Is Your Skin Microbiome Older Than Your Species?

The bacteria living on your cheeks right now may predate your species by tens of millions of years. When researchers compared the microbes on human skin to those on the skin of chimpanzees, gorillas, and other primates, they found something startling: the bacterial family trees matched the primate family trees almost perfectly. The microbes, it seems, have been co-evolving with their primate hosts since long before Homo sapiens emerged. You didn't inherit your skin microbiome from your parents alone. You inherited it from your evolutionary lineage.

How do we know the bacteria are that old?

The evidence comes from phylogenetic analysis—mapping the evolutionary relationships between species. When scientists at the University of Colorado Boulder analyzed skin bacteria from 18 primate species, including humans, they found that certain bacterial lineages diverged at roughly the same time as their primate hosts. Corynebacterium species on chimpanzee skin, for instance, are more closely related to Corynebacterium on human skin than to Corynebacterium on distantly related primates. The bacteria appear to have been passed down through generations, diversifying as their hosts diversified. This vertical transmission suggests that the partnership between primates and their skin microbes is not a recent arrangement. It's ancient.

What does this mean for the bacteria on your face?

It means the microbes you share with chimpanzees and gorillas have had millions of years to adapt to primate skin—its oils, its pH, its immune defenses. Staphylococcus epidermidis, one of the most abundant bacteria on human skin, is also found on great apes. Cutibacterium acnes, the species associated with acne, has primate relatives too. These bacteria aren't opportunistic colonizers that happened to land on you. They're specialists, honed by deep evolutionary time to thrive in the specific environment of primate skin. (For more on how these bacterial communities function, see our overview of Corynebacterium species.)

But some of your microbes are much newer

Not everything on your skin is an ancient passenger. Humans have also picked up microbes from their environments—bacteria from soil, water, other animals, and each other. The microbial diversity on modern human skin is shaped by diet, geography, hygiene practices, and indoor living. Research on hunter-gatherer populations suggests that people living traditional lifestyles carry different microbial communities than urban populations, even though the core species are shared. Westernization has likely pruned some microbial lineages while favoring others. The oldest residents remain, but the neighborhood has changed.

Why this matters for your skin

If your skin microbiome has been co-evolving with primates for 20 million years, it's not easily replaceable or interchangeable. Disrupting it with aggressive cleansing or antimicrobial products may be more consequential than we thought—you're not just wiping away a temporary film of bacteria, but destabilizing a partnership that predates agriculture, cities, and soap itself.

References

• Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. Nat Rev Microbiol. 2018.
• Oh J, Byrd AL, Park M, et al. Temporal stability of the human skin microbiome. Cell. 2016.
• Flowers L, Grice EA. The Skin Microbiota: Balancing Risk and Reward. Cell Host Microbe. 2020.
• Ross AA, Müller KM, Weese JS, Neufeld JD. Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia. Proc Natl Acad Sci U S A. 2018.