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Human Skin Microbiome Is Largely Stable Over Time According to Metagenomic Study

NEW YORK (GenomeWeb) – The microbial communities living on people's skin are largely stable over time, according to a new study.

Researchers led by Julie Segre from the National Human Genome Research Institute and Heidi Kong of the National Cancer Institute swabbed various skin sites of a dozen healthy people over the course of months and years. As they reported today in Cell, metagenomic shotgun sequencing revealed that individuals retained their own unique microbial signatures over time.

"Here, we show that community stability persists regardless of the sampling time interval and despite constant exposure of skin communities to extrinsic factors," Segre, Kong, and their colleagues wrote in their paper. "Interestingly, the nature and degree of this stability is highly individual specific."

The researchers collected samples from 12 healthy people at 17 skin sites at three different time points, with one month to two months or one year to two years between sampling. From this, they generated nearly 600 samples and 720 gigabase pairs of shotgun microbial sequence data.

By comparing the community membership and structure at these time periods, the researchers found that an individual's short- and long-term microbial communities were more similar to each other than they were to the communities of other individuals at similar time periods.

The bacterial and fungal makeup of sebaceous sites was particularly stable. But even dry sites like the palm of the hand that are commonly exposed to environmental sources of other microbes were stable over time. Feet, the researchers noted, harbored the least stable microbiome.

The researchers also reported that stability was generally anti-correlated with community diversity. Feet, with their high diversity and moist environment, were likely to be less stable than low-diversity sebaceous sites. No site exhibited changes in diversity levels over time, suggesting to the researchers that community diversity is homeostatic.

Segre, Kong, and their colleagues also found that individuals have specific microbial signatures. Using a supervised random forests algorithm, they identified taxa that could differentiate each individual, and could also tell whether those taxa were present at subsequent time points. A small number of species retained their discriminatory power over time, and low-abundance ones generally could better distinguish individuals and were more stable over time, they noted.

To dive into whether microbial strains are stable over time, the researchers focused on Propionibacterium acnes, finding that its strains appear to be stable over time, across body sites. Further, when the researchers looked at SNPs shared among P. acnes in longitudinal samples, they likewise uncovered SNV stability over time.

The researchers also compared the functional gene content of P. acnes strains that the individuals housed to find that individuals could have similar pangenomic capacity through different combinations of strains. Thus, even though individuals have distinct P. acnes strain signatures, they have similar functional capacities.

They similarly examined the stability of Staphylococcus epidermidis strains over time, again finding that multi-phyletic communities of S. epidermidis strains are maintained and that strains among individuals over time are more similar than those found between individuals.

This suggested to the researchers that new strains are rarely acquired from the environment.

The researchers added that what they've learned about the healthy skin microbiome could provide insight for studies of people with skin conditions like eczema, or with primary immune deficiencies.

"Future studies can use the knowledge of the relative stability of the skin microbial communities in healthy adults to understand how various exposures or disease state may alter these skin microbes," Segre said in a statement. "For example, studies in acne patients could explore whether specific strains bloom during adolescent acne flares or change with medications such as antibiotics."

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