Personal microbiomes and next-generation sequencing for laboratory-based education.

Sequencing and bioinformatics technologies have advanced rapidly in recent years, driven largely by developments in next-generation sequencing (NGS) technology. Given the increasing importance of these advances, there is a growing need to incorporate concepts and practices relating to NGS into undergraduate and high school science curricula. We believe that direct access to sequencing and bioinformatics will improve the ability of students to understand the information obtained through these increasingly ubiquitous research tools. In this commentary, we discuss approaches and challenges for bringing NGS into the classroom based on our experiences in developing and running a microbiome project in high school and undergraduate courses. We describe strategies for maximizing student engagement through establishing personal relevance and utilizing an inquiry-based structure. Additionally, we address the practical issues of incorporating cutting edge technologies into an established curriculum. Looking forward, we anticipate that NGS educational experiments will become more commonplace as sequencing costs continue to decrease and the workflow becomes more user friendly.

[1]  Daniel Patrick Smith,et al.  Forensic analysis of the microbiome of phones and shoes , 2015, Microbiome.

[2]  Leonard A. Annetta,et al.  Is inquiry possible in light of accountability?: A quantitative comparison of the relative effectiveness of guided inquiry and verification laboratory instruction , 2010 .

[3]  Vincent N. Lunetta,et al.  The Laboratory in Science Education: Foundations for the Twenty-First Century , 2004 .

[4]  D. Walt,et al.  Lessons learned from the introduction of personalized genotyping into a medical school curriculum , 2011, Genetics in Medicine.

[5]  Scott A Strobel,et al.  Plant endophytes as a platform for discovery-based undergraduate science education. , 2007, Nature chemical biology.

[6]  Jennifer C. Drew,et al.  Whole genome sequencing in the undergraduate classroom: outcomes and lessons from a pilot course. , 2008, Journal of microbiology & biology education.

[7]  Shawneequa L. Callier Swabbing Students: Should Universities Be Allowed to Facilitate Educational DNA Testing? , 2012, The American journal of bioethics : AJOB.

[8]  A. Klindworth,et al.  Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies , 2012, Nucleic acids research.

[9]  I. Makarevitch,et al.  Killing two birds with one stone: Model plant systems as a tool to teach the fundamental concepts of gene expression while analyzing biological data. , 2017, Biochimica et biophysica acta. Gene regulatory mechanisms.

[10]  Katherine H. Huang,et al.  Identifying personal microbiomes using metagenomic codes , 2015, Proceedings of the National Academy of Sciences.

[11]  A. Kasarskis,et al.  Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study , 2013, Genome Medicine.

[12]  Katherine M. Hyland,et al.  Participatory Genomic Testing as an Educational Experience. , 2016, Trends in genetics : TIG.

[13]  B. Drayton,et al.  A Study of the Literature on Lab-Based Instruction in Biology , 2015 .

[14]  Justin F Shaffer,et al.  Brewing for Students: An Inquiry-Based Microbiology Lab , 2015, Journal of microbiology & biology education.

[15]  Erez Lieberman Aiden,et al.  The expanding scope of DNA sequencing , 2012, Nature Biotechnology.

[16]  M. LaBonte,et al.  An alternative laboratory designed to address ethical concerns associated with traditional TAS2R38 student genotyping , 2015, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[17]  Jack T. H. Wang,et al.  Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome† , 2015, Journal of microbiology & biology education.

[18]  Jason Stenson,et al.  Humans differ in their personal microbial cloud , 2015, PeerJ.