Metagenomic analysis of RNA viruses in a fresh water lake

PLoS ONE

Volumn 4, Issue 9, 2009, Pages

  Djikeng, Appolinaire ^a   Kuzmickas, Ryan ^a   Anderson, Norman G ^b   Spiro, David J ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b Viral Defense Foundation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; ENDEMIC DISEASE; FEVER; HONEYBEE; LAKE ECOSYSTEM; METAGENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; RNA VIRUS; UNITED STATES; VIRAL GENETICS; VIRUS CELL INTERACTION; VIRUS IDENTIFICATION; VIRUS INFECTIVITY; VIRUS TRANSMISSION; COMPUTER PROGRAM; ECOLOGY; GENETIC DATABASE; GENETIC PROCEDURES; GENETIC VARIABILITY; GENETICS; MICROBIOLOGY; PHYLOGENY; SEQUENCE ALIGNMENT; VIROLOGY; VIRUS GENOME;

ACUTE BEE PARALYSIS VIRUS; ADENOVIRIDAE; ANIMALIA; APIS MELLIFERA; AVES; BANNA VIRUS; COXSACKIEVIRUS; DSRNA VIRUSES; ECHOVIRUS; HEXAPODA; INFLUENZA A VIRUS; NORWALK VIRUS; RNA VIRUSES;

FRESH WATER;

DATABASES, GENETIC; ECOLOGY; FRESH WATER; GENETIC TECHNIQUES; GENETIC VARIATION; GENOME, VIRAL; MARYLAND; PHYLOGENY; RNA VIRUSES; SEQUENCE ALIGNMENT; SOFTWARE; WATER MICROBIOLOGY;

EID: 70349675587     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007264     Document Type: Article

References (35)

1. Edwards RA, Rohwer F (2005) Viral metagenomics. Nat Rev Microbiol 3: 504-510.
2. 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.
3. 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: e3.
4. 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.
5. 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.
6. Culley AI, Lang AS, Suttle CA (2003) High diversity of unknown picorna-like viruses in the sea. Nature 424: 1054-1057.
7. Culley AI, Lang AS, Suttle CA (2007) The complete genomes of three viruses assembled from shotgun libraries of marine RNA virus communities. Virol J 4: 69.
8. Culley AI, Lang AS, Suttle CA (2006) Metagenomic analysis of coastal RNA virus communities. Science 312: 1795-1798.
9. Breitbart M, Rohwer F (2005) Here a virus, there a virus, everywhere the same virus? Trends Microbiol 13: 278-284.
10. Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, et al. (2006) The marine viromes of four oceanic regions. PLoS Biol 4: e368.
11. Short CM, Suttle CA (2005) Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl Environ Microbiol 71: 480-486.
12. Breitbart M, Miyake JH, Rohwer F (2004) Global distribution of nearly identical phage-encoded DNA sequences. FEMS Microbiol Lett 236: 249-256.
13. Watanabe RA, Fryer JL, Rohovec JS (1988) Molecular filtration for recovery of waterborne viruses of fish. Appl Environ Microbiol 54: 1606-1609.
14. Djikeng A, Halpin R, Kuzmickas R, Depasse J, Feldblyum J, et al. (2008) Viral genome sequencing by random priming methods. BMC Genomics 9: 5.
15. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
16. Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, et al. (2008) Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE 3: e2836.
17. Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17: 377-386.
18. Goldberg SM, Johnson J, Busam D, Feldblyum T, Ferriera S, et al. (2006) A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci U S A 103: 11240-11245.
19. Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M (2007) CAMERA: a community resource for metagenomics. PLoS Biol 5: e75.
20. Williamson SJ, Rusch DB, Yooseph S, Halpern AL, Heidelberg KB, et al. (2008) The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples. PLoS ONE 3: e1456.
21. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5: e77.
22. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
23. Tringe SG, von MC, Kobayashi A, Salamov AA, Chen K, et al. (2005) Comparative metagenomics of microbial communities. Science 308: 554-557.
24. Bench SR, Hanson TE, Williamson KE, Ghosh D, Radosovich M, et al. (2007) Metagenomic characterization of Chesapeake Bay virioplankton. Appl Environ Microbiol 73: 7629-7641.
25. Garcia MH, Ivanova N, Kunin V, Warnecke F, Barry KW, et al. (2006) Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol 24: 1263-1269.
26. Martin-Cuadrado AB, Lopez-Garcia P, Alba JC, Moreira D, Monticelli L, et al. (2007) Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS ONE 2: e914.
27. Nabeshima T, Thi NP, Guillermo P, Parquet MC, Yu F, et al. (2008) Isolation and molecular characterization of Banna virus from mosquitoes, Vietnam. Emerg Infect Dis 14: 1276-1279.
28. Chen B, Tao S (1996) Arbovirus survey in China in recent ten years. Chin Med J (Engl) 109: 13-15.
29. de Miranda Jr, Drebot M, Tyler S, Shen M, Cameron CE, et al. (2004) Complete nucleotide sequence of Kashmir bee virus and comparison with acute bee paralysis virus. J Gen Virol 85: 2263-2270.
30. Van MM, Dullemans AM, Verbeek M, Van Den Heuvel JF, Clerivet A, et al. (2002) Sequence analysis and genomic organization of Aphid lethal paralysis virus: a new member of the family Dicistroviridae. J Gen Virol 83: 3131-3138.
31. Allan GM, Ellis JA (2000) Porcine circoviruses: a review. J Vet Diagn Invest 12: 3-14.
32. Biagini P (2004) Human circoviruses. Vet Microbiol 98: 95-101.
33. Cox-Foster DL, Conlan S, Holmes EC, Palacios G, Evans JD, et al. (2007) A metagenomic survey of microbes in honey bee colony collapse disorder. Science 318: 283-287.
34. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, et al. (2003) Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 185: 6220-6223.
35. Bench SR, Hanson TE, Williamson KE, Ghosh D, Radosovich M, et al. (2007) Metagenomic characterization of Chesapeake Bay virioplankton. Appl Environ Microbiol 73: 7629-7641.