Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing

Abstract

The human skin is a complex ecosystem that hosts a heterogeneous flora. Until recently, the diversity of the cutaneous microbiota was mainly investigated for bacteria through culture based assays subsequently confirmed by molecular techniques. There are now many evidences that viruses represent a significant part of the cutaneous flora as demonstrated by the asymptomatic carriage of beta and gamma-human papillomaviruses on the healthy skin. Furthermore, it has been recently suggested that some representatives of the Polyomavirus genus might share a similar feature. In the present study, the cutaneous virome of the surface of the normal-appearing skin from five healthy individuals and one patient with Merkel cell carcinoma was investigated through a high throughput metagenomic sequencing approach in an attempt to provide a thorough description of the cutaneous flora, with a particular focus on its viral component. The results emphasize the high diversity of the viral cutaneous flora with multiple polyomaviruses, papillomaviruses and circoviruses being detected on normal-appearing skin. Moreover, this approach resulted in the identification of new Papillomavirus and Circovirus genomes and confirmed a very low level of genetic diversity within human polyomavirus species. Although viruses are generally considered as pathogen agents, our findings support the existence of a complex viral flora present at the surface of healthy-appearing human skin in various individuals. The dynamics and anatomical variations of this skin virome and its variations according to pathological conditions remain to be further studied. The potential involvement of these viruses, alone or in combination, in skin proliferative disorders and oncogenesis is another crucial issue to be elucidated.

The diversity and host interactions of Propionibacterium acnes bacteriophages on human skin

“…They are a reservoir of diversity-generating elements (Rohwer and Thurber, 2009) and regulate both the abundance and diversity of their bacterial hosts by predation (Suttle et al, 1990;Waterbury and Valois, 1993;Rohwer, 2003;Rodriguez-Valera et al, 2009). Although the skin bacterial community has been studied by several groups (Gao et al, 2007;Costello et al, 2009;Grice et al, 2009;Kong et al, 2012;The Human Microbiome Project Consortium, 2012;Blaser et al, 2013;Fitz-Gibbon et al, 2013;Nakatsuji et al, 2013), relatively few studies have characterized the skin viral community (Foulongne et al, 2012;Ma et al, 2014;Wylie et al, 2014). In particular, the composition and dynamics of bacteriophages and their interactions with bacterial hosts on the skin are not well understood.…”

Improved detection reveals active β-papillomavirus infection in skin lesions from kidney transplant recipients

“…17,18 Nearly all adults are persistently infected in the skin with many viruses belonging to the human papillomavirus (HPV) family. 19,20 Although they appear not to cause overt clinical symptoms in a great majority of infected individuals, they can cause cancer, either in skin or in genital sites, particularly in subjects with impaired immune function. [21][22][23][24][25] To date, more than 150 HPV types have been completely sequenced and classified into five genera (and a series of intragenus species, indicated by Arabic numbers) based on DNA sequence analysis.…”

Human papillomavirus and posttransplantation cutaneous squamous cell carcinoma: A multicenter, prospective cohort study

“…HPV constitute an important part of the normal human skin virome 6, 7, 19, 20. There is strong evidence from laboratory studies to suggest that HPV plays a role in cSCC carcinogenesis, principally through synergy with UVR 13, 14, 15.…”

“…The virome component of the human microbiome is known to play an important role in disease,4, 5 and HPV is particularly prevalent in the normal skin virome 6, 7. HPVs are double‐stranded DNA viruses that are classified into 5 genera (α, β, γ, μ, and ν) 8, 9.…”