Advanced sequencing technologies and their wider impact in microbiology

Journal of Experimental Biology - Tập 210 Số 9 - Trang 1518-1525 - 2007
Neil Hall1
1School of Biological Sciences, Biosciences Building, Crown Street,University of Liverpool, Liverpool L69 7ZB, UK

Tóm tắt

SUMMARYIn the past 10 years, microbiology has undergone a revolution that has been driven by access to cheap high-throughput DNA sequencing. It was not long ago that the cloning and sequencing of a target gene could take months or years,whereas now this entire process has been replaced by a 10 min Internet search of a public genome database. There has been no single innovation that has initiated this rapid technological change; in fact, the core chemistry of DNA sequencing is the same as it was 30 years ago. Instead, progress has been driven by large sequencing centers that have incrementally industrialized the Sanger sequencing method. A side effect of this industrialization is that large-scale sequencing has moved out of small research labs, and the vast majority of sequence data is now generated by large genome centers. Recently,there have been advances in technology that will enable high-throughput genome sequencing to be established in research labs using bench-top instrumentation. These new technologies are already being used to explore the vast microbial diversity in the natural environment and the untapped genetic variation that can occur in bacterial species. It is expected that these powerful new methods will open up new questions to genomic investigation and will also allow high-throughput sequencing to be more than just a discovery exercise but also a routine assay for hypothesis testing. While this review will concentrate on microorganisms, many of the important arguments about the need to measure and understand variation at the species, population and ecosystem level will hold true for many other biological systems.

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Tài liệu tham khảo

Bennett, S. (2004). Solexa Ltd. Pharmacogenomics5,433-438.

Bennett, S. T., Barnes, C., Cox, A., Davies, L. and Brown,C. (2005). Toward the 1,000 dollars human genome. Pharmacogenomics6,373-382.

Bertrand, H., Poly, F., Van, V. T., Lombard, N., Nalin, R.,Vogel, T. M. and Simonet, P. (2005). High molecular weight DNA recovery from soils prerequisite for biotechnological metagenomic library construction. J. Microbiol. Methods62, 1-11.

Blattner, F. R., Plunkett, G., III, Bloch, C. A., Perna, N. T.,Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K.,Mayhew, G. F. et al. (1997). The complete genome sequence of Escherichia coli K-12. Science277,1453-1474.

Braslavsky, I., Hebert, B., Kartalov, E. and Quake, S. R.(2003). Sequence information can be obtained from single DNA molecules. Proc. Natl. Acad. Sci. USA100,3960-3964.

Breitbart, M., Hewson, I., Felts, B., Mahaffy, J. M., Nulton,J., Salamon, P. and Rohwer, F. (2003). Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol.185,6220-6223.

Breitbart, M., Felts, B., Kelley, S., Mahaffy, J. M., Nulton,J., Salamon, P. and Rohwer, F. (2004). Diversity and population structure of a near-shore marine-sediment viral community. Proc. Biol. Sci.271,565-574.

Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D. H.,Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M. et al.(2000). Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol.18,630-634.

Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher,C., Harris, D., Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E., III et al. (1998). Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature393,537-544.

Culley, A. I., Lang, A. S. and Suttle, C. A.(2006). Metagenomic analysis of coastal RNA virus communities. Science312,1795-1798.

Curtis, T. P. and Sloan, W. T. (2005). Microbiology. Exploring microbial diversity – a vast below. Science309,1331-1333.

Curtis, T. P., Sloan, W. T. and Scannell, J. W.(2002). Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA99,10494-10499.

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. (2006). Community genomics among stratified microbial assemblages in the ocean's interior. Science311,496-503.

Edwards, R. A., Rodriguez-Brito, B., Wegley, L., Haynes, M.,Breitbart, M., Peterson, D. M., Saar, M. O., Alexander, S., Alexander, E. C.,Jr and Rohwer, F. (2006). Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics7, 57.

El-Sayed, N. M., Myler, P. J., Blandin, G., Berriman, M.,Crabtree, J., Aggarwal, G., Caler, E., Renauld, H., Worthey, E. A.,Hertz-Fowler, C. et al. (2005). Comparative genomics of trypanosomatid parasitic protozoa. Science309,404-409.

Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A.,Kirkness, E. F., Kerlavage, A. R., Bult, C. J., Tomb, J. F., Dougherty, B. A.,Merrick, J. M. et al. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science269,496-512.

Fukiya, S., Mizoguchi, H., Tobe, T. and Mori, H.(2004). Extensive genomic diversity in pathogenic Escherichia coli and Shigella strains revealed by comparative genomic hybridization microarray. J. Bacteriol.186,3911-3921.

Gans, J., Wolinsky, M. and Dunbar, J. (2005). Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science309,1387-1390.

Gardner, M. J., Hall, N., Fung, E., White, O., Berriman, M.,Hyman, R. W., Carlton, J. M., Pain, A., Nelson, K. E., Bowman, S. et al.(2002a). Genome sequence of the human malaria parasite Plasmodium falciparum.Nature419,498-511.

Gardner, M. J., Shallom, S. J., Carlton, J. M., Salzberg, S. L.,Nene, V., Shoaibi, A., Ciecko, A., Lynn, J., Rizzo, M., Weaver, B. et al.(2002b). Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature419,531-534.

Gill, S. R., Pop, M., Deboy, R. T., Eckburg, P. B., Turnbaugh,P. J., Samuel, B. S., Gordon, J. I., Relman, D. A., Fraser-Liggett, C. M. and Nelson, K. E. (2006). Metagenomic analysis of the human distal gut microbiome. Science312,1355-1359.

Goffeau, A., Aert, R., Agostini-Carbone, M. L., Ahmed, A.,Aigle, M., Alberghina, L., Albermann, K., Albers, M., Aldea, M., Alexandraki,D. et al. (1997). The yeast genome directory. Nature387(Suppl.),1-105.

Goldberg, S. M., Johnson, J., Busam, D., Feldblyum, T.,Ferriera, S., Friedman, R., Halpern, A., Khouri, H., Kravitz, S. A., Lauro, F. M. et al. (2006). A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc. Natl. Acad. Sci. USA103,11240-11245.

Hall, N., Pain, A., Berriman, M., Churcher, C., Harris, B.,Harris, D., Mungall, K., Bowman, S., Atkin, R., Baker, S. et al.(2002). Sequence of Plasmodium falciparum chromosomes 1,3-9 and 13. Nature419,527-531.

Hall, N., Karras, M., Raine, J. D., Carlton, J. M., Kooij, T. W., Berriman, M., Florens, L., Janssen, C. S., Pain, A., Christophides, G. K. et al. (2005). A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science307,82-86.

Hyman, R. W., Fung, E., Conway, A., Kurdi, O., Mao, J., Miranda,M., Nakao, B., Rowley, D., Tamaki, T., Wang, F. et al.(2002). Sequence of Plasmodium falciparum chromosome 12. Nature419,534-537.

Jurinke, C., van den Boom, D., Cantor, C. R. and Koster, H.(2002). The use of MassARRAY technology for high throughput genotyping. Adv. Biochem. Eng. Biotechnol.77, 57-74.

Kasianowicz, J. J., Brandin, E., Branton, D. and Deamer, D. W. (1996). Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. USA93,13770-13773.

Klenk, H. P., Clayton, R. A., Tomb, J. F., White, O., Nelson, K. E., Ketchum, K. A., Dodson, R. J., Gwinn, M., Hickey, E. K., Peterson, J. D. et al. (1997). The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.Nature390,364-370.

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.(2001). Initial sequencing and analysis of the human genome. Nature409,860-921.

Lim, H. K., Chung, E. J., Kim, J. C., Choi, G. J., Jang, K. S.,Chung, Y. R., Cho, K. Y. and Lee, S. W. (2005). Characterization of a forest soil metagenome clone that confers indirubin and indigo production on Escherichia coli.Appl. Environ. Microbiol.71,7768-7777.

Madabhushi, R. S. (1998). Separation of 4-color DNA sequencing extension products in noncovalently coated capillaries using low viscosity polymer solutions. Electrophoresis19,224-230.

Manichanh, C., Rigottier-Gois, L., Bonnaud, E., Gloux, K.,Pelletier, E., Frangeul, L., Nalin, R., Jarrin, C., Chardon, P., Marteau, P. et al. (2006). Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut55,205-211.

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. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature437,376-380.

Medini, D., Donati, C., Tettelin, H., Masignani, V. and Rappuoli, R. (2005). The microbial pan-genome. Curr. Opin. Genet. Dev.15,589-594.

Mikkelsen, T., Hiller, L. W., Eichler, E. E., Zody, M. C.,Jaffe, D. B., Yang, S. P., Enard, W., Hellmannm, I., Linbald-toh, K. and Altheide, T. K. (2005). Initial sequence of the chimpanzee genome and comparison with the human genome. Nature437, 69-87.

Mills, D. K., Entry, J. A., Voss, J. D., Gillevet, P. M. and Mathee, K. (2006). An assessment of the hypervariable domains of the 16S rRNA genes for their value in determining microbial community diversity: the paradox of traditional ecological indices. FEMS Microbiol. Ecol.57,496-503.

Prober, J. M., Trainor, G. L., Dam, R. J., Hobbs, F. W.,Robertson, C. W., Zagursky, R. J., Cocuzza, A. J., Jensen, M. A. and Baumeister, K. (1987). A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science238,336-341.

Qiu, W. G., Schutzer, S. E., Bruno, J. F., Attie, O., Xu, Y.,Dunn, J. J., Fraser, C. M., Casjens, S. R. and Luft, B. J.(2004). Genetic exchange and plasmid transfers in Borrelia burgdorferi sensu stricto revealed by three-way genome comparisons and multilocus sequence typing. Proc. Natl. Acad. Sci. USA101,14150-14155.

Ronaghi, M., Karamohamed, S., Pettersson, B., Uhlen, M. and Nyren, P. (1996). Real-time DNA sequencing using detection of pyrophosphate release. Anal. Biochem.242, 84-89.

Sanger, F., Nicklen, S. and Coulson, A. R.(1977). DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA74,5463-5467.

Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X.,McCutcheon, J. P., Rosenbaum, A. M., Wang, M. D., Zhang, K., Mitra, R. D. and Church, G. M. (2005). Accurate multiplex polony sequencing of an evolved bacterial genome. Science309,1728-1732.

Smith, L. M., Sanders, J. Z., Kaiser, R. J., Hughes, P., Dodd,C., Connell, C. R., Heiner, C., Kent, S. B. and Hood, L. E.(1986). Fluorescence detection in automated DNA sequence analysis. Nature321,674-679.

Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. M., Huse,S. M., Neal, P. R., Arrieta, J. M. and Herndl, G. J. (2006). Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc. Natl. Acad. Sci. USA103,12115-12120.

Storm, A. J., Chen, J. H., Zandbergen, H. W. and Dekker, C.(2005a). Translocation of double-strand DNA through a silicon oxide nanopore. Phys. Rev. E Stat. Nonlin. Soft Matter Phys.71,051903.

Storm, A. J., Storm, C., Chen, J., Zandbergen, H., Joanny, J. F. and Dekker, C. (2005b). Fast DNA translocation through a solid-state nanopore. Nano. Lett.5,1193-1197.

Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C.,Medini, D., Ward, N. L., Angiuoli, S. V., Crabtree, J., Jones, A. L., Durkin,A. S. et al. (2005). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial“pan-genome”. Proc. Natl. Acad. Sci. USA102,13950-13955.

Velicer, G. J., Raddatz, G., Keller, H., Deiss, S., Lanz, C.,Dinkelacker, I. and Schuster, S. C. (2006). Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. Proc. Natl. Acad. Sci. USA103,8107-8112.

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. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science304, 66-74.

Waterston, R. H., Lindblad-Toh, K., Birney, E., Rogers, J.,Abril, J. F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An,P. et al. (2002). Initial sequencing and comparative analysis of the mouse genome. Nature420,520-562.

Wicker, T., Schlagenhauf, E., Graner, A., Close, T. J., Keller,B. and Stein, N. (2006). 454 sequencing put to the test using the complex genome of barley. BMC Genom.7, 275.

Zhang, T., Breitbart, M., Lee, W. H., Run, J. Q., Wei, C. L.,Soh, S. W., Hibberd, M. L., Liu, E. T., Rohwer, F. and Ruan, Y.(2006). RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol.4, e3.

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Journal of Experimental Biology

Tập 210 Số 9

1518-1525

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