Dual barcoded shotgun expression library sequencing, or Dub-seq, is a novel high-throughput method for discovering gene function in microbes under various environmental conditions. It was developed by scientists in the Environmental Genomics and Systems Biology (EGSB) Division under the aegis of the Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA) program. In a seminal paper published January 18 in Nature Communications, the Dub-seq team presented details of the technique and proof-of-concept work showing that the approach is reproducible, economical, scalable, and identifies both known and novel gene functions.
In a letter to the editor published July 6 in Nature Biotechnology, the KBase team presented a comprehensive overview of the platform and an assessment of its scientific impact. The paper describes the unique features and infrastructure of the platform, in addition to highlighting scientific use cases that demonstrate its significance for biology research.
While advances in sequencing technologies have enabled researchers to access the genomes of thousands of microbes and make them publicly available, the task of assigning functions to the genes uncovered has lagged behind due to the limited capacity of functional analysis approaches. To help overcome this bottleneck, Berkeley Lab researchers, led by Adam Arkin and Adam Deutschbauer in Biosciences’ Environmental Genomics and Systems Biology (EGSB) Division and Matthew Blow at the DOE Joint Genome Institute (JGI), have developed a workflow that enables large-scale, genome-wide assays of gene importance across many conditions.
To characterize the functions of genes in newly discovered bacteria, microbiologists introduce mutations using mobile DNA snippets called transposons delivered via a vector. But finding an effective transposon mutagenesis system for a novel microorganism through trial and error can be a time-consuming and expensive endeavor.
To streamline the process, Environmental Genomics and Systems Biology (EGSB) Division researchers, led by Adam Deutschbauer and Adam Arkin, have developed a new technique to test hundreds of different transposon vector variants in parallel within what the investigators term “magic pools.”
The approach was detailed in mSystems, an open access journal from the American Society for Microbiology.
A high-throughput, cost effective method for discovering gene function in microbes under various environmental conditions is among the winners of R&D Magazine’s 2017 R&D 100 Award. The technology, called Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), was developed by Adam Arkin, Adam Deutschbauer, Vivek Mutalik, and Pavel Novichkov of the Environmental Genomics and Systems Biology (EGSB) Division. Dub-seq … Read more »