Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides


A fundamental goal in biotechnology and biology is the development of approaches to better understand the genetic basis of traits. Here we report a versatile method, trackable multiplex recombineering (TRMR), whereby thousands of specific genetic modifications are created and evaluated simultaneously. To demonstrate TRMR, in a single day we modified the expression of >95% of the genes in Escherichia coli by inserting synthetic DNA cassettes and molecular barcodes upstream of each gene. Barcode sequences and microarrays were then used to quantify population dynamics. Within a week we mapped thousands of genes that affect E. coli growth in various media (rich, minimal and cellulosic hydrolysate) and in the presence of several growth inhibitors (β-glucoside, D-fucose, valine and methylglyoxal). This approach can be applied to a broad range of traits to identify targets for future genome-engineering endeavors.

DOI: 10.1038/nbt.1653

5 Figures and Tables

Citations per Year

410 Citations

Semantic Scholar estimates that this publication has 410 citations based on the available data.

See our FAQ for additional information.

Cite this paper

@article{Warner2010RapidPO, title={Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides}, author={Joseph R Warner and Philippa J. Reeder and Anis Karimpour-Fard and Lauren B.A. Woodruff and Ryan T. Gill}, journal={Nature Biotechnology}, year={2010}, volume={28}, pages={856-862} }