Resident viruses and their interactions with the immune system

Nature Immunology

Volumn 14, Issue 7, 2013, Pages 654-659

  Duerkop, Breck A ^a   Hooper, Lora V ^a,b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTIVE IMMUNITY; ADENOVIRUS; BACTERIOPHAGE; CELLULAR IMMUNITY; CORONAVIRUS; CYTOMEGALOVIRUS; HUMAN; IMMUNE SYSTEM; IMMUNITY; INNATE IMMUNITY; LYMPHOCYTIC CHORIOMENINGITIS VIRUS; MERKEL CELL POLYOMAVIRUS; METAGENOMICS; NONHUMAN; PRIORITY JOURNAL; REVIEW; SIMIAN IMMUNODEFICIENCY VIRUS; VIRULENCE; VIRUS CELL INTERACTION; VIRUS ENTRY; VIRUS IMMUNITY;

GASTROINTESTINAL TRACT; HOST-PATHOGEN INTERACTIONS; HUMANS; MOUTH; NASAL CAVITY; RESPIRATORY SYSTEM; SKIN; VIRUSES;

EID: 84879373236     PISSN: 15292908     EISSN: 15292916     Source Type: Journal    
DOI: 10.1038/ni.2614     Document Type: Review

References (57)

1. Hooper, L.V., Littman, D.R. & Macpherson, A.J. Interactions between the microbiota and the immune system. Science 336, 1268-1273 (2012).
2. Lozupone, C.A., Stombaugh, J.I., Gordon, J.I., Jansson, J.K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220-230 (2012).
3. White, D.W., Suzanne Beard, R. & Barton, E.S. Immune modulation during latent herpesvirus infection. Immunol. Rev. 245, 189-208 (2012).
4. Handley, S.A. et al. Pathogenic simian immunodefciency virus infection is associated with expansion of the enteric virome. Cell 151, 253-266 (2012).
5. Reyes, A. et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334-338 (2010).
6. Minot, S. et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21, 1616-1625 (2011).
7. Foulongne, V. et al. Human skin microbiota: high diversity of DNA viruses identifed on the human skin by high throughput sequencing. PLoS ONE 7, e38499 (2012).
8. Zhang, T. et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 4, e3 (2006).
9. Turnbaugh, P.J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480-484 (2009).
10. Pride, D.T. et al. Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. ISME J. 6, 915-926 (2012).
11. Breitbart, M. et al. Viral diversity and dynamics in an infant gut. Res. Microbiol. 159, 367-373 (2008).
12. Weinbauer, M.G. Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28, 127-181 (2004). (Pubitemid 38510500)
13. DeMarini, D.M. & Lawrence, B.K. Prophage induction by DNA topoisomerase II poisons and reactive-oxygen species: role of DNA breaks. Mutat. Res. 267, 1-17 (1992).
14. Duerkop, B.A., Clements, C.V., Rollins, D., Rodrigues, J.L. & Hooper, L.V. A composite bacteriophage alters colonization by an intestinal commensal bacterium. Proc. Natl. Acad. Sci. USA 109, 17621-17626 (2012).
15. Kim, M.S., Park, E.J., Roh, S.W. & Bae, J.W. Diversity and abundance of single-stranded DNA viruses in human feces. Appl. Environ. Microbiol. 77, 8062-8070 (2011).
16. Canchaya, C., Fournous, G., Chibani-Chennouf, S., Dillmann, M.L. & Brussow, H. Phage as agents of lateral gene transfer. Curr. Opin. Microbiol. 6, 417-424 (2003). (Pubitemid 37075363)
17. Pride, D.T., Salzman, J. & Relman, D.A. Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses. Environ. Microbiol. 14, 2564-2576 (2012).
18. Ivanov, I.I. et al. Specifc microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 4, 337-349 (2008).
19. Mazmanian, S.K., Liu, C.H., Tzianabos, A.O. & Kasper, D.L. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122, 107-118 (2005). (Pubitemid 40977944)
20. Kuss, S.K. et al. Intestinal microbiota promote enteric virus replication and systemic pathogenesis. Science 334, 249-252 (2011).
21. Ichinohe, T. et al. Microbiota regulates immune defense against respiratory tract infuenza A virus infection. Proc. Natl. Acad. Sci. USA 108, 5354-5359 (2011).
22. Kane, M. et al. Successful transmission of a retrovirus depends on the commensal microbiota. Science 334, 245-249 (2011).
23. Schowalter, R.M., Pastrana, D.V., Pumphrey, K.A., Moyer, A.L. & Buck, C.B. Merkel cell polyomavirus and two previously unknown polyomaviruses are chronically shed from human skin. Cell Host Microbe 7, 509-515 (2010).
24. Miller, C.S., Avdiushko, S.A., Kryscio, R.J., Danaher, R.J. & Jacob, R.J. Effect of prophylactic valacyclovir on the presence of human herpesvirus DNA in saliva of healthy individuals after dental treatment. J. Clin. Microbiol. 43, 2173-2180 (2005). (Pubitemid 40656223)
25. Lazarevic, V. et al. Analysis of the salivary microbiome using culture-independent techniques. J. Clin. Bioinforma. 2, 4 (2012).
26. Bogaert, D. et al. Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PLoS ONE 6, e17035 (2011).
27. Nokso-Koivisto, J., Kinnari, T.J., Lindahl, P., Hovi, T. & Pitkaranta, A. Human picornavirus and coronavirus RNA in nasopharynx of children without concurrent respiratory symptoms. J. Med. Virol. 66, 417-420 (2002). (Pubitemid 34111785)
28. Minot, S., Grunberg, S., Wu, G.D., Lewis, J.D. & Bushman, F.D. Hypervariable loci in the human gut virome. Proc. Natl. Acad. Sci. USA 109, 3962-3966 (2012).
29. Victoria, J.G. et al. Metagenomic analyses of viruses in stool samples from children with acute faccid paralysis. J. Virol. 83, 4642-4651 (2009).
30. Finkbeiner, S.R. et al. Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog. 4, e1000011 (2008).
31. Lee, Y.K. & Mazmanian, S.K. Has the microbiota played a critical role in the evolution of the adaptive immune system? Science 330, 1768-1773 (2010).
32. McFall-Ngai, M. Adaptive immunity: care for the community. Nature 445, 153 (2007). (Pubitemid 46095705)
33. Vaishnava, S. et al. The antibacterial lectin RegIIIγ promotes the spatial segregation of microbiota and host in the intestine. Science 334, 255-258 (2011).
34. Salzman, N.H. et al. Enteric defensins are essential regulators of intestinal microbial ecology. Nat. Immunol. 11, 76-83 (2010).
35. Lysholm, F. et al. Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing. PLoS ONE 7, e30875 (2012).
36. Willner, D. et al. Metagenomic analysis of respiratory tract DNA viral communities in cystic fbrosis and non-cystic fbrosis individuals. PLoS ONE 4, e7370 (2009).
37. Brandl, K. et al. Vancomycin-resistant enterococci exploit antibiotic-induced innate immune defcits. Nature 455, 804-807 (2008).
38. Fukuda, S. et al. Bifdobacteria can protect from enteropathogenic infection through production of acetate. Nature 469, 543-547 (2011).
39. Virgin, H.W., Wherry, E.J. & Ahmed, R. Redefning chronic viral infection. Cell 138, 30-50 (2009).
40. Barton, E.S. et al. Herpesvirus latency confers symbiotic protection from bacterial infection. Nature 447, 326-329 (2007). (Pubitemid 46788830)
41. Zuniga, E.I., Liou, L.Y., Mack, L., Mendoza, M. & Oldstone, M.B. Persistent virus infection inhibits type I interferon production by plasmacytoid dendritic cells to facilitate opportunistic infections. Cell Host Microbe 4, 374-386 (2008).
42. Inchley, C.J. & Howard, J.G. The immunogenicity of phagocytosed T4 bacteriophage: cell replacement studies with splenectomized and irradiated mice. Clin. Exp. Immunol. 5, 189-198 (1969).
43. Nelson, J., Ormrod, D.J., Wilson, D. & Miller, T.E. Host immune status in uraemia III. Humoral response to selected antigens in the rat. Clin. Exp. Immunol. 42, 234-240 (1980). (Pubitemid 10008789)
44. Gorski, A. et al. Bacteriophages and transplantation tolerance. Transplant. Proc. 38, 331-333 (2006).
45. Eriksson, F. et al. Tumor-specifc bacteriophages induce tumor destruction through activation of tumor-associated macrophages. J. Immunol. 182, 3105-3111 (2009).
46. Mori, K., Kubo, T., Kibayashi, Y., Ohkuma, T. & Kaji, A. Anti-vaccinia virus effect of M13 bacteriophage DNA. Antiviral Res. 31, 79-86 (1996). (Pubitemid 26183122)
47. Duerr, D.M., White, S.J. & Schluesener, H.J. Identifcation of peptide sequences that induce the transport of phage across the gastrointestinal mucosal barrier. J. Virol. Methods 116, 177-180 (2004). (Pubitemid 38117081)
48. Hamzeh-Mivehroud, M., Mahmoudpour, A., Rezazadeh, H. & Dastmalchi, S. Non-specifc translocation of peptide-displaying bacteriophage particles across the gastrointestinal barrier. Eur. J. Pharm. Biopharm. 70, 577-581 (2008).
49. Keller, R. & Engley, F.B. Jr. Fate of bacteriophage particles introduced into mice by various routes. Proc. Soc. Exp. Biol. Med. 98, 577-580 (1958).
50. Rescigno, M. et al. Dendritic cells express tight junction proteins and penetrate gut epithelial monolayers to sample bacteria. Nat. Immunol. 2, 361-367 (2001). (Pubitemid 33706348)
51. Barfoot, R. et al. Some properties of dendritic macrophages from peripheral lymph. Immunology 68, 233-239 (1989). (Pubitemid 19246567)
52. Gorski, A. et al. Bacteriophage translocation. FEMS Immunol. Med. Microbiol. 46, 313-319 (2006).
53. Lepage, P. et al. Dysbiosis in infammatory bowel disease: a role for bacteriophages? Gut 57, 424-425 (2008). (Pubitemid 351288109)
54. Yan, N. & Chen, Z.J. Intrinsic antiviral immunity. Nat. Immunol. 13, 214-222 (2012).
55. Sun, L., Wu, J., Du, F., Chen, X. & Chen, Z.J. Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science 339, 786-791 (2013).
56. Wu, J. et al. Cyclic GMP-AMP is an endogenous second messenger in innate immune signaling by cytosolic DNA. Science 339, 826-830 (2013).
57. Doulatov, S. et al. Tropism switching in Bordetella bacteriophage defnes a family of diversity-generating retroelements. Nature 431, 476-481 (2004). (Pubitemid 39329589)