Over 90 percent of the human cutaneous virome is made up of unclassifiable “dark matter”
Studies of the human microbiome have gained popularity in recent years, but just how much do we really know about the helpful (and harmful) microbes living in the human body? A recent study by a team of dermatologists and microbiologists at the University of Pennsylvania (UPenn) in the US, has revealed we have a lot left to learn – during a viral DNA analysis of 16 healthy volunteers, the team found that over 90 percent of the DNA viruses on human skin are “dark matter” that isn’t identifiable (1). “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,” says Elizabeth Grice, senior author of the paper and assistant professor of dermatology. “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 needle in the haystack,” she adds.
To overcome the problem, Grice and her colleagues used viral DNA purification techniques on virus-like particles (VLPs) before performing shotgun metagenomics sequencing on the purified samples. A database search showed that over 90 percent of the detected DNA did not match any known genomes. Much of the viral material identified belonged to the Caudovirales order (tailed bacteriophages), although most were not classed to family level. This suggests a strong link between the viruses and bacteria found on the skin, as phages can alter the phenotype of their host bacteria. The team found evidence of transmissible genes which could confer antibiotic resistance, virulence and pathogenicity, implying that the skin virome may play a significant role in health and disease. As for the viruses that could be identified, the most abundant, perhaps unsurprisingly, was the skin-cell infecting HPV. The UPenn team hope that their work will help to establish a baseline for future study of the skin virome and the ways it changes during disease, and encourage other researchers to design their own studies of the virome – to this end, they have made their methods, including the algorithms they devised to analyze their data, freely available. They also plan to continue their work, and are now using the methods they have developed to study the genomic variability of skin viruses, and to observe how the skin virome changes in response to influences, such as UV radiation exposure and antibiotic treatments.
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References
- GD Hannigan et al., “The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome”, mBio, 6, e1578–15 (2015). PMID: 26489866.
