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Swabs to Genomes Workflow… as a class!

For the last few years our lab has been really excited about the idea of having undergraduates culture bacterial isolates and sequence their genomes.  Starting with the Undergraduate Built Environment Genomes Project in 2011, we went on to re-write and upgrade the assembly pipeline that we use, followed by the publication of the “Swabs to genomes: a comprehensive workflow” paper describing the entire process.   Along the way we’ve published over 20 Genome Announcements with undergraduate authors (usually as the first author).  I feel that we have the process down fairly well in the lab and currently have undergraduates running through isolates from seagrass, feline anal sacs, and the built environment.

However, we have never tried the next logical step… running this as a class in a 10 week quarter.   A couple of years ago we got three students in the lab and we basically gave them the workflow and said “try this and see how long it takes”.  One bailed after a month, one bailed after a few months and one published a Genome Announcement 1.5 years later.  Hardly a ringing endorsement for doing it in a single quarter, though probably not the best test.

A sample student plate
A sample student plate

Enter Ashley Vater, a graduate student at UC Davis, who came to our lab asking for help finding a bacteriophage of an abalone pathogen using metagenomics.  Turned out she had registered to teach a freshman seminar on “big data” and thought some metagenomics might be the way to go.   Well we talked her out of that and talked her into co-instructing Swabs to Genomes with me as a Spring Quarter freshman seminar.  Once that was decided we (most she) hurriedly threw together class materials, a syllabus, learning goals etc.  We got some students enrolled, spread some aquaculture abalone feces on plates and got started right away on Week 1.  The goal is to have annotated and publishable genomes by Week 10!

The class only meets for 2 hours, once a week, so there’s a fair bit of magic that happens between classes.  For example last week the students extracted DNA from overnight cultures, but we will run the PCRs, and they will check them on gels in class.  There just aren’t enough class days for all the wet lab work.

And of course (this is the Eisen lab after all) we are making the students blog about the experience.  Every week, one group of students will write a blog post about what we did that week.   These can all be found here on microBEnet.

At the end of the quarter, Ashley and I will write a summary of how it all went… what worked and what didn’t work.  In addition we’ll post all of the class materials in hopes that others will try something similar.   We’d love to have any input… and it would be especially great if people commented on the student blogs.


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 “Swabs to Genomes Workflow… as a class!

  1. We’re running high-throughput cultivation “real research” sections for freshman biology lab, now for the second semester. We should compare notes!

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