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Skin Microbiome Visual Abstract

How Much Does the Skin Microbiome Change Over Time?

Julia Oh

7/14/2016


By Julia Oh, Ph.D.


Assistant Professor at the Jackson Laboratory for Genomic Medicine

Like a forest, plain or desert, our skin has different ecologies. We have oily sites like our face and torso, dry sites like our hands and forearms, and moist sites like our feet and armpits. And all over our skin, we have tremendous numbers of microbes—bacteria, fungi and viruses that make up what is called the skin microbiome.

There are dangerous germs that can make us sick, and you probably have heard a lot about them. Most microbes, however, are good for us. For example, they help in developing and maintaining our immune system, and can help to protect against infections.

I have spent most of the last few years working on methods to characterize what are the microbes on our skin, including who is there and what are they doing. Our previous research has shown that our skin’s microbes are very much shaped by where on the skin they are found, and what that skin site is like. For example, oily sites have a lot of bacteria and fungi that grow well with oil. Sites in and around the nose might have a lot of bacteriophages, which are bacterial viruses. Relatively dry sites like the hands tend to be very diverse, with a lot of different types of bacteria. Foot sites tend to look very different—likely because they get exposed to different environments as we walk around, and the skin there is also quite different, thick and scaly.

The skin is probably one of the most continually perturbed parts of our bodies—we are constantly showering, washing, touching things and other people, and moving from one place to another. Understanding whether and how our skin microbes change over time is important to understanding how changes in microbial communities may lead to disease or health. In our recently published paper, we studied the stability of our skin communities over time and found some surprising results.

Skin Microbiome Visual AbstractImage courtesy of Cell. www.cell.com

Our first question was, how stable is the skin microbiome? Despite how exposed our skin is, we found that skin microbes were generally stable over both short and long time periods. Foot sites were least stable. This might be because there is some selective pressure exerted at oilier sites on the body that isn’t present in the feet. Alternately, maybe our immune system is less active in our extremities, given lower blood flow and thicker skin on our feet, which might change the immune surveillance. We also saw that stability could be an individual-specific quality—some individuals could have extraordinarily stable communities, while others had more fluctuations. Again, this could be caused by a combination of factors, from hygiene and other behaviors, temperature, environment, to the immune status. Surprisingly, even though we’re constantly touching things, the hands were relatively stable.

We also asked, what wasn’t stable? We did an analysis looking at transience, or appearance/disappearance of species over time. When species are low in abundance, they tend to be appear/disappear more often. Generally, though, when a microbe is high in abundance, it tends to be really stable. There was one exception—human viruses, which could appear/disappear even if they were abundant. We looked a little farther and found that the DNA viruses didn’t appear to obey the same rules that other microbes do, in terms of skin-site specificity. In retrospect, this makes sense because DNA viruses infect human cells—and they’re not as dependent as bacteria might be in growing in a particular skin site. Interestingly, we also saw that viruses tended to be very specific to an individual. While most of us have a core set of bacteria and fungi, the same wasn’t true for the human viruses—we tend to have our own unique set of them.

Finally, we asked, where do we get our microbes from? Are we constantly re-acquiring them from the environment or other people, or do we constantly replenish our own microbes? To understand this, we did an analysis that is kind of like what the cops do on CSI—look at single differences in the DNA. Except here, we are looking at differences in microbial DNA, not human DNA. If they remain the same, it’s very probable that we retain the same strains over time. We saw that distributions remained very stable over time—so our resident skin microbes likely live in deeper crevices of the skin (or in our hair follicles) where they constantly grow and replenish our skin.

In summary, we were surprised to see such striking stability in the microbiome at most of our skin sites. Especially in the hands, because they are constantly in use and are continually being cleaned. But this was in healthy individuals—future studies need to look at individuals who have defective immune systems, those who often get skin disease, or people who take antibiotics often, since their skin communities might be quite different.

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