Human skin Microbiota: High diversity of DNA viruses identified on the human skin by high throughput sequencing

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Foulongne, Vincent ^a   Sauvage, Virginie ^b   Hebert, Charles ^c   Dereure, Olivier ^a   Cheval, Justine ^c   Gouilh, Meriadeg Ar ^b   Pariente, Kevin ^c   Segondy, Michel ^a   Burguière, Ana ^b   Manuguerra, Jean Claude ^b   Caro, Valérie ^b   Eloit, Marc ^b,c,d  

^a INSERM   (France)

^b INSTITUT PASTEUR   (France)

^c Pathoquest   (France)

^d ECOLE NATIONALE VÉTÉRINAIRE D ALFORT   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; ARTICLE; CIRCOVIRUS; CLINICAL ARTICLE; CONTROLLED STUDY; DNA VIRUS; FEMALE; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; MALE; MERKEL CELL TUMOR; METAGENOMICS; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PAPILLOMA VIRUS; POLYOMA VIRUS; SKIN FLORA; VIRUS DETECTION; VIRUS GENOME; VIRUS IDENTIFICATION;

BACTERIA; BACTERIOPHAGES; CIRCOVIRIDAE; DNA VIRUSES; GENOME, BACTERIAL; GENOME, VIRAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOME; PAPILLOMAVIRIDAE; PHYLOGENY; POLYOMAVIRIDAE; SKIN;

EID: 84862522999     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038499     Document Type: Article

References (44)

1. Grice EA, Segre JA, (2011) The skin microbiome. Nat Rev Microbiol 9(4): 244-53.
2. Gao Z, Tseng CH, Pei Z, Blaser MJ, (2007) Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci U S A 104(8): 2927-32.
3. Antonsson A, Erfurt C, Hazard K, Holmgren V, Simon M, et al. (2003) Prevalence and type spectrum of human papillomaviruses in healthy skin samples collected in three continents. J Gen Virol 84(7): 1881-6.
4. Antonsson A, Karanfilovska S, Lindqvist PG, Hnasson BG, (2003) General acquisition of human papillomavirus infections of skin occurs in early infancy. J Clin Microbiol 41(6): 2509-14.
5. Chen AC, McMillan NA, Antonsson A, (2008) Human papillomavirus type spectrum in normal skin of individuals with or without a history of frequent sun exposure. J Gen Virol 89(11): 2891-7.
6. Forslund O, (2007) Genetic diversity of cutaneous human papillomaviruses. J Gen Virol 88(10): 2662-9.
7. Kohler A, Gottschling M, Forster J, Rowert-Hubert J, Stockfleth E, et al. (2010) Genomic characterization of a novel human papillomavirus (HPV-117) with a high viral load in a persisting wart. Virology 399(1): 129-33.
8. Kohler A, Gottschling M, Manning K, Lehmann MD, Schuz E, et al. (2011) Genomic characterization of ten novel human papillomavirus from keratotic lesions of immunosuppressed patients. J Gen Virol 92(7): 1585-1594.
9. Feng H, Shuda M, Chang Y, Moore PS, (2008) Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319(5866): 1096-100.
10. Shuda M, Feng H, Kwun HJ, Rosen ST, Gjoerup O, et al. (2008) T antigen mutations are a human tumor-specific signature for Merkel cell polyomavirus. Proc Natl Acad Sci U S A 105(42): 16272-7.
11. Foulongne V, Kluger N, Dereure O, Mercier G, Moles JP, et al. (2010) Merkel cell polyomavirus in cutaneous swabs. Emerg Infect Dis 16(4): 685-7.
12. Schowalter RM, Pastrana DV, Pumphrey KA, Moyer AL, Buck CB, (2010) Merkel cell polyomavirus and two previously unknown polyomaviruses are chronically shed from human skin. Cell Host Microbe 7(6): 509-15.
13. Wieland U, Mauch C, Kreuter A, Krieg T, Pfister H, (2009) Merkel cell polyomavirus DNA in persons without merkel cell carcinoma. Emerg Infect Dis 15(9): 1496-8.
14. Sauvage V, Foulongne V, Cheval J, Ar Gouilh M, Pariente K, et al. (2011) Human polyomavirus related to African green monkey lymphotropic polyomavirus. Emerg Infect Dis 17(8): 1364-70.
15. Scuda N, Hofmann J, Clavignac-Spencer S, Ruprecht K, Liman P, et al. (2011) A Novel human polyomavirus closely related to the african green monkey-derived lymphotropic polyomavirus. J Virol 85(9): 4586-90.
16. Li L, Kapoor A, Slikas B, Bamidele OS, Wang C, et al. (2010) Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol 84(4): 1674-82.
17. Sauvage V, Cheval J, Foulongne V, Ar Gouilh MA, Pariente K, et al. (2011) Identification of the first human gyrovirus, a virus related to chicken anemia virus. J Virol 85(15): 7948-50.
18. Grice EA, Kong HH, Renaud G, Young AC, NISC comparative sequencing program, et al (2008) A diversity profile of the human skin microbiota. Genome Res 18(7): 1043-50.
19. Breitbart M, Salamon P, Mahaffy JM, Segall AM, et al. (2002) Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci U S A 99(22): 14250-5.
20. Delwart EL, (2007) Viral metagenomics. Rev Med Virol. 17(2): 115-31.
21. Li SK, Leung RK, Guo HX, Wei JF Wang JH, et al. (2011) Detection and identification of plasma bacterial and viral elements in HIV/AIDS patients in comparison to healthy adults. Clin Microbiol Infect2011 Oct 4 doi:10.1111/j.1469-0691.2011.03690.
22. Victoria JG, Kapoor A, Li L, Blinkova O, Slikas B, et al. (2009) Metagenomic analyses of viruses in stool samples from children with acute flaccid paralysis. J Virol 83(9): 4642-51.
23. Giardina E, Pietrangeli I, Martone C, Zampatti S, Marsala P, et al. (2009) Whole genome amplification and real-time PCR in forensic casework. BMC Genomics 10: 159.
24. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, et al. (2009) Topographical and temporal diversity of the human skin microbiome. Science 324(5931): 1190-2.
25. Kong HH, (2011) Skin microbiome: genomics-based insights into the diversity and role of skin microbes. Trends Mol Med 17(6): 320-8.
26. Paulino LC, Tseng CH, Strober BE, Blaser MJ, (2006) Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions. J Clin Microbiol 44: 2933-41.
27. Antonsson A, Forslund O, Ekberg H, Sterner G, Hansson BG, (2000) The ubiquity and impressive genomic diversity of human skin papillomaviruses suggest a commensalic nature of these viruses. J Virol 74(24): 11636-41.
28. Hsu JY, Chen AC, Keleher A, McMillan NA, Antonsson A, (2009) Shared and persistent asymptomatic cutaneous human papillomavirus infections in healthy skin. J Med Virol 81(8): 1444-9.
29. Weissenborn SJ, Neale R, De Koning MN, Waterboer T, Abeni D, et al. (2009) Prevalence and multiplicity of cutaneous beta papilloma viruses in plucked hairs depend on cellular DNA input. J Virol Methods 161(2): 280-3.
30. Bernard H U, Burk R D, Chen Z, Van Doorslaer K, Hausen H, et al. (2010) Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 401(1): 70-9.
31. Cheval J, V Sauvage, Frangeul L, Dacheux L, Guigon G, et al. (2011) Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. J Clin Microbiol 49(9): 3268-75.
32. Duncavage EJ, Pfeifer JD, (2011) Human polyomaviruses 6 and 7 are not detectable in Merkel cell polyomavirus-negative Merkel cell carcinoma. J Cutan Pathol 38(10): 790-6.
33. Schrama D, Buck CB, Houben R, Becker JC, (2012) No Evidence for Association of HPyV6 or HPyV7 with Different Skin Cancers. J Invest Dermatol 132(1): 239-41.
34. Biagini P, (2004) Human circoviruses. Vet Microbiol. 98: 95-101.
35. Li L, Shan T, Soji OB, Alam MM, Kunz TH, et al. (2011) Possible cross-species transmission of circoviruses and cycloviruses among farm animals. J Gen Virol. 92(4): 768-72.
36. Gao Z, Tseng CH, Strober BE, Pei Z, Blaser MJ, (2008) Substantial alterations of the cutaneous bacterial biota in psoriatic lesions. PLoS One 3(7): e2719.
37. Grice EA, Snitkin ES, Yockey LJ, Bermudez DM, Liechty KW, et al. (2011) Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response. Proc Natl Acad Sci U S A 107(33): 14799-804.
38. Dubina M, GoldenbergG (2009) Viral-associated nonmelanoma skin cancers: a review. Am J Dermatopathol 31(6): 561-73.
39. Feltkamp MC, De Koning MN, Bavinck JN, Ter Schegget J, (2008) Betapapillomaviruses: innocent bystanders or causes of skin cancer. J Clin Virol 43(4): 353-60.
40. Tuttleton Arron S, Jennings L, Nindl I, Rosl F, Bouwes Bavinck JN, et al. (2011) Viral oncogenesis and its role in nonmelanoma skin cancer. Br J Dermatol 164(6): 1201-13.
41. Calder KB, Smoller BR, (2010) New insights into merkel cell carcinoma. Adv Anat Pathol 17(3): 155-61.
42. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28(10): 2731-2739.
43. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32(5): 1792-1797.
44. Drummond AJ, Rambaut A, (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214-214.