Diversity and abundance of single-stranded DNA viruses in human feces

Applied and Environmental Microbiology

Volumn 77, Issue 22, 2011, Pages 8062-8070

  Kim, Min Soo ^a   Park, Eun Jin ^a   Roh, Seong Woon ^a   Bae, Jin Woo ^a  

^a Kyung Hee University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

454-PYROSEQUENCING; AQUATIC ENVIRONMENTS; BACTEROIDES; CAPSID PROTEINS; CONTIGS; DOUBLE STRANDED DNA; FECAL SAMPLES; HEALTHY INDIVIDUALS; HIGH-THROUGHPUT; HUMAN FECAL; HUMAN FECES; PHYLOGENETIC ANALYSIS; PREVOTELLA; PUBLIC DATABASE; SINGLE-STRANDED DNA; SINGLE-STRANDED DNA (SS-DNA); ULTRACENTRIFUGATION; VIRAL DNA;

CENTRIFUGATION; DNA;

VIRUSES;

SINGLE STRANDED DNA; VIRUS DNA;

ABUNDANCE; AQUATIC ENVIRONMENT; BACTERIUM; DATABASE; DNA; FECES; FILTRATION; INFECTIVITY; MOLECULAR ANALYSIS; PHYLOGENETICS; PROTEIN; PUBLIC HEALTH; SPECIES DIVERSITY; VIRUS;

ARTICLE; BIODIVERSITY; CLUSTER ANALYSIS; DENSITY GRADIENT CENTRIFUGATION; DNA SEQUENCE; DNA VIRUS; FECES; FILTRATION; GENETICS; HUMAN; ISOLATION AND PURIFICATION; NUCLEIC ACID AMPLIFICATION; PHYLOGENY; SEQUENCE HOMOLOGY; VIROLOGY; VIRUS LOAD;

BIODIVERSITY; CENTRIFUGATION, DENSITY GRADIENT; CLUSTER ANALYSIS; DNA VIRUSES; DNA, SINGLE-STRANDED; DNA, VIRAL; FECES; FILTRATION; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; VIRAL LOAD;

EID: 83055177100     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.06331-11     Document Type: Article

References (67)

1. Angly, F. E., et al. 2006. The marine viromes of four oceanic regions. PLoS Biol. 4:e368.
2. Ashelford, K. E., M. J. Day, and J. C. Fry. 2003. Elevated abundance of bacteriophage infecting bacteria in soil. Appl. Environ. Microbiol. 69:285-289.
3. Baker, G. C., J. J. Smith, and D. A. Cowan. 2003. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 55:541-555.
4. Breitbart, M., et al. 2008. Viral diversity and dynamics in an infant gut. Res. Microbiol. 159:367-373.
5. Breitbart, M., et al. 2003. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185:6220-6223.
6. Breitbart, M., and F. Rohwer. 2005. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13:278-284.
7. Canchaya, C., G. Fournous, S. Chibani-Chennoufi, M. L. Dillmann, and H. Brussow. 2003. Phage as agents of lateral gene transfer. Curr. Opin. Microbiol. 6:417-424.
8. Cole, J. R., et al. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37:D141-D145.
9. Danovaro, R., E. Manini, and A. Dell'Anno. 2002. Higher abundance of bacteria than of viruses in deep Mediterranean sediments. Appl. Environ. Microbiol. 68:1468-1472.
10. Danovaro, R., and M. Serresi. 2000. Viral density and virus-to-bacterium ratio in deep-sea sediments of the eastern Mediterranean. Appl. Environ. Microbiol. 66:1857-1861.
11. De Filippo, C., et al. 2010. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. U. S. A. 107:14691-14696.
12. Desnues, C., et al. 2008. Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 452:340-343.
13. Dethlefsen, L., S. Huse, M. L. Sogin, and D. A. Relman. 2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6:e280.
14. Dinsdale, E. A., et al. 2008. Functional metagenomic profiling of nine biomes. Nature 452:629-632.
15. Drake, L. A., K. H. Choi, A. G. Edward Haskell, and F. C. Dobbs. 1998. Vertical profiles of virus-like particles and bacteria in the water column and sediments of Chesapeake Bay, U. S. A. Aquatic Microb. Ecol. 16:17-25.
16. Edwards, R. A., and F. Rohwer. 2005. Viral metagenomics. Nat. Rev. Microbiol. 3:504-510.
17. Frank, D. N., et al. 2007. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. U. S. A. 104:13780-13785.
18. Gomez-Alvarez, V., T. K. Teal, and T. M. Schmidt. 2009. Systematic artifacts in metagenomes from complex microbial communities. ISME J. 3:1314-1317.
19. Hall, T. A. 1999. BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
20. Hehemann, J. H., et al. 2010. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464:908-912.
21. Helton, R. R., L. Liu, and K. E. Wommack. 2006. Assessment of factors influencing direct enumeration of viruses within estuarine sediments. Appl. Environ. Microbiol. 72:4767-4774.
22. Huson, D. H., A. F. Auch, J. Qi, and S. C. Schuster. 2007. MEGAN analysis of metagenomic data. Genome Res. 17:377-386.
23. Kim, K. H., et al. 2008. Amplification of uncultured single-stranded DNA viruses from rice paddy soil. Appl. Environ. Microbiol. 74:5975-5985.
24. Kristensen, D. M., A. R. Mushegian, V. V. Dolja, and E. V. Koonin. 2010. New dimensions of the virus world discovered through metagenomics. Trends Microbiol. 18:11-19.
25. Larsen, N., et al. 2010. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 5:e9085.
26. Lepage, P., et al. 2008. Dysbiosis in inflammatory bowel disease: a role for bacteriophages? Gut 57:424-425.
27. Ley, R. E., D. A. Peterson, and J. I. Gordon. 2006. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124:837-848.
28. López-Bueno, A., et al. 2009. High diversity of the viral community from an Antarctic lake. Science 326:858-861.
29. Lozupone, C. A., et al. 2008. The convergence of carbohydrate active gene repertoires in human gut microbes. Proc. Natl. Acad. Sci. U. S. A. 105: 15076-15081.
30. Maslowski, K. M., et al. 2009. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature 461:1282-1286.
31. Morowitz, M. J., et al. 2011. Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc. Natl. Acad. Sci. U. S. A. 108:1128-1133.
32. Nelson, K. E., et al. 2010. A catalog of reference genomes from the human microbiome. Science 328:994-999.
33. Niu, B., L. Fu, S. Sun, and W. Li. 2010. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics 11:187.
34. Park, E. J., et al. 2010. Metagenomic analysis of the viral community in fermented Foods. Appl. Environ. Microbiol. 77:1284-1291.
35. Patel, A., et al. 2007. Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nat. Protoc. 2:269-276.
36. Polz, M. F., and C. M. Cavanaugh. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64:3724-3730.
37. Qin, J., et al. 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59-65.
38. Reyes, A., et al. 2010. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466:334-338.
39. Roberts, A. P., et al. 2008. Revised nomenclature for transposable genetic elements. Plasmid 60:167-173.
40. Rohwer, F., D. Prangishvili, and D. Lindell. 2009. Roles of viruses in the environment. Environ. Microbiol. 11:2771-2774.
41. Roossinck, M. J. 2011. The good viruses: viral mutualistic symbioses. Nat. Rev. Microbiol. 9:99-108.
42. Rosario, K., C. Nilsson, Y. W. Lim, Y. Ruan, and M. Breitbart. 2009. Metagenomic analysis of viruses in reclaimed water. Environ. Microbiol. 11:2806-2820.
43. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
44. Schloss, P. D., et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541.
45. Sokol, H., et al. 2008. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl. Acad. Sci. U. S. A. 105:16731-16736.
46. Suttle, C. A. 2007. Marine viruses-major players in the global ecosystem. Nat. Rev. Microbiol. 5:801-812.
47. Suttle, C. A. 1994. The significance of viruses to mortality in aquatic microbial communities. Microb. Ecol. 28:237-243.
48. Tamames, J., and A. Moya. 2008. Estimating the extent of horizontal gene transfer in metagenomic sequences. BMC Genomics 9:136.
49. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
50. Tap, J., et al. 2009. Towards the human intestinal microbiota phylogenetic core. Environ. Microbiol. 11:2574-2584.
51. Tasse, L., et al. 2010. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res. 20:1605-1612.
52. Thompson, J. R., L. A. Marcelino, and M. F. Polz. 2002. Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR.' Nucleic Acids Res. 30:2083-2088.
53. Thurber, R. V. 2009. Current insights into phage biodiversity and biogeography. Curr. Opin. Microbiol. 12:582-587.
54. Thurber, R. V., M. Haynes, M. Breitbart, L. Wegley, and F. Rohwer. 2009. Laboratory procedures to generate viral metagenomes. Nat. Protoc. 4:470-483.
55. Tucker, K. P., R. Parsons, E. M. Symonds, and M. Breitbart. 2010. Diversity and distribution of single-stranded DNA phages in the North Atlantic Ocean. ISME J. 5:822-830.
56. Turnbaugh, P. J., et al. 2007. The human microbiome project. Nature 449: 804-810.
57. Turnbaugh, P. J., et al. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027-1031.
58. Wang, X., et al. 2010. Cryptic prophages help bacteria cope with adverse environments. Nat. Commun. 1:147.
59. Weinbauer, M. G. 2004. Ecology of prokaryotic viruses. FEMS Microbiol. Rev. 28:127-181.
60. Wen, L., et al. 2008. Innate immunity and intestinal microbiota in the development of type 1 diabetes. Nature 455:1109-1113.
61. Wilhelm, S. W., and C. A. Suttle. 1999. Viruses and nutrient cycles in the sea. Bioscience 49:781-788.
62. Willner, D., et al. 2009. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS One 4:e7370.
63. Wommack, K. E., and R. R. Colwell. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64:69-114.
64. Xu, J., et al. 2007. Evolution of symbiotic bacteria in the distal human intestine. Plos Biol. 5:e156.
65. Yooseph, S., et al. 2007. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. Plos Biol. 5:e16.
66. Yu, Z., and M. Morrison. 2004. Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36:808-812.
67. Zhang, T., et al. 2006. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 4:0108-0118.