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Chapter 38 : Construction of BAC and Fosmid Libraries from Naturally Occurring Microbial Populations

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Construction of BAC and Fosmid Libraries from Naturally Occurring Microbial Populations, Page 1 of 2

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Abstract:

This chapter discusses one potential approach involving genomic characterization of the naturally occurring microbial genomes, without the requirement of isolating individual microbes one by one in pure culture. It describes some of the methodological options and considerations, and presents a few of the protocols that have been used successfully for preparing genomic libraries from natural microbial assemblages. Some of the earliest large-fragment genome libraries from natural microbial populations made use of bacteriophage lambda cloning protocols. Today, advanced vector systems such as fosmids and bacterial artificial chromosomes (BACs) are now in wide use. BAC and fosmid libraries are useful tools that can be used to sidestep many thorny problems that still inhibit the accurate characterization of naturally occurring microbial communities. They represent useful tools for conducting sequence surveys to determine the phylogenetic and functional content and properties inherent in native microbial populations. They can also serve as reagents for gene discovery, gene expression, and functional genomic characterization of naturally occurring microbes, some still resistant to cultivation techniques. BAC and fosmid libraries can also serve as useful reagents in microarray construction and analyses of naturally occurring microbial dynamics and variability.

Citation: Delong E. 2007. Construction of BAC and Fosmid Libraries from Naturally Occurring Microbial Populations, p 879-885. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch38

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Chromosomal DNA
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FIGURE 1

Comparison of BAC (A), traditional fosmid (B), and blunt-end fosmid (C) cloning of DNA fragments for environmental genomic studies.

Citation: Delong E. 2007. Construction of BAC and Fosmid Libraries from Naturally Occurring Microbial Populations, p 879-885. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch38
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References

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1. Béjà, O.,, L. Aravind,, E. V. Koonin,, M. T. Suzuki,, A. Hadd,, L. P. Nguyen,, S. B. Jovanovich,, C. M. Gates,, R. A. Feldman,, J. L. Spudich,, E. N. Spudich,, and E. F. DeLong. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:19021906.
2. Béjà, O.,, M. T. Suzuki,, J. F. Heidelberg,, W. C. Nelson,, C. M. Preston,, T. Hamada,, J. A. Eisen,, C. M. Fraser,, and E. F. DeLong. 2002. Unsuspected diversity among marine aerobic anoxygenic phototrophs. Nature 415:630633.
3. Béjà , O.,, M. T. Suzuki,, E. V. Koonin,, L. Aravind,, A. Hadd,, L. P. Nguyen,, R. Villacorta,, M. Amjadi,, C. Garrigues,, S. B. Jovanovich,, R. A. Feldman,, and E. F. DeLong. 2000. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ. Microbiol. 2:516529.
4. Doolittle, R. F. 2002. Microbial genomes opened up. Nature 392:339342.
5. Hughes, J. B.,, J. J. Hellmann,, T. H. Ricketts,, and B. J. Bohannan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67:43994406.
6. Kim, U.-J.,, H. Shizuya,, P. Dejong,, B. Birren,, and M. Simon. 1992. Stable propagation of cosmid sized human DNA inserts in an F-factor based vector. Nucleic Acids Res. 20:10831185.
7. Marsh, T. L.,, P. Saxman,, J. Cole,, and J. Tiedje. 2000. Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Appl. Environ. Microbiol. 66:36163620.
8. Olsen, G. J.,, D. J. Lane,, S. J. Giovannoni,, N. R. Pace,, and D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40: 337365.
9. Pace, N. R. 1997. A molecular view of microbial diversity and the biosphere. Science 276:734740.
10. Pace, N. R.,, D. A. Stahl,, G. J. Olsen,, and D. J. Lane. 1985. Analyzing natural microbial populations by rRNA sequences. ASM News 51:412.
11. Quaiser, A.,, T. Ochsenreiter,, H. P. Klenk,, A. Kletzin,, A. H. Treusch,, G. Meurer,, J. Eck,, C. W. Sensen,, and C. Schleper. 2002. First insight into the genome of an uncultivated crenarchaeote from soil. Environ. Microbiol. 4: 603611.
12. Rondon, M. R.,, P. R. August,, A. D. Bettermann,, S. F. Brady,, T. H. Grossman,, M. R. Liles,, K. A. Loiacono,, B. A. Lynch,, I. A. MacNeil,, C. Minor,, C. L. Tiong,, M. Gilman,, M. S. Osburne,, J. Clardy,, J. Handelsman,, and R. M. Goodman. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:25412547.
13. Rondon, M. R.,, S. J. Raffel,, R. M. Goodman,, and J. Handelsman. 1999. Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus. Proc. Natl. Acad. Sci. USA 96:64516455.
14. Schleper, C.,, E. F. DeLong,, C. M. Preston,, R. A. Feldman,, K. Y. Wu,, and R. V. Swanson. 1998. Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilic archaeon Cenarchaeum symbiosum. J. Bacteriol. 180:50035009.
15. Shizuya, H.,, B. Birren,, U. J. Kim,, V. Mancino,, T. Slepak,, Y. Tachiiri,, and M. Simon. 1992. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Sci. USA 89:87948797.
16. Shizuya, H.,, and H. Kouros-Mehr. 2001. The development and applications of the bacterial artificial chromosome cloning system. Keio J. Med. 50:2630.
17. Song, J.,, F. Dong,, J. W. Lilly,, R. M. Stupar,, and J. Jiang. 2001. Instability of bacterial artificial chromosome (BAC) clones containing tandemly repeated DNA sequences. Genome 44:463469.
18. Stein, J. L.,, T. L. Marsh,, K. Y. Wu,, H. Shizuya,, and E. F. DeLong. 1996. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J. Bacteriol. 178:591599.
19. Suzuki, M.,, M. S. Rappe,, and S. J. Giovannoni. 1998. Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol. 64:45224529.

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