Probing individual environmental bacteria for viruses by using microfluidic digital PCR

Science

Volumn 333, Issue 6038, 2011, Pages 58-62

  Tadmor, Arbel D ^a   Ottesen, Elizabeth A ^b   Leadbetter, Jared R ^a   Phillips, Rob ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; BACTERIUM; GENE TRANSFER; GENETIC MARKER; GENOMICS; MICROBIAL COMMUNITY; POLYMERASE CHAIN REACTION; PROBE; VIRUS;

ALLELE; ARTICLE; BACTERIAL CELL; ENVIRONMENT; GENE TRANSFER; ISOPTERA; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; MICROFLUIDIC ANALYSIS; MOLECULAR PROBE; NONHUMAN; ORGANISMAL INTERACTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; VIRUS CELL INTERACTION; VIRUS GENE;

ALLELES; AMINO ACID SEQUENCE; ANIMALS; BACTERIOPHAGES; ECOSYSTEM; ENDODEOXYRIBONUCLEASES; GENES, RRNA; GENES, VIRAL; GENETIC VARIATION; INTESTINES; ISOPTERA; MICROBIAL INTERACTIONS; MICROFLUIDIC ANALYTICAL TECHNIQUES; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; PROPHAGES; SEQUENCE ALIGNMENT; TREPONEMA;

BACTERIA (MICROORGANISMS); ISOPTERA;

EID: 79959855149     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1200758     Document Type: Article

References (41)

1. C. A. Suttle, Nat. Rev. Microbiol. 5, 801 (2007).
2. M. B. Sullivan et al., Environ. Microbiol. 12, 3035 (2010).
3. D. Lindell et al., Nature 449, 83 (2007).
4. F. E. Angly et al., PLoS Biol. 4, e368 (2006).
5. S. J. Williamson et al., PLoS ONE 3, e1456 (2008).
6. P. Hugenholtz, Genome Biol. 3, reviews0003 (2002).
7. R. A. Edwards, F. Rohwer, Nat. Rev. Microbiol. 3, 504 (2005).
8. E. A. Dinsdale et al., Nature 452, 629 (2008).
9. D. M. Kristensen, A. R. Mushegian, V. V. Dolja, E. V. Koonin, Trends Microbiol. 18, 11 (2010).
10. A. F. Andersson, J. F. Banfield, Science 320, 1047 (2008).
11. R. N. Zare, S. Kim, Annu. Rev. Biomed. Eng. 12, 187 (2010).
12. E. A. Ottesen, J. W. Hong, S. R. Quake, J. R. Leadbetter, Science 314, 1464 (2006).
13. Y. Marcy et al., Proc. Natl. Acad. Sci. U.S.A. 104, 11889 (2007).
14. L. Warren, D. Bryder, I. L. Weissman, S. R. Quake, Proc. Natl. Acad. Sci. U.S.A. 103, 17807 (2006).
15. S. Dube, J. Qin, R. Ramakrishnan, PLoS ONE 3, e2876 (2008).
16. F. Rohwer, R. Edwards, J. Bacteriol. 184, 4529 (2002).
17. T. M. Rose et al., Nucleic Acids Res. 26, 1628 (1998).
18. Materials and methods are available as supporting material on Science Online.
19. Supporting text is available as supporting material on Science Online.
20. A. Tholen, B. Schink, A. Brune, FEMS Microbiol. Ecol. 24, 137 (1997).
21. Y. Hongoh, M. Ohkuma, T. Kudo, FEMS Microbiol. Ecol. 44, 231 (2003).
22. F. Warnecke et al., Nature 450, 560 (2007).
23. J. R. Leadbetter, T. M. Schmidt, J. R. Graber, J. A. Breznak, Science 283, 686 (1999).
24. T. G. Lilburn et al., Science 292, 2495 (2001).
25. S. D. Moore, P. E. Prevelige Jr., Curr. Biol. 12, R96 (2002).
26. V. B. Rao, M. Feiss, Annu. Rev. Genet. 42, 647 (2008).
27. S. Chai et al., J. Mol. Biol. 224, 87 (1992).
28. K. Eppler, E. Wyckoff, J. Goates, R. Parr, S. Casjens, Virology 183, 519 (1991).
29. S. Casjens, Mol. Microbiol. 49, 277 (2003).
30. M. S. Mitchell, S. Matsuzaki, S. Imai, V. B. Rao, Nucleic Acids Res. 30, 4009 (2002).
31. S. Sun et al., Cell 135, 1251 (2008).
32. K. D. Pruitt, T. Tatusova, D. R. Maglott, Nucleic Acids Res. 33, D501 (2005).
33. Percent identity was measured across 235 unambiguous aligned amino acids.
34. A. P. Martin, Appl. Environ. Microbiol. 68, 3673 (2002).
35. M. Hamady, C. Lozupone, R. Knight, ISME J. 4, 17 (2010).
36. S. R. Casjens et al., J. Bacteriol. 187, 1091 (2005).
37. N. Wolfe et al., Glob. Change Hum. Health 1, 10 (2000).
38. L. Moore, G. Rocap, S. Chisholm, Nature 393, 465 (1998).
39. J. R. Thompson et al., Appl. Environ. Microbiol. 70, 4103 (2004).
40. S. G. Acinas, R. Sarma-Rupavtarm, V. Klepac-Ceraj, M. F. Polz, Appl. Environ. Microbiol. 71, 8966 (2005).
41. P. D. Schloss, J. Handelsman, Appl. Environ. Microbiol. 71, 1501 (2005).