Undergraduate Research: Built Environment Genomes

This project, started in December 2011, aimed at generating bacterial reference genomes from the built environment.  The goal was to provide a group of undergraduates with a substantial research experience while also conducting outreach related to the microbiology of the built environment.

Students collected samples from various built environments then cultured and identified a number of bacteria.  A subset of these were chosen for genome sequencing, one per student.  The students extracted DNA and prepared it for Illumina sequencing.  This was followed by de novo genome assembly, annotation, and preparation of a series of “Genome Announcement” papers.

This project was managed by David Coil with help from Jenna Lang.  Holly Bik, Aaron Darling, and Guilluame Jospin provided bioinformatic support.

Status of genomes:

Brachybacterium muris (Jonathon Lo): Paper here.   Genome assembly located here. Raw reads located here.

Microbacterium sp (Zach Bendiks): Paper here.  Genome assembly located here. Raw reads located here.

Curtobacterium flaccumfaciens (Jennifer Flanagan): Paper here.  Genome assembly here. Raw reads located here.

Dietzia sp (Amanda Diep): Paper here.  Genome assembly here.  Raw reads located here.

Kocuria rosea (Jessica Doctor): Paper here.  Genome assembly here.  Raw reads located here.

Leucobacter sp (Dakota Bevans, Hannah Holland-Moritz): Paper here.  Genome assembly here.  Raw reads located here.

Other information

See here for our project blog.  Also check out the video below describing the project: