Confidence intervals of similarity values determined for cloned SSU rRNA genes from environmental samples

Journal of Microbiological Methods

Volumn 65, Issue 1, 2006, Pages 144-152

  Fields, M W ^a   Schryver, J C ^b   Brandt, C C ^c   Yan, T ^c   Zhou, J Z ^c   Palumbo, A V ^c  

^a MIAMI UNIVERSITY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Clone; Environmental; Error analysis; Sequencing; SSU rRNA genes

Indexed keywords

GROUND WATER; SMALL SUBUNIT RIBOSOMAL RNA;

ARTICLE; CONFIDENCE INTERVAL; CONTROLLED STUDY; ENVIRONMENT; ERROR; GENE SEQUENCE; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

BASE SEQUENCE; CONFIDENCE INTERVALS; DNA, BACTERIAL; FRESH WATER; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 33644951885     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2005.07.001     Document Type: Article

References (19)

1. H.D. Brunk An Introduction to Mathematical Statistics 1975 Xerox Publishing Company Lexington, MA
2. J. Colinge, and G. Feger Detecting the impact of sequencing errors on SAGE data Bioinformatics 17 2001 840 842
3. T.P. Curtis, W.T. Sloan, and J.W. Scannell Estimating prokaryotic diversity and its limits Proc. Natl. Acad. Sci. U. S. A. 99 2002 10494 10499
4. D.E. Dykhuizen Santa Rosalia revisited: why are there so many species of bacteria? Antonie van Leeuwenhoek 73 1998 25 33
5. G.E. Fox, J.D. Wisotzkey, and P. Jurtshuk How close is close - 16S ribosomal-RNA sequence identity may not be sufficient to guarantee species identity Int. J. Syst. Bacteriol. 42 1992 166 170
6. F. Hill, C. Gemund, V. Benes, W. Ansorge, and T.J. Gibson An estimate of large-scale sequencing accuracy EMBO Rep. 1 2000 29 31
7. S. Kumar, K. Tamura, I.B. Jakobsen, and M. Nei MEGA2: molecular evolutionary genetics analysis software Bioinformatics 17 2001 1244 1245
8. W. Ludwig, O. Strunk, S. Klugbauer, N. Klugbauer, M. Weizenegger, and J. Neumaier Bacterial phylogeny based on comparative sequence analysis Electrophoresis 19 1998 554 568
9. L. Øvreås Population and community level approaches for analysing microbial diversity in natural environments Ecol. Lett. 3 2000 236 251
10. N.R. Pace A molecular view of microbial diversity and the biosphere Science 276 1997 734 740
11. X.Y. Qiu, L.Y. Wu, H.S. Huang, P.E. McDonel, A.V. Palumbo, and J.M. Tiedje Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning Appl. Environ. Microbiol. 67 2001 880 887
12. E. Stackebrandt, and B.M. Goebel A place for DNA-DNA reassociation and 16S ribosomal-RNA sequence analysis in the present species definition in bacteriology Int. J. Syst. Bacteriol. 44 1994 846 849
13. J. Stollberg, J. Urschitz, Z. Urban, and C.D. Boyd A quantitative evaluation of SAGE Genome Res. 10 2000 1241 1248
14. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL-W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
15. C.R. Woese, and G.E. Fox Phylogenetic structure of the prokaryotic domain: the primary kingdoms Proc. Natl. Acad. Sci. U. S. A. 74 1977 5088 5090
16. C.R. Woese, O. Kandler, and M.L. Wheelis Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya Proc. Natl. Acad. Sci. U. S. A. 87 1990 4576 4579
17. J.Z. Zhou, M.A. Bruns, and J.M. Tiedje DNA recovery from soils of diverse composition Appl. Environ. Microbiol. 62 1996 316 322
18. J.Z. Zhou, M.E. Davey, J.B. Figueras, E. Rivkina, D. Gilichinsky, and J.M. Tiedje Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA Microbiology 143 1997 3913 3919
19. J.Z. Zhou, B.C. Xia, D.S. Treves, L.Y. Wu, T.L. Marsh, and R.V. O'Neill Spatial and resource factors influencing high microbial diversity in soil Appl. Environ. Microbiol. 68 2002 326 334