Gut Virome and Inflammatory Bowel Disease

Inflammatory Bowel Diseases

Volumn 22, Issue 7, 2016, Pages 1708-1712

  Lopetuso, Loris R ^a,b   Ianiro, Gianluca ^a   Scaldaferri, Franco ^a   Cammarota, Giovanni ^a   Gasbarrini, Antonio ^a  

^a FONDAZIONE POLICLINICO UNIVERSITARIO A GEMELLI IRCCS   (Italy)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

gut barrier; gut inflammation; gut microbiota; gut virome; IBD

Indexed keywords

CHRONIC INFLAMMATION; CLINICAL FEATURE; GUT VIROME; HUMAN; INFLAMMATORY BOWEL DISEASE; INTESTINE FLORA; PHYSIOLOGY; PRIORITY JOURNAL; REVIEW; GASTROINTESTINAL TRACT; PATHOPHYSIOLOGY; VIROLOGY;

GASTROINTESTINAL MICROBIOME; GASTROINTESTINAL TRACT; HUMANS; INFLAMMATORY BOWEL DISEASES;

EID: 84976329732     PISSN: 10780998     EISSN: 15364844     Source Type: Journal    
DOI: 10.1097/MIB.0000000000000807     Document Type: Review

References (61)

1. Cammarota G, Ianiro G, Cianci R, et al. The involvement of gut microbiota in inflammatory bowel disease pathogenesis: potential for therapy. Pharmacol Ther. 2015;149:191-212
2. Conceicao-Neto N, Zeller M, Lefrere H, et al. Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Sci Rep. 2015;5:16532
3. Scarpellini E, Ianiro G, Attili F, et al. The human gut microbiota and virome: potential therapeutic implications. Dig Liver Dis. 2015;47:1007-1012
4. Reyes A, Semenkovich NP, Whiteson K, et al. Going viral: nextgeneration sequencing applied to phage populations in the human gut. Nat Rev Microbiol. 2012;10:607-617
5. Virgin HW. The virome in mammalian physiology and disease. Cell. 2014;157:142-150
6. Rohwer F. Global phage diversity. Cell. 2003;113:141
7. Breitbart M, Hewson I, Felts B, et al. Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol. 2003;185:6220-6223
8. Finkbeiner SR, Allred AF, Tarr PI, et al. Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog. 2008;4:e1000011
9. Minot S, Sinha R, Chen J, et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 2011;21:1616-1625
10. Minot S, Grunberg S, Wu GD, et al. Hypervariable loci in the human gut virome. Proc Natl Acad Sci U S A. 2012;109:3962-3966
11. Minot S, Bryson A, Chehoud C, et al. Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A. 2013;110:12450-12455
12. Reyes A, Haynes M, Hanson N, et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature. 2010;466:334-338
13. Zhang T, Breitbart M, Lee WH, et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 2006;4:e3
14. Kapusinszky B, Minor P, Delwart E. Nearly constant shedding of diverse enteric viruses by two healthy infants. J Clin Microbiol. 2012;50:3427-3434
15. Ackermann HW. Phage classification and characterization. Methods Mol Biol. 2009;501:127-140
16. Reyes A, Wu M, McNulty NP, et al. Gnotobiotic mouse model of phagebacterial host dynamics in the human gut. Proc Natl Acad Sci U S A. 2013;110:20236-20241
17. Waller AS, Yamada T, Kristensen DM, et al. Classification and quantification of bacteriophage taxa in human gut metagenomes. ISME J. 2014;8: 1391-1402
18. Lim ES, Zhou Y, Zhao G, et al. Early life dynamics of the human gut virome and bacterial microbiome in infants. Nat Med. 2015;21:1228-1234
19. Sommer F, Backhed F. The gut microbiota-masters of host development and physiology. Nat Rev Microbiol. 2013;11:227-238
20. Lotka AJ. Elements of Physical Biology. Williams and Wilkins, 1925
21. Volterra V. Variations and fluctuations of the number of individuals in animal species living together. In: Animal Ecology. Chapman RN (ed). McGraw-Hill, 1931
22. Parsons RJ, Breitbart M, Lomas MW, et al. Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea. ISME J. 2012;6:273-284
23. Cortez MH, Weitz JS. Coevolution can reverse predator-prey cycles. Proc Natl Acad Sci U S A. 2014;111:7486-7491
24. Markine-Goriaynoff N, Gillet L, Van Etten JL, et al. Glycosyltransferases encoded by viruses. J Gen Virol. 2004;85:2741-2754
25. Lagier JC, Million M, Hugon P, et al. Human gut microbiota: repertoire and variations. Front Cell Infect Microbiol. 2012;2:136
26. Kernbauer E, Ding Y, Cadwell K. An enteric virus can replace the beneficial function of commensal bacteria. Nature. 2014;516:94-98
27. Barton ES, White DW, Cathelyn JS, et al. Herpesvirus latency confers symbiotic protection from bacterial infection. Nature. 2007;447:326-329
28. White DW, Keppel CR, Schneider SE, et al. Latent herpesvirus infection arms NK cells. Blood. 2010;115:4377-4383
29. Yager EJ, Szaba FM, Kummer LW, et al. gamma-Herpesvirus-induced protection against bacterial infection is transient. Viral Immunol. 2009;22:67-72
30. Canny SP, Goel G, Reese TA, et al. Latent gammaherpesvirus 68 infection induces distinct transcriptional changes in different organs. J Virol. 2014;88:730-738
31. Nelson DA, Petty CC, Bost KL. Infection with murine gammaherpesvirus 68 exacerbates inflammatory bowel disease in IL-10-deficient mice. Inflamm Res. 2009;58:881-889
32. White DW, Suzanne Beard R, Barton ES. Immune modulation during latent herpesvirus infection. Immunol Rev. 2012;245:189-208
33. MacDuff DA, Reese TA, Kimmey JM, et al. Phenotypic complementation of genetic immunodeficiency by chronic herpesvirus infection. eLife. 2015:4
34. Barrett JC, Hansoul S, Nicolae DL, et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet. 2008;40:955-962
35. Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007;447:661-678
36. Rioux JD, Xavier RJ, Taylor KD, et al. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet. 2007;39:596-604
37. Hampe J, Franke A, Rosenstiel P, et al. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet. 2007;39:207-211
38. Mead PS, Slutsker L, Dietz V, et al. Food-related illness and death in the United States. Emerg Infect Dis. 1999;5:607-625
39. Cadwell K, Patel KK, Maloney NS, et al. Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine. Cell. 2010;141:1135-1145
40. Baldridge MT, Nice TJ, McCune BT, et al. Commensal microbes and interferon-lambda determine persistence of enteric murine norovirus infection. Science. 2015;347:266-269
41. Nice TJ, Baldridge MT, McCune BT, et al. Interferon-lambda cures persistent murine norovirus infection in the absence of adaptive immunity. Science. 2015;347:269-273
42. Lindblad-Toh K, Garber M, Zuk O, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011;478:476-482
43. Casanova JL, Abel L, Quintana-Murci L. Immunology taught by human genetics. Cold Spring Harb Symp Quant Biol. 2013;78:157-172
44. Quintana-Murci L, Clark AG. Population genetic tools for dissecting innate immunity in humans. Nat Rev Immunol. 2013;13:280-293
45. Perez-Brocal V, Garcia-Lopez R, Vazquez-Castellanos JF, et al. Study of the viral and microbial communities associated with Crohn's disease: a metagenomic approach. Clin Transl Gastroenterol. 2013;4:e36
46. Lepage P, Colombet J, Marteau P, et al. Dysbiosis in inflammatory bowel disease: a role for bacteriophages? Gut. 2008;57:424-425
47. Modi SR, Lee HH, Spina CS, et al. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature. 2013;499:219-222
48. Norman JM, Handley SA, Baldridge MT, et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015;160: 447-460
49. Brooks J, Watson AJ. The enteric virome in inflammatory bowel disease. Gastroenterology. 2015;149:1120-1121
50. Wang W, Jovel J, Halloran B, et al. Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria. Inflamm Bowel Dis. 2015;21: 1419-1427
51. Kwun HJ, Han HJ, Lee WJ, et al. Transactivation of the human endogenous retrovirus K long terminal repeat by herpes simplex virus type 1 immediate early protein. Virus Res. 2002;86:93-100
52. Lee WJ, Kwun HJ, Kim HS, et al. Activation of the human endogenous retrovirus W long terminal repeat by herpes simplex virus type 1 immediate early protein. Mol Cell. 2003;15:75-80
53. Nellaker C, Yao Y, Jones-Brando L, et al. Transactivation of elements in the human endogenous retrovirus W family by viral infection. Retrovirology. 2006;3:44
54. Sicat J, Sutkowski N, Huber BT. Expression of human endogenous retrovirus HERV-K18 superantigen is elevated in juvenile rheumatoid arthritis. J Rheumatol. 2005;32:1821-1831
55. Ruprecht K, Obojes K, Wengel V, et al. Regulation of human endogenous retrovirus W protein expression by herpes simplex virus type 1: implications for multiple sclerosis. J Neurovirol. 2006;12:65-71
56. Stauffer Y, Theiler G, Sperisen P, et al. Digital expression profiles of human endogenous retroviral families in normal and cancerous tissues. Cancer Immun. 2004;4:2
57. Perez-Brocal V, Garcia-Lopez R, Nos P, et al. Metagenomic analysis of Crohn's disease patients identifies changes in the virome and microbiome related to disease status and therapy, and detects potential interactions and biomarkers. Inflamm Bowel Dis. 2015;21:2515-2532
58. Madsen CD, Eugen-Olsen J, Kirk O, et al. TTV viral load as a marker for immune reconstitution after initiation of HAART in HIV-infected patients. HIV Clin Trials. 2002;3:287-295
59. Thom K, Petrik J. Progression towards AIDS leads to increased Torque teno virus and Torque teno minivirus titers in tissues of HIV infected individuals. J Med Virol. 2007;79:1-7
60. McElvania TeKippe E, Wylie KM, Deych E, et al. Increased prevalence of anellovirus in pediatric patients with fever. PLoS One. 2012;7: e50937
61. De Paepe M, Leclerc M, Tinsley CR, et al. Bacteriophages: an underestimated role in human and animal health? Front Cell Infect Microbiol. 2014;4:39