their functions by “biogeography” (body part) and individual.

To gather the necessary data, Oh and her colleagues swabbed samples — 263 samples at eight different skin sites — from fifteen healthy adults. Before the sampling, participants were instructed not to wash for twenty four hours. Why? Well, for one: because soap has been shown to be toxic to several species of skin microbe.

After collecting the samples, the researchers then used a procedure called shotgun sequencing to analyze the skin microbiome of each individual. Shotgun sequencing involves blasting DNA into smaller chunks (as with a shotgun), then reassembling these chunks into readable sequences. It’s amazing what computers can do these days.

Uncharted Microbes

Even after shotgun sequencing, much of the microbial DNA from the skin samples remained mysterious. It had never been seen before, and there were no reference guides — print, digital or otherwise — to identify this “microbial dark matter.”

So to map this mystery DNA, Oh and her colleagues created their own reference guide, calling it “the first multi-kingdom skin microbial gene catalogue.” Using this catalogue, the researchers found that most of the uncharted DNA belonged to skin bacteria, though there were also some eukaryotes — microbes with membranes — in the mix. Less than 1% of the unclassified DNA belonged to viruses.

Dark matter or otherwise, the data showed that bacterial species — P. acnes and S. epidermidis, for example — dominated at most skin sites. But although bacteria were clear winners in abundance and diversity, fungi and viruses also had strong epidermal showings, at least compared to their levels in human stool.  

For their part, fungi were found mostly on sebaceous, oily skin regions like the forehead. Viruses were more rare, but a few individuals had large colonies of molluscum contagiosum and human papillomavirus show up in their samples. For some reason, however, their skin appeared normal.

Resident microbes varied not only by body part, but also by individual. They varied so reliably, in fact, that the researchers could identify subjects with over 80% accuracy based solely on their microbial taxonomy. In other words, your skin microbiome is like your fingerprint: uniquely yours.

Microbial Uniqueness

Your skin crawls with life. It’s a diverse ecosystem of bacteria, fungi, viruses and other organisms invisible to the naked eye. It’s your skin microbiome.

From a microbial perspective, no two pieces of skin are the same. Your forehead is distinct from your toenail, and yourtoenail is distinct from my toenail.

How do these differences affect your health? That’s not clear.

But do they affect it? Almost certainly.

Stay tuned.


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