Research

Viruses/bacteriophages/phages are critical players in processes as diverse as global biogeochemical cycles and human health. Phages show high specificity to their target host, which in turn defend themselves using an array of mechanisms. However, to date, the specificity trait encoded in these interactions has not been studied systematically. Recently, we used three high-throughput genetic technologies (RB-TnSeq, Dub-seq, and CRISPRi) developed at the LBNL-UC Berkeley to globally map the functional interactions between diverse phages and their bacterial hosts. Phage predation and microbiome ecosystem function is influenced not only by diverse biotic conditions but also by abiotic biogeochemical conditions. We have multiple projects underway to isolate novel phages (double strand DNA phages, single strand DNA phages and single strand RNA phages), characterize their interactions with target bacteria and study their influence of microbiome function.  One of the larger goal is to predict phage susceptibility based on the genome sequence alone. These interaction studies are crucial in uncovering molecular mechanisms of interactions and engineering the functional traits in phages, phage capsids and chimeric phages for diverse applications as diverse as biodefense/biosecurity and agriculture productivity. 

Projects: 

• DOE BRaVE Phage Foundry

• NSF EDGE: Connecting host genotype to phage susceptiblity phenotype

• DOE ENIGMA - Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov), a Science Focus Area Program 

• DOE Virsoil: Ecology of Phage resistance

Linking genotype-to-phenotype is at the core of building any new biological product, whether the product is made up of DNA, RNA, Proteins, lipids, carbohydrate or their combinations. Towards this grand goal of connecting gentoype to phenotype, our teams conceptualized and developed a high-throughput overexpression characterization technology (dual barcoded shotgun expression library sequencing, Dub-seq) that is scalable, quantitative, and agnostic to the source of DNA and allow multiplex characterization of underlying function. So far, we have used Dub-seq technology to uncover stress and antibiotic tolerance traits, phage resistance phenotypes, and used in functional complementation approaches. This technology is easily amenable to characterize biological function encoded in the environmental DNA, phage genomes or the laboratory produced single-amplified-genomes from uncultivable bacterial clades. This technology has won 2017 R&D100 Award. Along with Dub-seq technology, we have also adopted technologies developed by our collaborators such as randomly barcoded Tn-seq (RB-TnSeq) and different CRISPR interference  (CRISPRi) systems for functional assessment of bacterial and phage genomes.

Projects: 

• DOE DOE ENIGMA - Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov), a Science Focus Area Program 

• DOE Virsoil: Ecology of Phage resistance

Microbial communities pervade everything from soil, air and water to humans and animals. We are made up of, and are covered by, a microbial jungle. Like every living entity, microbes have developed numerous ways to compete with each other to exist and multiply. Some produce nasty chemicals to deter others while some produce proteins that degrade those nasty chemicals in response as a counterattack. Some produce ‘stabbing needle’ types of protein machines (commonly known as Tailocins) to inhibit or kill specific members in a bacterial community while not impacting their kin. This strategy seems to provide sister cells a competitive advantage. Tailocins are phage-tail-like bacteriocins, closely related to phages, and share evolutionary relationship with toxin delivering Nano-scale sized protein machines called contractile injection systems. Using genetic tools developed at Berkeley Lab, we have characterized the interaction of these many tailocin particles with diverse pseudomonads and also the host factors involved in tailocin mediated killing and self-immunity. We are currently studying the design rules for engineering of these protein nano-machines to target specific bacteria. These studies have direct implication on using tailocins for microbiome manipulation and as therapeutics for recalcitrant bacterial infections.  

Projects:

• DOE DOE ENIGMA - Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov), a Science Focus Area Program 

Our inability to reliably predict quantitative behavior of sequence-controlled polymers limits their application potential. Every synthetic biology and biomanufacturing project starts with searching for genetic parts and tools to engineer bacteria of interest. We are passionate about designing, studying and cataloguing genetic parts and tools, and constructing biological insulation architecture to enable reliable and predictable engineering of diverse bacteria. As a part of larger team, we have created panels of public-domain standard biological parts that support reliable forward engineering of gene expression at genome scales for synthetic biology users and practitioners. We are currently developing datamining approaches to compile and curate functional genetic elements and empower future biological engineers and synthetic biologists to dream beyond laboratory model systems.  

Projects:

• DOE Kbase

• NSF BIOFAB