Microfluidic digital PCR enables multigene analysis of individual environmental bacteria

Science

Volumn 314, Issue 5804, 2006, Pages 1464-1467

  Ottesen, Elizabeth A ^a   Jong, Wook Hong ^b   Quake, Stephen R ^c   Leadbetter, Jared R ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b AUBURN UNIVERSITY   (United States)

^c Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CELL CULTURE; ECOSYSTEMS; ENZYMES;

MICROBIOTA; RIBOSOMAL RNA-BASED SPECIES; SYMBIONTS;

GENETIC ENGINEERING;

BACTERIUM; BIODIVERSITY; GENETIC ANALYSIS; GENOMICS; MICROBIAL COMMUNITY; POLYMERASE CHAIN REACTION;

ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BACTERIUM IDENTIFICATION; BIODIVERSITY; ECOSYSTEM; GENETIC ANALYSIS; ISOPTERA; MICROFLORA; MICROFLUIDICS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SYMBIONT; SYMBIOSIS; TECHNIQUE;

ANIMALS; BACTERIA; DIGESTIVE SYSTEM; DNA, RIBOSOMAL; FLUORESCENT DYES; FORMATE-TETRAHYDROFOLATE LIGASE; GENES, BACTERIAL; GENES, RRNA; ISOPTERA; MICROFLUIDIC ANALYTICAL TECHNIQUES; MICROFLUIDICS; PHYLOGENY; POLYMERASE CHAIN REACTION; RIBOTYPING; RNA, RIBOSOMAL, 16S; SPIROCHAETALES; SYMBIOSIS; TREPONEMA;

BACTERIA (MICROORGANISMS); ISOPTERA;

EID: 33845342557     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1131370     Document Type: Article

References (40)

1. N. D. Gray, I. M. Head, Environ. Microbiol. 3, 481 (2001).
2. E. Zuckerkandl, L. Pauling, J. Theor. Biol. 8, 357 (1965).
3. P. Hugenholtz, B. M. Goebel, N. R. Pace, J. Bacteriol. 180, 4765 (1998).
4. S. J. Sogin, M. L. Sogin, C. R. Woese, J. Mol. Evol. 1, 173 (1971).
5. C. S. Riesenfeld, P. D. Schloss, J. Handelsman, Annu. Rev. Genet. 38, 525 (2004).
6. G. W. Tyson et al., Nature 428, 37 (2004).
7. M. Strous et al., Nature 440, 790 (2006).
8. S. G. Tringe et al., Science 308, 554 (2005).
9. J. C. Venter et al., Science 304, 66 (2004); published online 4 March 2004 (10.1126/science.1093857).
10. O. Béjà et al., Science 289, 1902 (2000).
11. J. L. Nielsen, D. Christensen, M. Kloppenborg, P. H. Nielsen, Environ. Microbiol. 5, 202 (2003).
12. M. Manefield, A. S. Whiteley, R. I. Griffiths, M. J. Bailey, Appl. Environ. Microbiol. 68, 2002 (2002).
13. R. I. Amann, W. Ludwig, K. H. Schleifer, Microbiol. Rev. 59, 143 (1995).
14. K. Zwirglmaier, W. Ludwig, K. H. Schleifer, Mol. Microbiol. 51, 89 (2004).
15. K. Zhang et al., Nat. Biotechnol. 24, 680 (2006).
16. B. Vogelstein, K. W. Kinzler, Proc. Natl. Acad. Sci. U.S.A. 96, 9236 (1999).
17. T. Thorsen, S. J. Maerkl, S. R. Quake, Science 298, S80 (2002); published online 26 September 2002 (10.1126/science.1076996).
18. J. W. Hong, S. R. Quake, Nat. Biotechnol. 21, 1179 (2003).
19. H. Pang, H. H. Winkler, J. Bacteriol. 175, 3893 (1993).
20. F. A. Rainey, N. L. Ward-Rainey, P. H. Janssen, H. Hippe, E. Stackebrandt, Microbiology 142, 2087 (1996).
21. S. G. Acinas, R. Sarma-Rupavtarm, V. Klepac-Ceraj, M. F. Polz, Appl. Environ. Microbiol. 71, 8966 (2005).
22. J. A. Breznak, J. M. Switzer, Appl. Environ. Microbiol. 52, 623 (1986).
23. A. Brauman, M. D. Kane, M. Labat, J. A. Breznak, Science 257, 1384 (1992).
24. D. A. Odelson, J. A. Breznak, Appl. Environ. Microbiol. 45, 1602 (1983).
25. A. Tholen, A. Brune, Environ. Microbiol. 2, 436 (2000).
26. L. G. Ljungdahl, Annu. Rev. Microbiol. 40, 415 (1986).
27. T. M. Salmassi, J. R. Leadbetter, Microbiology 149, 2529 (2003).
28. M. T. Suzuki, L. T. Taylor, E. F. DeLong, Appl. Environ. Microbiol. 66, 4605 (2000).
29. See supporting material on Science Online.
30. 1))/(1!) or 6.2%.
31. Value ± 1 standard deviation; 13 termites served as source of cells for n = 32 sample panels. All sample panels that met our conditions for single-cell separation and contained at least one FTHFS-positive chamber were used in calculation of gut bacterial loads.
32. M. Ohkuma, T. Kudo, Appl. Environ. Microbiol. 62, 461 (1996).
33. T. G. Lilburn, T. M. Schmidt, J. A. Sreznak, Environ. Microbiol. 1, 331 (1999).
34. J. A. Breznak, H. S. Pankratz, Appl. Environ. Microbiol. 33, 406 (1977).
35. J. R. Leadbetter, J. A. Breinak, Appl. Environ. Microbiol. 62, 3620 (1996).
36. The binomial distribution function was used to calculate the probability that, in 13 of 28 trials, a sequence that is present in 5% of chambers (0 of 20 165-only chambers) would randomly colocalize with clone H group FTHFS sequences.
37. J. R. Leadbetter, T. M. Schmidt, J. R. Graber, J. A. Breznak, Science 283, 686 (1999).
38. T. G. Lilburn et al., Science 292, 249S (2001).
39. H. A. Schmidt, K. Strimmer, M. Vingron, A. von Haeseler, Bioinformatics 18, S02 (2002).
40. We thank M. Unger, A. Daridon, and L. Warren for advice and discussions. Supported by NIH grant 1RO1 HG002644-01A1, NIH National Research Service Award grant 5 T32 GM07616, an NIH Director's Pioneer Award, and NSF grant DEB-0321753. S.R.Q. is a founder, shareholder, and consultant for Fluidigm Corporation.