2017 / 02

Next Paper
DOI: 10.24075/brsmu.2017-02-04

METHOD

Library preparation for metagenomic sequencing with Illumina

Krasnenko AYu1, Eliseev AYu2, Borisevich DI1, Tsukanov KYu1, Davydova AI1, Ilinsky VV1
About authors

1 Genotek Inc., Moscow

2 Moscow South-West High School No. 1543, Moscow, Russia

Correspondence should be addressed: Anna Krasnenko
Nastavnicheskiy per. 17, str. 1, pod. 14, Moscow, 105120; moc.liamg@oknensarkanna

About paper

Acknowledgements: the authors thank Daria Plakhina and Ivan Stetsenok of Genotek for their help and Sergey Glagolev of Moscow South-West High School No. 1543 for his valuable advice and comments.

Contribution of the authors to this work: Krasnenko AYu, Eliseev AYu — analysis of literature, research planning and implementation, data analysis and interpretation; Borisevich DI, Tsukanov KYu — bioinformatic analysis; Davydova AI — drafting of a manuscript; Ilinsky VV — research planning, scientific advisor. All authors participated in editing of the manuscript.

Received: 2017-04-12 Accepted: 2017-04-24 Published online: 2017-05-31
|
  1. Mori H, Maruyama F, Kato H, Toyoda A, Dozono A, Ohtsubo Y, et al. Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes. DNA Res. 2014; 21 (2): 217–27.
  2. Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, García-Cobos S, et al. Application of next generation sequencing in clinical microbiology and infection prevention. J Biotechnol. 2017 Feb 10; 243: 16–24.
  3. Oulas A, Pavloudi C, Polymenakou P, Pavlopoulos GA, Papanikolaou N, Kotoulas G., et al. Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. Bioinform Biol Insights. 2015 May 5; 9: 75–88.
  4. Hamady M, Knight R. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res. 2009 Jul; 19 (7): 1141–52.
  5. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014 Sep; 12 (9): 635–45.
  6. Mardis ER. Next-generation sequencing platforms. Annu Rev Anal Chem (Palo Alto Calif). 2013; 6: 287–303.
  7. Fabrice A, Didier R. Exploring microbial diversity using 16S rRNA high-throughput methods. J Comput Sci Syst Biol. 2009; 2 (1): 74–92.
  8. Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 2011; 6 (12): e27310.
  9. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013 Jan 7; 41 (1): e1.
  10. Illumina Inc., Web Site [homepage on the Internet]. c2017 [cited 2017 Apr 10]. Next-Generation Sequencing (NGS) [cited 2017 Apr 10]; [about 2 screens]. Available from: https://www.illumina. com/technology/next-generation-sequencing.html
  11. Bag S, Saha B, Mehta O, Anbumani D, Kumar N, Dayal M, et al. An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples. Sci Rep. 2016 May 31; 6: 26775.
  12. Qubit 3.0 Fluorometer User Guide [file on the Internet]. Revision A.0. US: Thermo Fisher Scientific Inc. c2014 [cited 2017 Apr 10]: 67 p. Available from: https://tools.thermofisher.com/content/sfs/ manuals/qubit_3_fluorometer_man.pdf
  13. Polz MF, Cavanaugh CM. Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol. 1998 Oct; 64 (10): 3724–30.
  14. Reysenbach AL, Giver LJ, Wickham GS, Pace NR. Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol. 1992 Oct; 58 (10): 3417–8.
  15. Bru D, Martin-Laurent F, Philippot L. Quantification of the detrimental effect of a single primer-template mismatch by real- time PCR using the 16S rRNA gene as an example. Appl Environ Microbiol. 2008 Mar; 74 (5): 1660–3.
  16. Wu JH, Hong PY, Liu WT. Quantitative effects of position and type of single mismatch on single base primer extension. J Microbiol Methods. 2009 Jun; 77 (3): 267–75.
  17. Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M. CAMERA: a community resource for metagenomics. PLoS Biol. 2007 Mar; 5 (3): e75.
  18. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013 Jan; 41 (Database issue): D590–6.
  19. Mao D-P, Zhou Q, Chen C-Y, Quan Z-X. Coverage evaluation of universal bacterial primers using the metagenomic datasets. BMC Microbiol. 2012 May 3; 12: 66.
  20. Brownie J, Shawcross S, Theaker J, Whitcombe D, Ferrie R, Newton C, et al. The elimination of primer-dimer accumulation in PCR. Nucleic Acids Res. 1997 Aug 15; 25 (16): 3235–41.
  21. Lorenz TC. Polymerase Chain Reaction: Basic Protocol Plus Troubleshooting and Optimization Strategies. J Vis Exp. 2012 May 22; (63): e3998.
  22. Kircher M, Sawyer S, Meyer M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 2012 Jan; 40 (1): e3.
  23. 16S Metagenomic Sequencing Library Preparation. Preparing 16S Ribosomal RNA Gene Amplicons for the Illumina MiSeq System [file on the Internet]. [cited 2017 Apr 10]: 28 p. Available from: https://www.illumina.com/content/dam/illumina-support/ documents/documentation/chemistry_documentation/16s/16s-metagenomic-library-prep-guide-15044223-b.pdf
  24. MiSeq System Denature and Dilute Libraries Guide [file on the Internet]. San Diego: Illumina Inc.; c2016 [cited 2017 Apr 10]: 14 p. Available from: http://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/
  25. Rukovodstvo po sisteme MiSeq [file on the Internet]. San Diego:
  26. Collection of commonly used RDP Tools for easy building. In: GitHub [Git repository hosting service]. c2017 [cited 2017 Apr 10]. Available from: https://github.com/rdpstaff/RDPTools
  27. RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s. In: GitHub [Git repository hosting service]. c2017 [cited 2017 Apr 10]. Available from: https://github.com/rdpstaff/ classifier/tree/701e229dde7cbe53d4261301e23459d9161599
  28. The Ribosomal Database Project (RDP) [database on the Internet]. Release 11. East Lansing, MI: Michigan State University. c1992– 2014 [cited 2017 Apr 10]. Available from: https://rdp.cme.msu. edu/
  29. Collection of commonly used RDP Tools for easy building. In: GitHub [Git repository hosting service]. c2017 [cited 2017 Apr 10]. Available from: https://github.com/rdpstaff/RDPTools
  30. RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s. In: GitHub [Git repository hosting service]. c2017 [cited 2017 Apr 10]. Available from: https://github.com/rdpstaff/ classifier/tree/701e229dde7cbe53d4261301e23459d91615999d
  31. Jones MB, Highlander SK, Anderson EL, Li W, Dayrit M, Klitgord N, et al. Library preparation methodology can influence genomic and functional predictions in human microbiome research. Proc Natl Acad Sci U S A. 2015 Nov 10; 112 (45): 14024–9.