Skip to main content
Using Comparative Genomics for Inquiry-Based Learning to Dissect Virulence of Escherichia coli O157:H7 and Yersinia pestis
CBE - Life Sciences Education (2012)
  • David J. Baumler, University of Wisconsin-Madison
  • Lois M. Banta, Williams College
  • Kai F. Hung, Eastern Illinois University
  • Jodi A. Schwarz, Vassar College
  • Eric L. Cabot, University of Wisconsin-Madison
  • Jeremy D. Glasner, University of Wisconsin-Madison
  • Nicole T. Perna, University of Wisconsin - Madison
Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of Genomes database. In the second module, students use an alignment of five Yersinia pestis genomes to analyze single-nucleotide polymorphisms of three genes to classify strains into biovar groups. Students are then given sequences of bacterial DNA amplified from the teeth of corpses from the first and second pandemics of the bubonic plague and asked to classify these new samples. Learning-assessment results reveal student improvement in self-efficacy and content knowledge, as well as students’ ability to use BLAST to identify genomic islands and conduct analyses of virulence factors from E. coli O157:H7 or Y. pestis. Each of these educational modules offers educators new ready-to-implement resources for integrating comparative genomic topics into their curricula.
  • BLAST,
  • learning objectives,
  • genomics,
  • bioinformatics,
  • undergraduate biological science curricula
Publication Date
Spring 2012
Citation Information
David J. Baumler, Lois M. Banta, Kai F. Hung, Jodi A. Schwarz, et al.. "Using Comparative Genomics for Inquiry-Based Learning to Dissect Virulence of Escherichia coli O157:H7 and Yersinia pestis" CBE - Life Sciences Education Vol. 11 (2012)
Available at: