Practical application of self-organizing maps to interrelate biodiversity and functional data in NGS-based metagenomics

ISME Journal

Volumn 5, Issue 5, 2011, Pages 918-928

  Weber, Marc ^a   Teeling, Hanno ^a   Huang, Sixing ^a   Waldmann, Jost ^a,b   Kassabgy, Mariette ^a   Fuchs, Bernhard M ^a   Klindworth, Anna ^a   Klockow, Christine ^a,c   Wichels, Antje ^d   Gerdts, Gunnar ^d   Amann, Rudolf ^a   Glöckner, Frank Oliver ^a,c  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b Institute of Marine Biotechnology eV   (Germany)

^c JACOBS UNIVERSITY BREMEN   (Germany)

^d ALFRED WEGENER INSTITUTE FOR POLAR AND MARINE RESEARCH   (Germany)

Author keywords

binning; metagenomics; molecular ecology; self organizing map (SOM); taxonomic classification; TaxSOM

Indexed keywords

RNA 16S; SEA WATER;

BIODIVERSITY; GENOMICS; MOLECULAR ECOLOGY; PROTEIN; TAXONOMY;

ALGORITHM; ARTICLE; BIODIVERSITY; CLUSTER ANALYSIS; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; INTERNET; METAGENOMICS; METHODOLOGY; MICROBIOLOGY; PHYLOGENY; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; BIODIVERSITY; CLUSTER ANALYSIS; INTERNET; METAGENOMICS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEAWATER; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 79955071957     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2010.180     Document Type: Article

References (58)

1. Abe T, Sugawara H, Kinouchi M, Kanaya S, Ikemura T. (2005). Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res 12:281-290.
2. Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T. (2003). Informatics for unveiling hidden genome signatures. Genome Res 13:693-702. (Pubitemid 36511927)
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990). Basic local alignment search tool. J Mol Biol 215:403-410.
4. Amann RI, Ludwig W, Schleifer KH. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143-169.
5. Brady A, Salzberg SL. (2009). Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models. Nat Methods 6:673.
6. Burge C, Campbell AM, Karlin S. (1992). Over-and underrepresentation of short oligonucleotides in DNA sequences. Proc Natl Acad Sci USA 89:1358-1362.
7. Chan C-KK, Hsu AL, Tang S-L, Halgamuge SK. (2008a). Using growing self-organising maps to improve the binning process in environmental whole-genome shotgun sequencing. J Biomed Biotechnol 2008, doi:10.1155/2008/ 513701. (Pubitemid 351171854)
8. Chan CK, Hsu AL, Halgamuge SK, Tang SL. (2008b). Binning sequences using very sparse labels within a metagenome. BMC Bioinformat 9:215.
9. Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H. (2009). Continuous base identification for singlemolecule nanopore DNA sequencing. Nat Nanotechnol 4:265-270.
10. Deschavanne PJ, Giron A, Vilain J, Fagot G, Fertil B. (1999). Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol Biol Evol 16:1391-1399. (Pubitemid 29473232)
11. Diaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW. (2009). TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformat 10:56.
12. Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton AP et al. (2009). Community-wide analysis of microbial genome sequence signatures. Genome Biol 10: R85.
13. Eddy SR. (1996). Hidden Markov models. Curr Opin Struct Biol 6:361-365. (Pubitemid 26197437)
14. Eddy SR. (1998). Profile Hidden Markov Models. Bioinformatics 14:755-763. (Pubitemid 28552108)
15. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G et al. (2009). Real-time DNA sequencing from single polymerase molecules. Science 323:133-138.
16. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR et al. (1995). Wholegenome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
17. Gupta PK. (2008). Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 26:602-611.
18. Hanekamp K, Bohnebeck U, Beszteri B, Valentin K. (2007). PhyloGena-a user-friendly system for automated phylogenetic annotation of unknown sequences. Bioinformatics 23:793-801. (Pubitemid 47049912)
19. Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR, Butterfield DA et al. (2007). Microbial population structures in the deep marine biosphere. Science 318:97-100. (Pubitemid 47538040)
20. Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, Sogin ML. (2008). Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet 4: e1000255.
21. Huson DH, Auch AF, Qi J, Schuster SC. (2007). MEGAN analysis of metagenomic data. Genome Res 17:377-386. (Pubitemid 46376747)
22. Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP et al. (2003). Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 13:91-96.
23. Karlin S, Burge C. (1995). Dinucleotide relative abundance extremes: a genomic signature. Trends Genet 11:283-290.
24. Karlin S. (1998). Global dinucleotide signatures and analysis of genomic heterogeneity. Curr Opin Microbiol 1:598-610. (Pubitemid 128433649)
25. Karlin S, Campbell AM, Mrazek J. (1998). Comparative DNA analysis across diverse genomes. Annu Rev Genet 32:185-225. (Pubitemid 29045312)
26. Karlin S, Ladunga I. (1994). Comparisons of eukaryotic genomic sequences. Proc Natl Acad Sci USA 91:12832-12836.
27. Karlin S, Ladunga I, Blaisdell BE. (1994). Heterogeneity of genomes: measures and values. Proc Natl Acad Sci USA 91:12837-12841.
28. Kohonen T. (1982). Self-organized formation of topologically correct feature maps. Biol Cybernet 43:59-69. (Pubitemid 12139984)
29. Kohonen T. (1990). Self-organization maps. Proc IEEE 78:1464-1480.
30. Kohonen T, Kohonen T, Schroeder MR, Huang TS, Maps SO. (2001). Springer-Verlag New York Inc.: Secaucus, NJ.
31. Kohonen T, Oja E, Simula O, Visa A, Kangas J. (1996). Engineering applications of the self-organizing map. Proc IEEE 84:1358-1384.
32. Kottmann R, Kostadinov I, Duhaime MB, Buttigieg PL, Yilmaz P, Hankeln W et al. (2010). Megx net: integrated database resource for marine ecological genomics. Nucleic Acids Res 38: D391-D395.
33. Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F et al. (2008). Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res 36:2230.
34. Martin C, Diaz NN, Ontrup J, Nattkemper TW. (2008). Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification. Bioinformatics 24:1568-1574. (Pubitemid 351966154)
35. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC et al. (2007). Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods 4:495-500. (Pubitemid 46852075)
36. McHardy AC, Martin HG, Tsirigos A, Hugenholtz P, Rigoutsos I. (2007). Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods S 4:63-72. (Pubitemid 46029478)
37. Noguchi H, Park J, Takagi T. (2006). MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res 34:5623-5630. (Pubitemid 44742449)
38. Ochman H. (2007). Single-cell genomics. Environ Microbiol 9:7. (Pubitemid 46058990)
39. Pernthaler A, Pernthaler J, Amann R. (2002). Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68:3094-3101. (Pubitemid 34602035)
40. Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA et al. (2009). The NIH Human Microbiome Project. Genome Res 19:2317-2323.
41. Podell S, Gaasterland T. (2007). DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol S 8: R16.
42. Pride DT, Meinersmann RJ, Wassenaar TM, Blaser MJ. (2003). Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Res 13:145-158.
43. Reva ON, Tümmler B. (2004). Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns. BMC Bioinformat 5:90.
44. Rocha EP, Viari A, Danchin A. (1998). Oligonucleotide bias in Bacillus subtilis: general trends and taxonomic comparisons. Nucleic Acids Res 26:2971-2980. (Pubitemid 28297532)
45. Sandberg R, Winberg G, Branden CI, Kaske A, Ernberg I, Coster J. (2001). Capturing whole-genome characteristics in short sequences using a naive Bayesian classifier. Genome Res 11:1404-1409. (Pubitemid 32771547)
46. Schloss PD, Handelsman J. (2003). Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14:303-310. (Pubitemid 36782660)
47. Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M. (2007). CAMERA: a community resource for metagenomics. PLoS Biol 5: e75.
48. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR et al. (2006). Microbial diversity in the deep sea and the underexplored 'rare biosphere'. Proc Natl Acad Sci USA 103:12115-12120. (Pubitemid 44215820)
49. Sonnhammer EL, Eddy SR, Durbin R. (1997). Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28:405-420. (Pubitemid 27280344)
50. Sonnhammer EL, Eddy SR, Birney E, Bateman A, Durbin R. (1998). Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 26:320-322. (Pubitemid 28291550)
51. Teeling H, Meyerdierks A, Bauer M, Amann R, Glöckner FO. (2004). Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 6:938-947. (Pubitemid 39123248)
52. Temperton B, Field D, Oliver A, Tiwari B, Muhling M, Joint I et al. (2009). Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing. ISME J 3:792-796.
53. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW et al. (2005). Comparative metagenomics of microbial communities. Science S 308:554-557. (Pubitemid 40570586)
54. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM et al. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37-43. (Pubitemid 38332350)
55. Waldmann J. (2008). Phyloprint-Entwicklung und Anwendung eines Frameworks zur taxonomischen Klassifikation. Westfälische Wilhelms-Universität Münster, Department of Mathematics and Computer Science, Diploma Thesis, http://cs.uni-muenster.de/Professoren/Lippe/diplomarbeiten/html/Waldmann/.
56. Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO, et al. (2006). Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443:950-955. (Pubitemid 44646166)
57. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN et al. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462:1056-1060.
58. Zhou J, Bruns MA, Tiedje JM. (1996). DNA recovery from soils of diverse composition. Appl Environ Microbiol S 62:316-322. (Pubitemid 26047397)