STEMM: Sequencing Training Education using Microbial Metagenomics

Project No.
PI Name
Elizabeth Dinsdale
San Diego State Univeristy

Abstract 1

STEMM: Sequencing Training Education using Microbial Metagenomics

Presentation Type
Megan Morris, Matthew Haggerty, Kevin Walsh, Robert Edwards, Marilee Bresciani Ludvik


While the first year of the 21st century started with the sequencing of the human genome, metagenomic analysis of microbial communities has become an overwhelming offshoot of DNA sequencing technology and one that is highly accessible to undergraduate researchers. DNA sequencing technologies that is revolutionizing the medical and pharmaceutical fields and students need to become familiar with interpretation of the data to participate in the genomic era. The bioinformatic tools are rapidly developing and many Faculty are lacking the training to use teach these techniques. Metagenomics provides a multitude of ways to integrate ecological, biochemical, molecular and computational ideas and paradigms into undergraduate teaching. Our proposal will provide undergraduate students and faculty with the knowledge to use the latest technologies, practice at thinking critically, and ways to form partnerships across disciplines.


The major goals of the project are to:
1) Vertically integrate metagenomics into the undergraduate curriculum
2) Integrate DNA sequencing and metagenomic analysis across universities via faculty workshops
3) Analyze the effectiveness of our programs and identify ways that lead to the best outcomes for STEMS learning


We teach metagenomics in a range of classes from lower to upper level biology and computer science classes. We have conducted two Summer Faculty training course in metagenomics for 32 Faculty from around the USA This year we had 14 Faculty from a range of Universities/Colleges in the USA and two Professors from Mexico joined the course. We have developed a short intensive course that we have taught to undergraduates, graduates, Post-doctoral researcher and Faculty in San Diego Mexico, Brazil and Australia. These courses reach about 300 people a year. In each of the workshops and classes we have developed and conducted evaluations of learning outcomes. These evaluations are currently be compiled and the results are being prepared for publication. Several of the evaluations have proved to be ambiguous and therefore we are redeveloping those instruments.


Metagenomic courses are providing students with research experience and improving their abilities to conduct science causing many to re-assess their career pathways. During the summer Faculty workshop we agreed upon three shared learning outcomes and assessments. The three shared learning outcomes were; 1) define the terms genomics and metagenomics and explain the difference, 2) Explain how (meta)genomics is used to study (community) structure and/or function of microbes and 3) analyze metagenomic or genomic data. The measurement instruments will be 1) an open-ended exam question (pre- and post) and possibly multiple choice, 2) open-ended exam question is agreed upon method; 3) Apply a shared rubric or criteria checklist to the written evidence derived from process, which will vary by instructors. We will now be able to assess the various pedagogical methods for teaching genomics and metagenomics across multiple institutions providing an examination of the success of our program.

Broader Impacts

We have disseminated our results at invited seminars, scientific meetings, journal publications, student presentations and workshops in six countries. We participate in local Open Day, where 700 community members are involved, and this provides an opportunity to talk about DNA sequencing and the use of genomics in all areas of life.

Unexpected Challenges

Engaging Faculty in development of assessments. To deal with this we provided examples of assessments, which improved understanding and encouraged discussion. The increased discussion lead to a shared assessment vision.


Edwards, R. A., J.M. Haggerty, N. Cassman, J. C. Busch, K. Aguinaldo, S. Chinta, R. Morey, M. Houle Vaughn, T.T. Harkins, C. Teiling, K. Fredrikson, and E. A Dinsdale 2013 Microbes, metagenomes and marine mammals: enabling the next generation of scientist to enter the genomic era. BMC Genomics 14:600