1887

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
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    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
    Source: J. Microbiol. Biol. Educ. December 2017 vol. 18 no. 3 doi:10.1128/jmbe.v18i3.1363
MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • PDF
    399.70 Kb
  • XML
    33.13 Kb
  • HTML
    34.02 Kb

    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.

Key Concept Ranking

Chromosomal DNA
0.7571223
Food Microbiology
0.59912825
Clostridium botulinum
0.5909247
0.7571223

References & Citations

1. Metzker ML2010Sequencing technologies—the next generationNat Rev Genet11314610.1038/nrg2626 http://dx.doi.org/10.1038/nrg2626
2. Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER2013The next-generation sequencing revolution and its impact on genomicsCell155273810.1016/j.cell.2013.09.006240748593969849 http://dx.doi.org/10.1016/j.cell.2013.09.006
3. Horn S2012Target enrichment via DNA hybridization captureMethods Mol Biol84017718810.1007/978-1-61779-516-9_2122237535 http://dx.doi.org/10.1007/978-1-61779-516-9_21
4. Bolger AM, Lohse M, Usadel B2014Trimmomatic: a flexible trimmer for Illumina sequence dataBioinformatics302114212010.1093/bioinformatics/btu170246954044103590 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 PA2012SPAdes: a new genome assembly algorithm and its applications to single-cell sequencingJ Comput Biol1945547710.1089/cmb.2012.0021225065993342519 http://dx.doi.org/10.1089/cmb.2012.0021
6. Antipov D, Hartwick N, Shen M, Raiko M, Pevzner PA2016PlasmidSPAdes: assembling plasmids from whole genome sequencing dataBioinformatics323380338727466620
7. Clooney AG, Fouhy F, Sleator RD, O’Driscoll A, Stanton C, Cotter PD, Claesson MJ2016Comparing apples and oranges?: Next generation sequencing and its impact on microbiome analysisPLoS One11e014802810.1371/journal.pone.0148028268492174746063 http://dx.doi.org/10.1371/journal.pone.0148028
8. Shendure J, Ji H2008Next-generation DNA sequencingNat Biotechnol261135114510.1038/nbt148618846087 http://dx.doi.org/10.1038/nbt1486
9. Mardis ER2008Next-generation DNA sequencing methodsAnnu Rev Genomics Hum Genet938740210.1146/annurev.genom.9.081307.16435918576944 http://dx.doi.org/10.1146/annurev.genom.9.081307.164359
10. Glenn TC2011Field guide to next-generation DNA sequencersMol Ecol Resour1175976910.1111/j.1755-0998.2011.03024.x21592312 http://dx.doi.org/10.1111/j.1755-0998.2011.03024.x
11. Ansorge WJ2009Next generation DNA sequencing techniquesN Biotechnol2519520310.1016/j.nbt.2008.12.00919429539 http://dx.doi.org/10.1016/j.nbt.2008.12.009
12. Lu H, Giordano F, Ning Z2016Oxford nanopore MinION sequencing and genome assemblyGenom Proteom Bioinformatics1426527910.1016/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 S2014Impact of next generation sequencing techniques in food microbiologyCurr Genomics1529330910.2174/1389202915666140616233211251327994133952 http://dx.doi.org/10.2174/1389202915666140616233211
14. Gilchrist CA, Turner SD, Riley MF, Petri WA, Hewlett EL2015Whole-genome sequencing in outbreak analysisClin Microbiol Rev2854156310.1128/CMR.00075-13258768854399107 http://dx.doi.org/10.1128/CMR.00075-13
15. Roossinck MJ2016Deep sequencing for discovery and evolutionary analysis of plant virusesVirus Resin press10.1515/978140088325727876625 http://dx.doi.org/10.1515/9781400883257
jmbe.v18i3.1363.citations
jmbe/18/3
content/journal/jmbe/10.1128/jmbe.v18i3.1363
Loading

Citations loading...

Supplemental Material

Loading

Article metrics loading...

/content/journal/jmbe/10.1128/jmbe.v18i3.1363
2017-12-01
2017-12-11

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.

Highlighted Text: Show | Hide
Loading full text...

Full text loading...

/deliver/fulltext/jmbe/18/3/jmbe-18-62.html?itemId=/content/journal/jmbe/10.1128/jmbe.v18i3.1363&mimeType=html&fmt=ahah

Figures

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
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
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

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error