The Built Environment Reference Genome Collection… A First Taste

Over the last several years our lab has spent a fair bit of effort on collecting and sequencing genomes of bacteria from the built environment.  Genome sequences are useful for a number of reasons including facilitating metagenomics and understanding the actual metabolic capacity of particular microbes.  In particular we hope that genome sequences will facilitate experimental work on some of these organisms, a logical next step after the “what is there?” phase of the field has been exhausted. And since these bacteria have been all cultured they sidestep the whole “most things in the built environment are dead” problem.

This quest has led in a number of directions starting with our Undergraduate Reference Genome Project, through improving our genome assembler and publishing our workflow, to sending genome-sequenced built environment microbes to space.  Now we’re even experimenting with doing this sort of thing in the classroom.

But for awhile the thought was growing in our minds that instead of doing a bunch of genome sequencing projects ourselves, we should teach other labs how to do it and facilitate where possible.   To that end, the Alfred P. Sloan Foundation agreed that we could spend some of our grant on a “Built Environment Culturomics” project with exactly this goal.  We e-mail blasted everyone we knew that had funding from the Sloan Foundation to work on the microbiology of the built environment with the following proposal.

If they would send us bacterial genomic DNA, we would sequence and assemble the genomes of up to 20 organisms per lab.  In addition we would help the labs if they wanted to learn assembly, or any of the associated bioinformatics (validation, annotation etc.).  Lastly we would help the lab submit the data to NCBI, submit the cultures to a culture collection, and help with publishing as needed.

We have gotten a lot of interest, and so far have sequenced somewhere in the neighborhood of a 70 genomes (publications pending).  These include Pseudomonas strains from a hospital, house-associated bacteria from San Francisco, several bacterial species from plumbing systems, and bacteria from an athletic facility.  As we dig more into the analyses and publications we’ll post updates here.

We expect to do another couple of sequencing runs so if your lab has funding from the Sloan Foundation and you have bacterial strains that you’d like to sequence… give us a shout in the very near future!

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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