SILVA: Comprehensive Databases for Quality Checked and Aligned Ribosomal RNA Sequence Data Compatible with ARB

Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches

Volumn , Issue , 2011, Pages 393-398

  Prüsse, Elmar ^a   Quast, Christian ^a   Yilmaz, Pelin ^a,b   Ludwig, Wolfgang ^c   Peplies, Jörg ^d   Glöckner, Frank Oliver ^a,b  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b JACOBS UNIVERSITY BREMEN   (Germany)

^c TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^d RIBOCON GMBH   (Germany)

Author keywords

Primary intention of SILVA project reliable rRNA datasets, informative set of processing and quality values for each sequence; SILVA, and two LSU databases use of molecular markers with higher resolution than SSU rRNA; SILVA, comprehensive databases quality checked and aligned ribosomal RNA sequence data compatible with ARB

Indexed keywords

EID: 84857191880     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118010518.ch45     Document Type: Chapter

References (31)

1. Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
2. Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ. 2005. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol. 71:7724-7736.
3. Cole JR, et al. 2009. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acid Res. 37:D141-D145.
4. Dawyndt P, Vancanneyt M, De Meyer H, Swings J. 2005. Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources. IEEE Trans. Knowledge Data Eng. 17:1111-1126.
5. DeSantis TZ, et al. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 72:5069-5072.
6. Euzeby JP. 1997. List of bacterial names with standing in nomenclature: A folder available on the Internet. Int. J. Syst. Bacteriol. 47:590-592.
7. Field D, et al. 2008. The minimum information about a genome sequence (MIGS) specification. Nat. Biotechnol. 26:541-547.
8. Fox GE, Pechman KR, Woese CR. 1977. Comparative cataloging of 16S ribosomal ribonucleic acid: Molecular approach to procaryotic systematics. International Journal of Bacteriol. 27:44-57. Garrity GM, Bell JA, Lilburn TG. 2004. Bergey's Taxonomic Outline of the Prokaryotes. 5th ed. New York: Springer Verlag. Giovannoni SJ, DeLong EF, Olsen GJ, Pace NR. 1988. Phylogenetic groupspecific oligodeoxynucleotide probes for identification of single microbial cells. J. Bacteriol. 170:720-726.
9. Garrity GM, Bell JA, Lilburn TG. 2004. Bergey's Taxonomic Outline of the Prokaryotes. 5th ed. New York: Springer Verlag. Giovannoni SJ, DeLong EF, Olsen GJ, Pace NR. 1988. Phylogenetic groupspecific oligodeoxynucleotide probes for identification of single microbial cells. J. Bacteriol. 170:720-726.
10. Gutell RR, Larsen N, Woese CR. 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58:10-26.
11. Hong SH, Bunge J, Jeon SO, Epstein SS. 2006. Predicting microbial species richness. Proc. Natl. Acad. Sci. USA 103:117-122.
12. Korf I, Yandell M, Bedell J. 2003. BLAST. Beijing, Cambridge, Farnham, Köln, Paris, Sebastopol, Taipei, Tokyo: O'Reilly & Associates. Kottmann R et al. (2009) Megx.net: Integrated database resource for marine ecological genomics.
13. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nucleic Acid Res. 35:3100-3108.
14. Lee C, Grasso C, Sharlow MF. 2002. Multiple sequence alignment using partial order graphs. Bioinformatics 18:452-464.
15. Ludwig W, Schleifer KH. 2005. Molecular phylogeny of bacteria based on comparative sequence analysis of conserved genes. In Sapp J, ed. Microbial Phylogeny and Evolution, Concepts and Controversies. New York: Oxford University Press, pp. 70-98.
16. Ludwig W, et al. 2004. ARB: A software environment for sequence data. Nucleic Acid Res. 32:1363-1371.
17. Marchesi JR, Sato T, Weightman AJ, Martin TA, Fry JC, Hiom SJ, Wade WG. 1998. Design and evaluation of useful bacterium-specific PCR primers that amplify genes coding for bacterial 16S rRNA. Appl. Environ. Microbiol. 64:795-799.
18. Margulies M et al. 2006. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 441:120-120.
19. Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA. 1986. Microbial ecology and evolution: A ribosomal RNA approach. Annu. Rev. Microbiol. 40:337-365.
20. Pace NR. 2009. Mapping the tree of life: Progress and prospects. Microbiol. Mol. Biol. Rev. 73:565-576.
21. Pace NR, Stahl DA, Olsen GJ, Lane DJ. 1985. Analyzing natural microbial populations by rRNA sequences. ASM News 51:4-12.
22. Pedros-Alio C. 2006. Marine microbial diversity: Can it be determined? Trends Microbiol. 14:257-263.
23. Peplies J, Glöckner FO, Amann R, Ludwig W. 2004. Comparative sequence analysis and oligonucleotide probe design based on 23S rRNA genes of Alphaproteobacteria from North Sea bacterioplankton. Syst. Appl. Microbiol. 27:573-580.
24. Peplies J, Kottmann R, Ludwig W, Glöckner FO. 2008. A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. Syst. Appl. Microbiol. 31:251-257.
25. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig WG, Peplies J, Glöckner FO. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acid Res. 35:7188-7196.
26. Reeder J, Knight R. 2009. The "rare biosphere": A reality check. Nat. Methods 6:636-637.
27. Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP. 2002. DNA points the way ahead of taxonomy-In assessing new approaches, it's time for DNA's unique contribution to take a central role. Nature 418:479-479.
28. Tringe SG, Hugenholtz P. 2008. A renaissance for the pioneering 16S rRNA gene. Curr. Opin. Microbiol. 11:442-446.
29. Ward DM, Weller R, Bateson MM. 1990. 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345:63-65.
30. Wuyts J, De Rijk P, Van de Peer Y, Winkelmans T, De Wachter R. 2001. The European Large Subunit Ribosomal RNA Database. Nucleic Acid Res. 29:175-177.
31. Yarza P et al. 2008. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst. Appl. Microbiol. 31:241-250.