Rapid Tracking and Identifying Phages through Barcoding

A groundbreaking study from the Department of Energy's Lawrence Berkeley National Laboratory. This research introduces an innovative method to swiftly label and characterize bacteriophages, viruses that target bacteria, using the acclaimed CRISPR gene-editing technology. The team's approach holds the promise of transforming our ability to identify, track, and manipulate these elusive entities.

Central to the researchers' methodology is the mapping of the gene essentiality landscape of phages on a genome-wide scale. Employing CRISPR interference (CRISPRi) technology, the team systematically suppressed the expression of nearly every gene in two model phages, λ and P1. This groundbreaking effort marks the first systematic study of gene essentiality at such a scale in bacterial viruses.

Illustration of Phage Engineering method used in to perform barcoding
Illustration of Phage Engineering method used in their study The homologous recombination method was used to introduce random barcodes at nonessential genomic loci Additionally counter selection facilitated by the nuclease active Cas12a was employed to enrich the engineered phages The schematic outlines the steps for barcode insertion and counterselection focusing on the red locus for lambda phage and the res locus for P1 phage Credit Original study cited below

By discerning which genes are indispensable for the infection cycle and which are dispensable, the researchers provide a comprehensive understanding of phage gene essentiality. Crucially, this knowledge extends beyond specific phage types, highlighting an interconnectedness among phage genes that could unlock further insights into their functioning.

By putting certain genes on mute, the researchers stumbled upon a game-changing revelation in their study—the incorporation of barcodes into phage genomes. The objective was to pinpoint genes that weren't crucial for phage function and swap them with distinctive tags. These tags, comprising unique sequences of nucleic acids, operate much like the barcodes you find at your local supermarket. This ingenious move now allows scientists and clinicians to swiftly pinpoint and monitor various phages in a range of environments. This, in turn, equips researchers with a powerful tool to delve into diverse aspects of bacteriophages within a specific setting, opening up new avenues for scientific exploration.

Bacteriophages represent one of the most abundant and genetically diverse entities. By combining the power of CRISPR gene-editing technology with the practicality of barcoding, the researchers have opened new avenues for understanding, utilizing, and tracking bacteriophages. This pioneering work not only sheds light on the gene essentiality of phages but also paves the way for transformative applications across agriculture, environmental science, and healthcare. As we delve deeper into the microbial universe, the potential unleashed by this study offers a glimpse into a future where the untapped knowledge of phage gene function finds practical and impactful applications.

You can read their full paper here Denish Piya et al, Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages, PLOS Biology (2023). DOI: 10.1371/journal.pbio.3002416. Cover photo credit to the original study

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About the author

Hello there!

I'm Raphael Hans Lwesya. I have a deep interest in phage research and science communication. I strive to simplify complex ideas and present the latest phage-related research in an easy-to-digest format. Thank you for visiting The Phage blog. If you have any questions or suggestions, please feel free to leave a comment or contact me at [email protected].

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