home Miscellaneous, Training Everyone choose a genome (reference genome sequencing as an undergrad research project)

Everyone choose a genome (reference genome sequencing as an undergrad research project)

(cross-posted with modifications from the Eisen Lab blog)

Not enough reference genomes from the built environment?
Looking for ways to increase undergraduate participation in research?

The marriage of these two concepts seems fairly straightforward.   Bring undergraduates into the lab, have them culture microbes from the built environment, then sequence and assemble genomes… one per student.

That’s the process currently underway in the Eisen Lab, with support from microBEnet and the Sloan Foundation.

Eisen Lab

In addition to the obvious goal of sequencing reference genomes we hope to develop a workflow and protocols for undergraduate isolation and sequencing of reference genomes.  Ideally this would be transferable to other labs, even classrooms.

Currently there are 6 undergraduates involved in this project, having commenced in January.   Since then they have learned sterile technique, basic microbiology/molecular biology protocols, 16S PCR, basic cloning, and how to analyze 16S rRNA sequences.  Each one has now processed their own environmental samples and we’re in the process of screening candidates for sequencing and starting to prepare Illumina libraries.

In addition to the science, this project has a strong outreach component.   The students will be blogging about their experience on the lab blog and footage is being taken for a short “documentary” of the whole process.  Check this space for updates.



David Coil

David Coil is a Project Scientist in the lab of Jonathan Eisen at UC Davis. David works at the intersection between research, education, and outreach in the areas of the microbiology of the built environment, microbial ecology, and bacterial genomics. Twitter

5 thoughts on “Everyone choose a genome (reference genome sequencing as an undergrad research project)

  1. Cool. I am trying something similar based on the human microbiome project’s “100 most wanted” list that I saw at asm last year. We won’t be doing the sequencing this quarter, but the isolation and ident biochemically and by 16s. I hope to do the sequencing and annotation but am waiting to see how the wet work goes! These experiences for undergrads – any kind of discovery process really- go a long way toward getting them out of md mode and thinking about research.

  2. Paul,

    Glad to hear that you’re working on something similar with undergrads. Would you be interested in a guest blog post writing up your experiences and lessons learned? I think the more people share information about these kinds of projects the better.

    1. That could be fun – i give the final exam on Wed, so maybe after that :) Or slightly before, if I am procrastinating…

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