Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR
Abstract
Viruses may very well be the most abundant biological entities on the planet. Yet neither metagenomic studies nor classical phage isolation techniques have shed much light on the identity of the hosts of most viruses. We used a microfluidic digital polymerase chain reaction (PCR) approach to physically link single bacterial cells harvested from a natural environment with a viral marker gene. When we implemented this technique on the microbial community residing in the termite hindgut, we found genus-wide infection patterns displaying remarkable intragenus selectivity. Viral marker allelic diversity revealed restricted mixing of alleles between hosts, indicating limited lateral gene transfer of these alleles despite host proximity. Our approach does not require culturing hosts or viruses and provides a method for examining virus-bacterium interactions in many environments.
Additional Information
© 2011 American Association for the Advancement of Science. Received 22 November 2010; accepted 16 May 2011. We wish to thank D. Baltimore, S. Casjens, D. S. Fisher, R. W. Hendrix, H. J. Lee, M. Lindén, E. G. Matson, R. Milo, V. J. Orphan, S. R. Quake, A. Z. Rosenthal, E. M. Rubin and colleagues at JGI, D. Z. Soghoian, N. D. Wolfe, D. Wu, X. Zhang, and the anonymous referees for their advice and feedback. We also wish to thank E.G.M. and A.Z.R for their assistance in collection of specimens and E.G.M. for ZAS genomic DNA. This project was supported by the NIH Director's Pioneer Award, NIH American Recovery and Reinvestment Act grant number R01 GM085286-01S, U.S. Department of Energy grant no. DE-FG02-07ER64484, and NSF grant nos. EF-0523267 and CMMI-0758343 and by the Davidow Family Research Fund. GenBank accession numbers are given in table S10.Attached Files
Accepted Version - nihms348964.pdf
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Additional details
- PMCID
- PMC3261838
- Eprint ID
- 24314
- DOI
- 10.1126/science.1200758
- Resolver ID
- CaltechAUTHORS:20110706-095349883
- NIH
- R01 GM085286-01S
- Department of Energy (DOE)
- DE-FG02-07ER64484
- NSF
- EF-0523267
- NSF
- CMMI-0758343
- Davidow Family Research Fund
- Created
-
2011-07-06Created from EPrint's datestamp field
- Updated
-
2023-10-23Created from EPrint's last_modified field
- Caltech groups
- Division of Geological and Planetary Sciences