Researchers from the Perelman School of Medicine at the University of Pennsylvania surveyed the skin's virus population or "virome," which revealed most DNA viruses on healthy human skin are viral “dark matter” never described before. The research also included the development of a set of virome analysis tools to assist researchers for further examinations.
Understanding Microbes and Bacteria
Living on and inside humans, microbiomes and skin-resident bacteria can be vital toward:
- Warding off harmful infections,
- Maintaining proper skin immunity and
- Healing wounds.
However, they can also be harmful in causing diseases.
"There has been a real need for a better understanding of these viruses, given their potential effects on our skin cells as well as on our resident bacteria," said Elizabeth A. Grice, Ph.D., senior author and assistant professor of Dermatology at Penn Medicine. "Until now, relatively little work has been done in this area, in part because of the technical challenges involved. For example, a skin swab taken for analysis will contain mostly human and bacterial DNA and only a tiny amount of viral genetic material—the proverbial needles in the haystack."
Techniques and Research Analysis
Previous approaches in studying viral genetic material overlooks many viruses not already displayed in databases.
Using optimized techniques for isolating virus-like particles (VLPs) from skin swabs and for analyzing tiny amounts of genetic material, the team focused their sequencing and analysis on viral DNA without entirely depending on databases.
Expected results were revealed using samples from 16 healthy individuals. Analysis showed most abundant skin-cell infecting virus was human papilloma virus, which causes common warts and has been linked to skin cancers. However, most of the detected DNA from the VLPs did not match viral genes in existing databases.
"More than 90% was what we call viral dark matter—it had features of viral genetic material, but no taxonomic classification," said Grice.
The findings also clearly linked the skin virome to the skin microbiome, where most of the detected viral DNA appeared to belong to phage viruses, which infect and live within bacteria for long periods of time. When the researchers sequenced skin bacterial DNA from the same 16 subjects, they found it often contained tell-tale marks—or CRISPR spacers—of prior invasion by the same phage viruses.
Grice and her team are now using new methods to study the genomic variability of skin viruses, as well as changes in the skin virome in response to common factors such as ultraviolet radiation exposure and antibiotic use.