An automated phylogenetic tree-based Small subunit rRNA Taxonomy and Alignment Pipeline (STAP)

PLoS ONE

Volumn 3, Issue 7, 2008, Pages

  Wu, Dongying ^a   Hartman, Amber ^a,e   Ward, Naomi ^c,d   Eisen, Jonathan A ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF WYOMING   (United States)

^d Center of Marine Biotechnology   (United States)

^e JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL SUBUNIT RIBOSOMAL RNA; RIBOSOME RNA;

ARTICLE; AUTOMATION; COMPUTER PROGRAM; DATA ANALYSIS SOFTWARE; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; RNA SEQUENCE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TAXONOMY; BIOLOGY; EVALUATION; GENETICS; METHODOLOGY; NUCLEIC ACID DATABASE; RNA GENE;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENES, RRNA; PHYLOGENY; RNA, RIBOSOMAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EID: 50149086330     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002566     Document Type: Article

References (46)

1. Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 71(11): 5088-90.
2. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180(18): 1765-71.
3. Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276(5313): 734-40.
4. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, et al. (1985) Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl. Acad. Sci., USA 82: 6955-6959.
5. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, et al. (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev 60(2): 407-38.
6. Imhoff JF, Caumette P (2004) Recommended standards for the description of new species of anoxygenic phototrophic bacteria. Int J Syst Evol Microbiol 54(Pt 4): 1415-21.
7. Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71(2): 491-9.
8. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173(2): 697-703.
9. Liu WT, Marsh TL, Cheng H, Forney LJ (1997) Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl Environ Microbiol 63(11): 4516-22.
10. Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65(10): 4630-6.
11. Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology. Antonie Van Leeuwenhoek 73(1): 127-41.
12. Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, et al. (2002) High-density microarray of small-subunit ribosomal DNA probes. Appl Environ Microbiol 68(5): 2535-41.
13. Hughes JB, Hellmann JJ, Rickeus TH, Bohannan BJ (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67(10): 4399-406.
14. Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF, et al. (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73(1): 278-88.
15. Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55(3): 541-55.
16. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, et al. (2005) Re-evaluating prokaryotic species. Nat Rev Microbiol 3(9): 733-9.
17. Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nat Rev Microbiol; dio:10.1038/nrmicro1872.
18. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al. (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 128 (6978): 37-43.
19. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304(5667): 66-74.
20. Eisen JA (2007) Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. PLoS Biol 5(3): e82.
21. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, et al. (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science 314(5807): 1933-5.
22. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, et al. (2006) Microbial diversity in the deep sea and the underexplored "rare biosphere". Proc Natl Acad Sci USA 103(32): 12115-20.
23. Cole JR, Chai B, Farris RJ, Wang Q, Kulam-Syed-Mohideen SA, et al. (2007) The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res 35 (Database issue): D169-D172.
24. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. (2006) Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB. Appl Environ Microbiol 72: 5069-72.
25. Wuyts J, Perriere G, Van De Peer Y (2004) The European ribosomal RNA database. Nucleic Acids Res 32 (Database issue): D101-3.
26. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71(12): 8228-35.
27. Ludwig W, Strunk O, Westram R, Richter L, Meier H, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32(1): 1363-71.
28. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. (2005) Diversity of the Human Intestinal Microbial Flora. Science 308 (5728): 1635-38.
29. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Appl Environ Microbiol 73(16): 5261-7.
30. Weisburg WG, Giovannoni SJ, Woese CR (1989) The Deinococcus-Thermus phylum and the effect of rRNA composition of phylogenetic tree construction. Syst Appl Microbiol 11: 128-34.
31. Koski LB, Golding GB (2001) The closest BLAST hit is often not the nearest neighbor. J Mol Evol 52(6): 540-2.
32. Eisen JA (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8(3): 163-7.
33. Eisen JA, Hanawalt PC (1999) A phylogenomic study of DNA repair genes, proteins, and processes. Mutat Res 435(3): 171-213.
34. Eisen JA (2000) Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Genet Dev 10(6): 606-11.
35. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Molecular systematics Sinauer Associates. Sunderland, MA. pp 407-514.
36. Devulder G, Perrière G, Baty F, Flandrois JP (2003) BIBI, a bibinformatics bacterial identification tool. J Clin Microbiol 41(4): 1785-7.
37. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71(3): 1501-6.
38. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. (2001) The sequence of the human genome. Science 291: 1304-1351.
39. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12(10): 1611-8.
40. Thompson JD, Higgins DG, Gibson TJ (1994) 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: 4673-4680.
41. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52(5): 696-704.
42. Thompson JD, Gibson TJ, Plewniak F, Jeanmongin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24: 4876-4882.
43. Penn K, Wu D, Eisen JA, Ward N (2006) Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts. Applied and Environmental Microbiology 72(2): 1680-3.
44. García Martín H, Ivanova N, Kunin V, Warnecke F, Barry KW, et al. (2006) Metagenomic analysis of two enhanced biological phosphorus removal EBPR sludge communities. Nat Biotechnol 24(10): 1263-9.
45. DeSantis TZ Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, et al. (2006) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34(Web Server issue): W394-9.
46. Matz MV, Nielsen R (2005) A likelihood ratio test for species membership based on DNA sequence data. Philos Trans R Soc Lond B Biol Sci 360(1462): 1969-74.