Open resource metagenomics: A model for sharing metagenomic libraries

Standards in Genomic Sciences

Volumn 5, Issue 2, 2011, Pages 203-210

  Neufeld, J D ^a   Engel, K ^a   Cheng, J ^a   Moreno Hagelsieb, G ^b   Rose, D R ^a   Charles, T C ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

^b WILFRID LAURIER UNIVERSITY   (Canada)

Author keywords

Functional complementation; Metagenomic libraries; Sharing

Indexed keywords

EID: 83255175699     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1974654     Document Type: Article

References (26)

1. Canadian MetaMicroBiome Library. http://cm2bl.org
2. Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glöckner FO, Kolker E, Kowalchuk G, et al. Toward a standards-compliant genomic and metagenomic publication record. OMICS 2008; 12:157-160. PubMed doi:10.1089/omi.2008.A2B2
3. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed doi:10.1038/nbt1360
4. Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol 2011; 29:415-420. PubMed doi:10.1038/nbt.1823
5. Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 1996; 178:591-599. PubMed
6. Schmidt TM, DeLong EF, Pace NR. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol 1991; 173:4371-4378. PubMed
7. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 2000; 66:2541-2547. PubMed doi:10.1128/AEM.66.6.2541-2547.2000
8. Gillespie DE, Brady SF, Bettermann AD, Cianciotto NP, Liles MR, Rondon MR, Clardy J, Goodman RM, Handelsman J. Isolation of antibiotics turbomycin a and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 2002; 68:4301-4306. PubMed doi:10.1128/AEM.68.9.4301-4306.2002
9. Liles MR, Manske BF, Bintrim SB, Handelsman J, Goodman RM. A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl Environ Microbiol 2003; 69:2684-2691. PubMed doi:10.1128/AEM.69.5.2684-2691.2003
10. Riesenfeld CS, Goodman RM, Handelsman J. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 2004; 6:981-989. PubMed doi:10.1111/j.1462-2920.2004.00664.x
11. Wang C, Meek DJ, Panchal P, Boruvka N, Archibald FS, Driscoll BT, Charles TC. Isolation of poly-3-hydroxybutyrate metabolism genes from complex microbial communities by phenotypic complementation of bacterial mutants. Appl Environ Microbiol 2006; 72:384-391. PubMed doi:10.1128/AEM.72.1.384-391.2006
12. Hao Y, Winans SC, Glick BR, Charles TC. Identification and characterization of new LuxR/LuxI-type quorum sensing systems from metagenomic libraries. Environ Microbiol 2010; 12:105-117. PubMed doi:10.1111/j.1462-2920.2009.02049.x
13. Rolider A. Isolation and characterization of bacterial phosphorous metabolism genes from complex microbial communities. 2009; PhD thesis, University of Waterloo, http://hdl.handle.net/10012/4806
14. Schallmey M, Ly A, Wang C, Meglei G, Voget S, Streit WR, Driscoll BT, Charles TC. Harvesting of novel polyhydroxyalkanoate (PHA) synthase encoding genes from soil metagenome libraries using phenotypic screening and selection. FEMS Microbiol Lett 2011; 321:150-156. PubMed doi:10.1111/j.1574-6968.2011.02324.x
15. Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010; 60:249-266. PubMed doi:10.1099/ijs.0.016949-0
16. World Federation for Culture Collections. http://www.wfcc.info
17. Ward N, Eisen J, Fraser C, Stackebrandt E. Sequenced strains must be saved from extinction. Nature 2001; 414:148. PubMed doi:10.1038/35102737
18. Katzen F. Gateway® recombinational cloning: a biological operating system. Expert Opin Drug Discov 2007; 2:571-589. doi:10.1517/17460441.2.4.571
19. Kim JH, Feng Z, Bauer JD, Kallifidas D, Calle PY, Brady SF. Cloning large natural product gene clusters from the environment: Piecing environmental DNA gene clusters back together with TAR. Biopolymers 2010; 93:833-844. PubMed doi:10.1002/bip.21450
20. Meyer F, Paarmann D, D'Souza M, Olson R, Glass E, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A. The metagenomics RAST server-a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008; 9:386. PubMed doi:10.1186/1471-2105-9-386
21. Booth T, Gilbert J, Neufeld J, Ball J, Thurston M, Chipman K, Joint I, Field D. Handlebar: a flexible, web-based inventory manager for handling barcoded samples. Biotechniques 2007; 42:300-302. PubMed doi:10.2144/000112385
22. Jones JD, Gutterson N. An efficient mobilizable cosmid vector, pRK7813, and its use in a rapid method for marker exchange in Pseudomonas fluorescens strain HV37a. Gene 1987; 61:299-306. PubMed doi:10.1016/0378-1119(87)90193-4
23. House BL, Mortimer MW, Kahn ML. New recombination methods for Sinorhizobium meliloti genetics. Appl Environ Microbiol 2004; 70:2806-2815. PubMed doi:10.1128/AEM.70.5.2806-2815.2004
24. Hartley JL, Temple GF, Brasch MA. DNA cloning using in vitro site-specific recombination. Genome Res 2000; 10:1788-1795. PubMed doi:10.1101/gr.143000
25. Garrity GM, Thompson LM, Ussery DW, Paskin N, Baker D, Desmeth P, Schindel DE, Ong PS. Studies on monitoring and tracking genetic resources: an executive summary. Stand Genomic Sci 2009; 1:78-86. PubMed doi:10.4056/sigs.1491
26. Raes J, Korbel J, Lercher M, Von Mering C, Bork P. Prediction of effective genome size in metagenomic samples. Genome Biol 2007; 8:R10. PubMed doi:10.1186/gb-2007-8-1-r10