Phoenix 2: A locally installable large-scale 16S rRNA gene sequence analysis pipeline with Web interface

Journal of Biotechnology

Volumn 167, Issue 4, 2013, Pages 393-403

  Soh, Jung ^a   Dong, Xiaoli ^a   Caffrey, Sean M ^a   Voordouw, Gerrit ^a   Sensen, Christoph W ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

Gene sequence analysis; Hydrocarbon metagenomics; Microbial diversity; Pyrotags; Ribosomal RNA

Indexed keywords

GENE SEQUENCE ANALYSIS; METAGENOMICS; MICROBIAL DIVERSITY; PYROTAGS; RIBOSOMAL RNA;

HYDROCARBONS; RNA;

PIPELINES;

RNA 16S;

ARTICLE; BIOINFORMATICS; COMPUTER PROGRAM; GENE SEQUENCE; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PRIORITY JOURNAL; RNA GENE; SEQUENCE ANALYSIS;

GENE SEQUENCE ANALYSIS; HYDROCARBON METAGENOMICS; MICROBIAL DIVERSITY; PYROTAGS; RIBOSOMAL RNA;

ALGORITHMS; BIODIVERSITY; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; GENES, RRNA; INTERNET; METAGENOMICS; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS; SOFTWARE;

EID: 84883354914     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2013.07.004     Document Type: Article

References (54)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. Journal of Molecular Biology 1990, 215:403-410.
2. Berdugo-Clavijo C., Dong X., Soh J., Sensen C.W., Gieg L.M. Methanogenic biodegradation of two-ringed polycyclic aromatic hydrocarbons. FEMS Microbiology Ecology 2012, 81:124-133.
3. Borg I., Groenen P. Modern Multidimensional Scaling: Theory and Applications 1997, Springer, New York.
4. Bragg L., Stone G., Imelfort M., Hugenholtz P., Tyson G.W. Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nature Methods 2012, 9:425-426.
5. Bray J.R., Curtis J.T. An ordination of upland forest communities of southern Wisconsin. Ecological Monographs 1957, 27:325-349.
6. Callbeck C.M., Dong X., Chatterjee I., Agrawal A., Caffrey S.M., Sensen C.W., Voordouw G. Microbial community succession in a bioreactor modeling a souring low-temperature oil reservoir subjected to nitrate injection. Applied Microbiology and Biotechnology 2011, 91:799-810.
7. Chao A. Non-parametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 1984, 11:265-270.
8. Chao A., Lee S.M. Estimating the number of classes via sample coverage. Journal of the American Statistical Association 1992, 87:210-217.
9. Chun J., Lee J.H., Jung Y., Kim M., Kim S., Kim B.K., Lim Y.W. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. International Journal of Systematic and Evolutionary Microbiology 2007, 57:2259-2261.
10. Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G.M., Tiedje J.M. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research 2009, 37:D141-D145.
11. Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L. BLAST+: architecture and applications. BMC Bioinformatics 2009, 10:421.
12. Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., Peña A.G., Goodrich J.K., Gordon J.I., Huttley G.A., Kelley S.T., Knights D., Koenig J.E., Ley R.E., Lozupone C.A., McDonald D., Muegge B.D., Pirrung M., Reeder J., Sevinsky J.R., Turnbaugh P.J., Walters W.A., Widmann J., Yatsunenko T., Zaneveld J., Knight R. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 2010, 7:335-336.
13. Church G.M., Kieffer-Higgins S. Multiplex DNA sequencing. Science 1988, 240:185-188.
14. Clarridge J.E. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clinical Microbiology Reviews 2004, 17:840-862.
15. DeSantis T.Z., Hugenholtz P., Keller K., Brodie E.L., Larsen N., Piceno Y.M., Phan R., Andersen G.L. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Research 2006, 34:W394-W399.
16. Excoffier L., Smouse P.E., Quattro J.M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 1992, 131:479-491.
17. Fowler S.J., Dong X., Sensen C.W., Suflita J.M., Gieg L.M. Methanogenic toluene metabolism: community structure and intermediates. Environmental Microbiology 2012, 14:754-764.
18. Gaspar J.M., Thomas W.K. Assessing the consequences of denoising marker-based metagenomic data. PLoS ONE 2013, 8:e60458.
19. Gotelli N.J., Colwell R.K. Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecology Letters 2001, 4:379-391.
20. Gower J. Principal coordinates analysis. Encyclopedia of Biostatistics 1998, 3514-3518. John Wiley and Sons, Inc. P. Armitage, T. Coulton (Eds.).
21. Hamady M., Lozupone C., Knight R. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME Journal 2010, 4:17-27.
22. Huse S., Huber J., Morrison H., Sogin M., Welch D. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biology 2007, 8:R143.
23. Huson D.H., Richter D.C., Rausch C., Dezulian T., Franz M., Rupp R. Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinformatics 2007, 8:460.
24. Jaccard P. Étude comparative de la distribution florale dans une portion des Alpes et des Jura. Bulletin de la Société Vaudoise des Sciences Naturelles 1901, 37:547-579.
25. Kryachko Y., Dong X., Sensen C.W., Voordouw G. Compositions of microbial communities associated with oil and water in a mesothermic oil field. Antonie Van Leeuwenhoek 2012, 101:493-506.
26. Kunin V., Engelbrektson A., Ochman H., Hugenholtz P. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology 2010, 12:118-123.
27. Kunin V., Hugenholtz P. PyroTagger: a fast, accurate pipeline for analysis of rRNA amplicon pyrosequence data. The Open Journal 2010, 1-8.
28. Li W., Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
29. Lozupone C., Knight R. UniFrac: a new phylogenetic method for comparing microbial communities. Applied and Environmental Microbiology 2005, 71:8228-8235.
30. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., Jobb G., Förster W., Brettske I., Gerber S., Ginhart A.W., Gross O., Grumann S., Hermann S., Jost R., König A., Liss T., Lüssmann R., May M., Nonhoff B., Reichel B., Strehlow R., Stamatakis A., Stuckmann N., Vilbig A., Lenke M., Ludwig T., Bode A., Schleifer K.H. ARB: a software environment for sequence data. Nucleic Acids Research 2004, 32:1363-1371.
31. Michener C.D., Sokal R.R. A quantitative approach to a problem of classification. Evolution 1957, 11:490-499.
32. Olsen G.J., Woese C.R. Ribosomal RNA: a key to phylogeny. FASEB Journal 1993, 7:113-123.
33. Park H.S., Chatterjee I., Dong X., Wang S.H., Sensen C.W., Caffrey S.M., Jack T.R., Boivin J., Voordouw G. Effect of sodium bisulfite injection on the microbial community composition in a brackish-water-transporting pipeline. Applied and Environmental Microbiology 2011, 77:6908-6917.
34. Petrosino J.F., Highlander S., Luna R.A., Gibbs R.A., Versalovic J. Metagenomic pyrosequencing and microbial identification. Journal of Clinical Chemistry 2009, 55:856-866.
35. Pruesse E., Quast C., Knittel K., Fuchs B., Ludwig W., Peplies J., Glöckner F.O. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research 2007, 35:7188-7196.
36. Quince C., Lanzén A., Curtis T.P., Davenport R.J., Hall N., Head I.M., Read L.F., Sloan W.T. Accurate determination of microbial diversity from 454 pyrosequencing data. Nature Methods 2009, 6:639-641.
37. Quince C., Lanzen A., Davenport R.J., Turnbaugh P.J. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 2011, 12:38.
38. Ramos-Padrón E., Bordenave S., Lin S., Bhaskar I.M., Dong X., Sensen C.W., Fournier J., Voordouw G., Gieg L.M. Carbon and sulfur cycling by microbial communities in a gypsum-treated oil sands tailings pond. Environmental Science and Technology 2011, 45:439-446.
39. Reeder J., Knight R. Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nature Methods 2010, 7:668-669.
40. Schloss P.D. Evaluating different approaches that test whether microbial communities have the same structure. ISME Journal 2008, 2:265-275.
41. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 2009, 75:7537-7541.
42. Schloss P.D., Gevers D., Westcott S.L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 2011, 6:e27310.
43. Schloss P.D., Westcott S.L. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Applied and Environmental Microbiology 2011, 77:3219-3226.
44. Shannon C.E. A mathematical theory of communication. The Bell System Technical Journal 1948, 27:379-423. 623-656.
45. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 2003, 13:2498-2504.
46. Shyu C., Soule T., Bent S.J., Foster J.A., Forney L.J. MiCA: a Web-based tool for the analysis of microbial communities based on terminal-restriction fragment length polymorphisms of 16S and 18S rRNA genes. Microbial Ecology 2007, 53:562-570.
47. Simpson E.H. Measurement of diversity. Nature 1949, 163:688.
48. Sogin M.L., Morrison H.G., Huber J.A., Welch D.M., Huse S.M., Neal P.R., Arrieta J.M., Herndl G.J. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America 2006, 103:12115-12120.
49. Spearman C. The proof and measurement of association between two things. International Journal of Epidemiology 2010, 39:1137-1150.
50. Stewart C.N., Excoffier L. Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry). Journal of Evolutionary Biology 1996, 9:153-171.
51. Wang Q., Garrity G.M., Tiedje J.M., Cole J.R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 2007, 73:5261-5267.
52. White J.R., Nagarajan N., Pop M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Computational Biology 2009, 5:e1000352.
53. Yue J.C., Clayton M.K. A similarity measure based on species proportions. Communications in Statistics - Theory and Methods 2005, 34:2123-2131.
54. Zahl S. Jackknifing an index of diversity. Ecology 1977, 58:907-913.