Genomic sequencing of single microbial cells from environmental samples

Current Opinion in Microbiology

Volumn 11, Issue 3, 2008, Pages 198-204

  Ishoey, Thomas ^a   Woyke, Tanja ^b   Stepanauskas, Ramunas ^c   Novotny, Mark ^a   Lasken, Roger S ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b DOE JOINT GENOME INSTITUTE   (United States)

^c BIGELOW LABORATORY FOR OCEAN SCIENCES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

CELL ISOLATION; DNA SEQUENCE; GENE AMPLIFICATION; GENE SEQUENCE; GENOTYPE; REVIEW;

BACTERIA; GENOMICS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 45849153461     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2008.05.006     Document Type: Review

References (50)

1. Rappe M.S., and Giovannoni S.J. The uncultured microbial majority. Annu Rev Microbiol 57 (2003) 369-394
2. Amann R.I., Ludwig W., and Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59 (1995) 143-169
3. Olsen G.J., Lane D.J., Giovannoni S.J., Pace N.R., and Stahl D.A. Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40 (1986) 337-365
4. Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D., Paulsen I., Nelson K.E., Nelson W., et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 (2004) 66-74
5. Tringe S.G., von Mering C., Kobayashi A., Salamov A.A., Chen K., Chang H.W., Podar M., Short J.M., Mathur E.J., Detter J.C., et al. Comparative metagenomics of microbial communities. Science 308 (2005) 554-557
6. Beja O., Aravind L., Koonin E.V., Suzuki M.T., Hadd A., Nguyen L.P., Jovanovich S.B., Gates C.M., Feldman R.A., Spudich J.L., et al. Bacterial rhodops: evidence for a new type of phototrophy in the sea. Science 289 (2000) 1902-1906
7. Rusch D.B., Halpern A.L., Sutton G., Heidelberg K.B., Williamson S., Yooseph S., Wu D., Eisen J.A., Hoffman J.M., Remington K., et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5 (2007) e77
8. DeLong E.F., Preston C.M., Mincer T., Rich V., Hallam S.J., Frigaard N.U., Martinez A., Sullivan M.B., Edwards R., Brito B.R., et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311 (2006) 496-503
9. Hallam S.J., Konstantinidis K.T., Putnam N., Schleper C., Watanabe Y-i, Sugahara J., Preston C., de la Torre J., Richardson P.M., and DeLong E.F. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc Natl Acad Sci 103 (2006) 18296-18301
10. Tyson G.W., Chapman J., Hugenholtz P., Allen E.E., Ram R.J., Richardson P.M., Solovyev V.V., Rubin E.M., Rokhsar D.S., and Banfield J.F. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428 (2004) 37-43
11. Woyke T., Teeling H., Ivanova N.N., Hunteman M., Richter M., Gloeckner F.O., Boffelli D., Anderson I.J., Barry K.W., Shapiro H.J., et al. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature (2006)
12. Lasken R.S. Single-cell genomic sequencing using multiple displacement amplification. Curr Opin Microbiol 10 (2007) 510-516
13. Dean F.B., Hosono S., Fang L., Wu X., Faruqi A.F., Bray-Ward P., Sun Z., Zong Q., Du Y., Du J., et al. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci U S A 99 (2002) 5261-5266
14. Dean F.B., Nelson J.R., Giesler T.L., and Lasken R.S. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 11 (2001) 1095-1099
15. Hosono S., Faruqi A.F., Dean F.B., Du Y., Sun Z., Wu X., Du J., Kingsmore S.F., Egholm M., and Lasken R.S. Unbiased whole-genome amplification directly from clinical samples. Genome Res 13 (2003) 954-964
16. Raghunathan A., Ferguson Jr. H.R., Bornarth C.J., Song W., Driscoll M., and Lasken R.S. Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71 (2005) 3342-3347
17. Lasken R.S., Raghunathan A., Kvist T., Ishoey T., Westermann P., Ahring B.K., and Boissy R. Multiple displacement amplification from single bacterial cells. In: Hughes S., and Lasken R.S. (Eds). Whole Genome Amplification (2005), Scion Publishing Ltd. 119-147 Methods Express
18. Kvist T., Ahring B.K., Lasken R.S., and Westermann P. Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl Microbiol Biotechnol (2006)
19. Zhang K., Martiny A.C., Reppas N.B., Barry K.W., Malek J., Chisholm S.W., and Church G.M. Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24 (2006) 680-686
20. Marcy Y., Ouverney C., Bik E.M., Losekann T., Ivanova N., Martin H.G., Szeto E., Platt D., Hugenholtz P., Relman D.A., et al. Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci (2007) 0704662104
21. Podar M., Abulencia C.B., Walcher M., Hutchison D., Zengler K., Garcia J.A., Holland T., Cotton D., Hauser L., and Keller M. Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl Environ Microbiol 73 (2007) 3205-3214
22. Mussmann M., Hu F.Z., Richter M., de Beer D., Preisler A., Jorgensen B.B., Huntemann M., Glockner F.O., Amann R., Koopman W.J., et al. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol 5 (2007) e230
23. Stepanauskas R., and Sieracki M.E. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc Natl Acad Sci 104 (2007) 9052-9057
24. Giovannoni S.J., DeLong E.F., Schmidt T.M., and Pace N.R. Tangential flow filtration and preliminary phylogenetic analysis of marine picoplankton. Appl Environ Microbiol 56 (1990) 2572-2575
25. Shiomori T., Miyamoto H., Makishima K., Yoshida M., Fujiyoshi T., Udaka T., Inaba T., and Hiraki N. Evaluation of bedmaking-related airborne and surface methicillin-resistant Staphylococcus aureus contamination. J Hosp Infect 50 (2002) 30-35
26. Groschel D.H.M. Air sampling in hospitals. Ann N Y Acad Sci 353 (1980) 230-240
27. Andersen A.A. New sampler for the collection, sizing, and enumeration of viable airborne particles. J Bacteriol 76 (1958) 471-484
28. Omberg K., and Stentzenbach L. Indoor and outdoor air sampling. In: Emanuel P., Roos J.W., and Niyogi K. (Eds). Sampling for Biological Agents in the Environment (2008), ASM Press 133-164
29. Lin X., Reponen T., Willeke K., Grinshpun S.A., Foarde K.K., and Ensor D.S. Long-term sampling of airborne bacteria and fungi into a non-evaporating liquid. Atmos Environ 33 (1999) 4291-4298
30. Lin X., Reponen T., Willeke K., Wang Z., Grinshpun S.A., and Trunov M. Survival of airborne microorganisms during swirling aerosol collection. Aerosol Sci Technol 32 (2000) 184-196
31. Ishoy T., Kvist T., Westermann P., and Ahring B.K. An improved method for single cell isolation of prokaryotes from meso-, thermo- and hyperthermophilic environments using micromanipulation. Appl Microbiol Biotechnol 69 (2006) 510-514
32. Marcy Y., Ishoey T., Lasken R.S., Stockwell T.B., Walenz B.P., Halpern A.L., Beeson K.Y., Goldberg S.M.D., and Quake S.R. Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet 3 (2007) e155
33. Sekar R., Fuchs B.M., Amann R., and Pernthaler J. Flow sorting of marine bacterioplankton after fluorescence in situ hybridization. Appl Environ Microbiol 70 (2004) 6210-6219
34. Wallner G., Fuchs B., Spring S., Beisker W., and Amann R. Flow sorting of microorganisms for molecular analysis. Appl Environ Microbiol 63 (1997) 4223-4231
35. Huber R., Huber H., and Stetter K.O. Towards the ecology of hyperthermophiles: biotopes, new isolation strategies and novel metabolic properties. FEMS Microbiol Rev 24 (2000) 615-623
36. Jahn U., Gallenberger M., Paper W., Junglas B., Eisenreich W., Stetter K.O., Rachel R., and Huber H. Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique, intimate association of two archaea. J Bacteriol 190 (2008) 1743-1750
37. Karlin S., Campbell A.M., and Mrazek J. Comparative DNA analysis across diverse genomes. Annu Rev Genet 32 (1998) 185-225
38. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J Mol Biol 215 (1990) 403-410
39. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 (2005) 376-380
40. Bennett S. Solexa Ltd. Pharmacogenomics 5 (2004) 433-438
41. Lasken R.S., and Stockwell T.B. Mechanism of chimera formation during the multiple displacement amplification reaction. BMC Biotechnol 7 (2007) 19
42. Inoue J., Shigemori Y., and Mikawa T. Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein. Nucleic Acids Res 34 (2006) e69
43. Wu L., Liu X., Schadt C.W., and Zhou J. Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol 72 (2006) 4931-4941
44. Hongoh Y., Sharma V.K., Prakash T., Noda S., Taylor T.D., Kudo T., Sakaki Y., Toyoda A., Hattori M., and Ohkuma M. Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell. Proc Natl Acad Sci 105 (2008) 5555-5560
45. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., et al. The sequence of the human genome. Science 291 (2001) 1304-1351
46. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., et al. Initial sequencing and analysis of the human genome. Nature 409 (2001) 860-921
47. Levy S., Sutton G., Ng P.C., Feuk L., Halpern A.L., Walenz B.P., Axelrod N., Huang J., Kirkness E.F., Denisov G., et al. The diploid genome sequence of an individual human. PLoS Biol 5 (2007) e254
48. Coleman M.L., Sullivan M.B., Martiny A.C., Steglich C., Barry K., Delong E.F., and Chisholm S.W. Genomic islands and the ecology and evolution of Prochlorococcus. Science 311 (2006) 1768-1770
49. Attie O., Bruno J.F., Xu Y., Qiu D., Luft B.J., and Qiu W.G. Co-evolution of the outer surface protein C gene (ospC) and intraspecific lineages of Borrelia burgdorferi sensu stricto in the northeastern United States. Infect Genet Evol 7 (2007) 1-12
50. Glockner G., Schulte-Spechtel U., Schilhabel M., Felder M., Suhnel J., Wilske B., and Platzer M. Comparative genome analysis: selection pressure on the Borrelia vls cassettes is essential for infectivity. BMC Genomics 7 (2006) 211