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Science 1 December 2006:
Vol. 314. no. 5804, pp. 1464 - 1467
DOI: 10.1126/science.1131370
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Reports

Microfluidic Digital PCR Enables Multigene Analysis of Individual Environmental Bacteria

Elizabeth A. Ottesen,1 Jong Wook Hong,2 Stephen R. Quake,3 Jared R. Leadbetter4*

Gene inventory and metagenomic techniques have allowed rapid exploration of bacterial diversity and the potential physiologies present within microbial communities. However, it remains nontrivial to discover the identities of environmental bacteria carrying two or more genes of interest. We have used microfluidic digital polymerase chain reaction (PCR) to amplify and analyze multiple, different genes obtained from single bacterial cells harvested from nature. A gene encoding a key enzyme involved in the mutualistic symbiosis occurring between termites and their gut microbiota was used as an experimental hook to discover the previously unknown ribosomal RNA–based species identity of several symbionts. The ability to systematically identify bacteria carrying a particular gene and to link any two or more genes of interest to single species residing in complex ecosystems opens up new opportunities for research on the environment.

1 Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
2 Materials Research and Education Center, Samuel Ginn College of Engineering, Auburn University, Auburn, AL 36849, USA.
3 Department of Bioengineering and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
4 Environmental Science and Engineering Program, California Institute of Technology, Pasadena, CA 91125, USA.

* To whom correspondence should be addressed. E-mail: jleadbetter{at}caltech.edu

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THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
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Nucleic Acids Res. 36, 4689-4698
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Planktonic and Sediment-Associated Aerobic Methanotrophs in Two Seep Systems along the North American Margin.
P. L. Tavormina, W. Ussler III, and V. J. Orphan (2008)
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From the Cover: Digital PCR for the molecular detection of fetal chromosomal aneuploidy.
Y. M. D. Lo, F. M. F. Lun, K. C. A. Chan, N. B. Y. Tsui, K. C. Chong, T. K. Lau, T. Y. Leung, B. C. Y. Zee, C. R. Cantor, and R. W. K. Chiu (2007)
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Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time.
R. Stepanauskas and M. E. Sieracki (2007)
PNAS 104, 9052-9057
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Science. ISSN 0036-8075 (print), 1095-9203 (online)