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Build the Read: A Hands-On Activity for Introducing Microbiology Students to Next-Generation DNA Sequencing and Bioinformatics

    Authors: Guerrino Macori1,*, Angelo Romano2, Lucia Decastelli2, Paul D. Cotter1
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    Affiliations: 1: Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland; APC Microbiome Institute, Cork, Ireland; 2: Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta, Torino, Italy
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Received 04 June 2017 Accepted 08 August 2017 Published 01 December 2017
    • ©2017 Author(s). Published by the American Society for Microbiology

    • [open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.
    • †Supplemental materials available at http://asmscience.org/jmbe
    • *Corresponding author. Mailing address: Teagasc Food Research Centre, FoodBiosciences Department, Moorepark, Cork, Ireland. Phone: +353 (01) 805 9531. E-mail: [email protected].
    Source: J. Microbiol. Biol. Educ. December 2017 vol. 18 no. 3 doi:10.1128/jmbe.v18i3.1363
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    Abstract:

    Next-Generation Sequencing (NGS) is the current standard for providing genomic data, by virtue of the ability of the technology to generate a considerable amount of information rapidly and at low cost. The data generated can be of key importance to research and addressing issues in public health and, thus, is relevant to society. Unsurprisingly, content relating to the principle and chemistry underlying Next-Generation Sequencing is presented to almost every microbiology-related class, to professionals across multiple fields and, to the general public as popular science. The most commonly utilized NGS platforms (MiSeq, NextSeq and HighSeq) are those provided by Illumina. In this paper, we describe a hands-on activity for students to represent the chemistry underlying Illumina-based NGS, by creating representative reads using LEGO blocks, to link indexes, assemble the sequence and ‘identify’ the bacteria from which the DNA originated, thereby, in the process introducing the participants to the basic principles of bioinformatics.

References & Citations

1. Metzker ML 2010 Sequencing technologies—the next generation Nat Rev Genet 11 31 46 10.1038/nrg2626 http://dx.doi.org/10.1038/nrg2626
2. Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER 2013 The next-generation sequencing revolution and its impact on genomics Cell 155 27 38 10.1016/j.cell.2013.09.006 24074859 3969849 http://dx.doi.org/10.1016/j.cell.2013.09.006
3. Horn S 2012 Target enrichment via DNA hybridization capture Methods Mol Biol 840 177 188 10.1007/978-1-61779-516-9_21 22237535 http://dx.doi.org/10.1007/978-1-61779-516-9_21
4. Bolger AM, Lohse M, Usadel B 2014 Trimmomatic: a flexible trimmer for Illumina sequence data Bioinformatics 30 2114 2120 10.1093/bioinformatics/btu170 24695404 4103590 http://dx.doi.org/10.1093/bioinformatics/btu170
5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA 2012 SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing J Comput Biol 19 455 477 10.1089/cmb.2012.0021 22506599 3342519 http://dx.doi.org/10.1089/cmb.2012.0021
6. Antipov D, Hartwick N, Shen M, Raiko M, Pevzner PA 2016 PlasmidSPAdes: assembling plasmids from whole genome sequencing data Bioinformatics 32 3380 3387 27466620
7. Clooney AG, Fouhy F, Sleator RD, O’Driscoll A, Stanton C, Cotter PD, Claesson MJ 2016 Comparing apples and oranges?: Next generation sequencing and its impact on microbiome analysis PLoS One 11 e0148028 10.1371/journal.pone.0148028 26849217 4746063 http://dx.doi.org/10.1371/journal.pone.0148028
8. Shendure J, Ji H 2008 Next-generation DNA sequencing Nat Biotechnol 26 1135 1145 10.1038/nbt1486 18846087 http://dx.doi.org/10.1038/nbt1486
9. Mardis ER 2008 Next-generation DNA sequencing methods Annu Rev Genomics Hum Genet 9 387 402 10.1146/annurev.genom.9.081307.164359 18576944 http://dx.doi.org/10.1146/annurev.genom.9.081307.164359
10. Glenn TC 2011 Field guide to next-generation DNA sequencers Mol Ecol Resour 11 759 769 10.1111/j.1755-0998.2011.03024.x 21592312 http://dx.doi.org/10.1111/j.1755-0998.2011.03024.x
11. Ansorge WJ 2009 Next generation DNA sequencing techniques N Biotechnol 25 195 203 10.1016/j.nbt.2008.12.009 19429539 http://dx.doi.org/10.1016/j.nbt.2008.12.009
12. Lu H, Giordano F, Ning Z 2016 Oxford nanopore MinION sequencing and genome assembly Genom Proteom Bioinformatics 14 265 279 10.1016/j.gpb.2016.05.004 http://dx.doi.org/10.1016/j.gpb.2016.05.004
13. Mayo B, Rachid CT, Alegría Á, Leite AM, Peixoto RS, Delgado S 2014 Impact of next generation sequencing techniques in food microbiology Curr Genomics 15 293 309 10.2174/1389202915666140616233211 25132799 4133952 http://dx.doi.org/10.2174/1389202915666140616233211
14. Gilchrist CA, Turner SD, Riley MF, Petri WA, Hewlett EL 2015 Whole-genome sequencing in outbreak analysis Clin Microbiol Rev 28 541 563 10.1128/CMR.00075-13 25876885 4399107 http://dx.doi.org/10.1128/CMR.00075-13
15. Roossinck MJ 2016 Deep sequencing for discovery and evolutionary analysis of plant viruses Virus Res in press 10.1515/9781400883257 27876625 http://dx.doi.org/10.1515/9781400883257

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2017-12-01
2020-07-07

Abstract:

Next-Generation Sequencing (NGS) is the current standard for providing genomic data, by virtue of the ability of the technology to generate a considerable amount of information rapidly and at low cost. The data generated can be of key importance to research and addressing issues in public health and, thus, is relevant to society. Unsurprisingly, content relating to the principle and chemistry underlying Next-Generation Sequencing is presented to almost every microbiology-related class, to professionals across multiple fields and, to the general public as popular science. The most commonly utilized NGS platforms (MiSeq, NextSeq and HighSeq) are those provided by Illumina. In this paper, we describe a hands-on activity for students to represent the chemistry underlying Illumina-based NGS, by creating representative reads using LEGO blocks, to link indexes, assemble the sequence and ‘identify’ the bacteria from which the DNA originated, thereby, in the process introducing the participants to the basic principles of bioinformatics.

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Author and Article Information

  • Received 04 June 2017 Accepted 08 August 2017 Published 01 December 2017
  • ©2017 Author(s). Published by the American Society for Microbiology

  • [open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.
  • †Supplemental materials available at http://asmscience.org/jmbe
  • *Corresponding author. Mailing address: Teagasc Food Research Centre, FoodBiosciences Department, Moorepark, Cork, Ireland. Phone: +353 (01) 805 9531. E-mail: [email protected].

Figures

Build the Read: A Hands-On Activity for Introducing Microbiology Students to Next-Generation DNA Sequencing and Bioinformatics
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Citation: Macori G, Romano A, Decastelli L, Cotter P. 2017. Build the read: a hands-on activity for introducing microbiology students to next-generation dna sequencing and bioinformatics . J. Microbiol. Biol. Educ. 18(3): doi:10.1128/jmbe.v18i3.1363
/content/jmbe/10.1128/jmbe.v18i3.1363.f1-jmbe-18-62
FIGURE 1

Bricks fixed in the flow-cell. In the simulation are represented 8 reads of 7 bases, each with indexes of 3 base lengths. (See Appendix 2 for the list of materials and notes for the instructor.)

jmbe/18/3/jmbe-18-62f1_thmb.gif
jmbe/18/3/jmbe-18-62f1.gif
Image of FIGURE 1

Click to view

FIGURE 1

Bricks fixed in the flow-cell. In the simulation are represented 8 reads of 7 bases, each with indexes of 3 base lengths. (See Appendix 2 for the list of materials and notes for the instructor.)

Source: J. Microbiol. Biol. Educ. December 2017 vol. 18 no. 3 doi:10.1128/jmbe.v18i3.1363
Download as Powerpoint
/content/jmbe/10.1128/jmbe.v18i3.1363.f2-jmbe-18-62
FIGURE 2

Simulation of part 1 and part 2 of the exercise The picture shows the reads that have been built with their indexes (a) and their overlapping (b), assembling a contig.

jmbe/18/3/jmbe-18-62f2_thmb.gif
jmbe/18/3/jmbe-18-62f2.gif
Image of FIGURE 2

Click to view

FIGURE 2

Simulation of part 1 and part 2 of the exercise The picture shows the reads that have been built with their indexes (a) and their overlapping (b), assembling a contig.

Source: J. Microbiol. Biol. Educ. December 2017 vol. 18 no. 3 doi:10.1128/jmbe.v18i3.1363
Download as Powerpoint
/content/jmbe/10.1128/jmbe.v18i3.1363.f3-jmbe-18-62
FIGURE 3

Possible extensions of the exercise. Simulation of the amplification and cluster generation. The hand simulates the consequential addition of bases during the sequence by synthesis reaction while the smartphone acquires the sequential pictures, simulating the solid-phase cluster amplification and acquisition of the images of the flow-cell by sequencers.

jmbe/18/3/jmbe-18-62f3_thmb.gif
jmbe/18/3/jmbe-18-62f3.gif
Image of FIGURE 3

Click to view

FIGURE 3

Possible extensions of the exercise. Simulation of the amplification and cluster generation. The hand simulates the consequential addition of bases during the sequence by synthesis reaction while the smartphone acquires the sequential pictures, simulating the solid-phase cluster amplification and acquisition of the images of the flow-cell by sequencers.

Source: J. Microbiol. Biol. Educ. December 2017 vol. 18 no. 3 doi:10.1128/jmbe.v18i3.1363
Download as Powerpoint

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