Viral Metagenomics

Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats

Volumn , Issue , 2011, Pages 3-13

  Williamson, Shannon J ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

DsDNA viral genotypic diversity; Viral genome, metagenomics; Viruses, and population biology

Indexed keywords

EID: 84886644714     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118010549.ch2     Document Type: Chapter

References (69)

1. Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, et al. 2009. Next-generation sequencing and metagenomic analysis: A universal diagnostic tool in plant virology. Mol. Plant Pathol. 10:537-545.
2. Allander T, Tammi MT, Eriksson M, Bjerkner A, Tiveljung-Lindell A, et al. 2005. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc. Natl. Acad. Sci. USA 102:12891-12896.
3. Andrews-Pfannkoch C, Fadrosh DW, Thorpe J, Williamson SJ. 2010. Hydroxyapatite-mediated separation of dsDNA, ssDNA and RNA genotypes from natural viral assemblages and metagenomic library construction. Appl. Environ. Microbiol. 5039-5045.
4. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, et al. 2006. The marine viromes of four oceanic regions. PLoS Biol. 4:e368.
5. Bench SR, Hanson TE, Williamson KE, Gosh D, Radosovich M, et al. 2007. Metagenomic characterization of Chesapeake Bay virioplankton. Appl. Environ. Microbiol. 73:7629-7641.
6. Blinkova O, Kapoor A, Victoria J, Jones M, Wolfe N, et al. 2009. Cardioviruses are genetically diverse and cause common enteric infections in South Asian children. J. Virol. 83:4631-4641.
7. Breitbart M, Rohwer F. 2005. Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. Biotechniques 39:729-736.
8. Breitbart M, Salamon P, Andresen B, Mahaffy J, Segall A, et al. 2002. Genomic analysis of uncultured marine viral communities. Proc. Natl. Acad. Sci. USA 99:14250-14255.
9. Breitbart M, Hewson I, Felts B, Mahaffy J, Nulton J, et al. 2003. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185:6220-6223.
10. Breitbart M, Felts B, Kelley S, Mahaffy J, Nulton J, et al. 2004a. Diversity and population structure of a near-shore marine-sediment viral community. Proc. R. Soc. Lond. B Biol. Sci. 271:565-574.
11. Breitbart M, Wegley L, Leeds S, Schoenfeld T, Rohwer F. 2004b. Phage community dynamics in hot springs. Appl. Environ. Microbiol. 70:1633-1640.
12. Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, et al. 2008. Viral diversity and dynamics in an infant gut. Res. Microbiol. 159:367-373.
13. Bryan MJ, Burroughs NJ, Spence EM, Clokie MR, Mann NH, et al. 2008. Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer. PLoS ONE 3:e2048.
14. Clokie MR, Shan J, Bailey S, Jia Y, Krisch HM, et al. 2006. Transcription of a 'photosynthetic' T4-type phage during infection of a marine cyanobacterium. Environ. Microbiol. 8:827-835.
15. Coetzee B, Freeborough MJ, Maree HJ, Celton JM, Rees DJ, et al. 2010. Deep sequencing analysis of viruses infecting grapevines: Virome of a vineyard. Virology 400:157-163.
16. Cornax R, Morinigo MA, Gonzalez-Jaen F, Alonso MC, Borrego JJ. 1994. Bacteriophages presence in human faeces of healthy subjects and patients with gastrointestinal disturbances. Zentralbl. Bakteriol. 281:214-224.
17. Culley AI, Lang AS, Suttle CA. 2006. Metagenomic analysis of coastal RNA virus communities. Science 312:1795-1798.
18. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, et al. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311:496-503.
19. Desnues C, Rodriguez-Brito B, Rayhawk S, Kelley S, Tran T, et al. 2008. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452:340-343.
20. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, et al. 2008. Functional metagenomic profiling of nine biomes. Nature 455:830.
21. Djikeng A, Kuzmickas R, Anderson NG, Spiro DJ. 2009. Metagenomic analysis of RNA viruses in a fresh water lake. PLoS ONE. 4:e7264.
22. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. 2005. Diversity of the human intestinal microbial flora. Science 308:1635-1638.
23. Edwards R, Rohwer F. 2005. Viral metagenomics. Nat. Rev. Microbiol. 3:504-510.
24. Feng H, Shuda M, Chang Y, Moore PS. 2008. Clonal integration of a polyomavirus in human Merkel cell carcinoma. Science 319:1096-1100.
25. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, et al. 2007. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Appl. Environ. Microbiol. 73:7059-7066.
26. Finkbeiner SR, Allred AF, Tarr PI, Klein EJ, Kirkwood CD, et al. 2008. Metagenomic analysis of human diarrhea: Viral detection and discovery. PLoS Pathog. 4:e1000011.
27. Furuse K, Osawa S, Kawashiro J, Tanaka R, Ozawa A, et al. 1983. Bacteriophage distribution in human faeces: Continuous survey of healthy subjects and patients with internal and leukaemic diseases. J. Gen. Virol. 64(Pt 9): 2039-2043.
28. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, et al. 2006. Metagenomic analysis of the human distal gut microbiome. Science 312:1355-13559.
29. Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM. 1998. Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products. Chem. Biol. 5:R245-R249.
30. Kempe S, Kazmierczak J, Landmann G, Konuk T, Reimer A, et al. 1991. Largest known microbialites discovered in Lake Van, Turkey. Nature 349:605-608.
31. Kim K-H, Chang H-W, Nam Y-D, Roh SW, Kim M-S, et al. 2008. Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Appl. Environ. Microbiol. 74:5975-5985.
32. Lapidot M, Friedmann M, Pilowsky M, Ben-Joseph R, Cohen S. 2001. Effect of host plant resistance to tomato yellow leaf curl virus (TYLCV) on virus acquisition and transmission by its whitefly vector. Phytopathology 91:1209-1213.
33. 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. 84:1674-1682.
34. Lindell D, Sullivan MB, Johnson ZI, Tolonen AC, Rohwer F, et al. 2004. Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proc. Natl. Acad. Sci. USA 101:11013-11018.
35. Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm, SW. 2005. Photosynthesis genes in marine viruses yield proteins during host infection. Nature 438:86-89.
36. Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, et al. 2007. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature 449:83-86.
37. Lopez-Bueno A, Tamames J, Velazquez D, Moya A, Quesada A, et al. 2009. High diversity of the viral community from an Antarctic lake. Science 326:858-861.
38. Mann NH. 2005. The third age of phage. PLoS Biol. 3:753-755.
39. Mann NH, Cook A, Millard A, Bailey S, Clokie M. 2003. Marine ecosystems: Bacterial photosynthesis genes in a virus. Nature 424:741.
40. Mann NH, Clokie MRJ, Millard A, Cook A, Wilson WH, et al. 2005. The genome of S-PM2, a "photosynthetic" T4-type bacteriophage that infects marine Synechococcus strains. J. Bacteriol. 187:3188-3200.
41. McDaniel L, Breitbart M, Mobberley J, Long A, Haynes M, et al. 2008. Metagenomic analysis of lysogeny in Tampa Bay: Implications for prophage gene expression. PLoS ONE 3:e3263.
42. Nakamura S, Yang CS, Sakon N, Ueda M, Tougan T, et al. 2009. Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS ONE 4:e4219.
43. Ng TFF, Manire C, Borrowman K, Langer T, Ehrhart L, et al. 2009a. Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics. J. Virol. 83:2500-2509.
44. Ng TFF, Suedmeyer WK, Wheeler E, Gulland F, Breitbart M. 2009b. Novel anellovirus discovered from a mortality event of captive California sea lions. J. Gen. Virol. 90:1256-1261.
45. Palacios G, Druce J, Du L, Tran T, Birch C, et al. 2008. A new arenavirus in a cluster of fatal transplant-associated diseases. N. Engl. J. Med. 358:991-998.
46. Porter K, Russ BE, Dyall-Smith ML. 2007. Virus-host interactions in salt lakes. Curr. Opin. Microbiol. 10:418-424.
47. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59-65.
48. Rodriguez-Brito B, Li L, Wegley L, Furlan M, Angly F, et al. 2010. Viral and microbial community dynamics in four aquatic environments. ISME J. 739-751.
49. Rohwer F, Thurber RV. 2009. Viruses manipulate the marine environment. Nature 459:207-212.
50. Schoenfeld T, Patterson M, Richardson PM, Wommack KE, Young M, et al. 2008. Assembly of viral metagenomes from yellowstone hot springs. Appl. Environ. Microbiol. 74:4164-4174.
51. Sharon I, Tzahor S, Williamson S, Shmoish M, Man-Aharonovich D, et al. 2007. Viral photosynthetic reaction center genes and transcripts in the marine environment. ISME J. 1:492-501.
52. Sharon I, Alperovitch A, Rohwer F, Haynes M, Glaser F, et al. 2009. Photosystem I gene cassettes are present in marine virus genomes. Nature 461:258-262.
53. Sullivan MB, Waterbury JB, Chisholm SW. 2003. Cyanophages infecting the oceanic cyanobacterium Prochlorococcus. Nature 424:1047-1051.
54. Sullivan MB, Coleman ML, Weigele P, Rohwer F, Chisholm SW. 2005. Three Prochlorococcus cyanophage genomes: Signature features and ecological interpretations. PLoS Biol. 3:e144.
55. Sullivan MB, Lindell D, Lee JA, Thompson LR, Bielawski JP, et al. 2006. Prevalence and evolution of core photosystem II genes in marine cyanobacterial viruses and their hosts. PLoS Biol. 4:e234.
56. Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. 2009. Laboratory procedures to generate viral metagenomes. Nat. Protoc. 4:470-483.
57. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, et al. 2007. The human microbiome project. Nature 449:804-810.
58. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. 2009. A core gut microbiome in obese and lean twins. Nature 457:480-484.
59. Vega Thurber RL, Barott KL, Hall D, Liu H, Rodriguez-Mueller B, et al. 2008. Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proc. Natl. Acad. Sci. USA 105:18413-18418.
60. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74.
61. Vogel TM, Simonet P, Jansson JK, Hirsch PR, Tiedje JM, et al. 2009. TerraGenome: A consortium for the sequencing of a soil metagenome. Nat. Rev. Microbiol. 7:252-252.
62. Weigele PR, Pope WH, Pedulla ML, Houtz JM, Smith AL, et al. 2007. Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus. Environ. Microbiol. 9:1675-1695.
63. Whitman WB, Coleman DC, Wiebe WJ. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95:6578-83.
64. Williamson KE, Wommack KE, Radosevich M. 2003. Sampling natural viral communities from soil for culture-independent analyses. Appl. Environ. Microbiol. 69:6628-6633.
65. Williamson SJ, Cary SC, Williamson KE, Helton RR, Bench SR, et al. 2008a. Lysogenic virus-host interactions predominate at deepsea diffuse-flow hydrothermal vents. ISME J. 2:1112-1121.
66. Williamson SJ, Rusch DB, Yooseph S, Halpern AL, Heidelberg KB, et al. 2008b. The Sorcerer II Global Ocean Sampling Expedition: Metagenomic characterization of viruses within aquatic microbial samples. PLoS ONE 3:e1456.
67. Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, et al. 2009. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS ONE 4:e7370.
68. Wommack KE, Bhavsar J, Ravel J. 2008. Metagenomics: Read length matters. Appl. Environ. Microbiol. 74:1453-1463.
69. Zhang T, Breitbart M, Lee WH, Run JQ, Wei CL, et al. 2006. RNA viral community in human feces: Prevalence of plant pathogenic viruses. PLoS Biol. 4:108-118.