The Raman Laboratory develops new tool for mapping phage-bacterial interactions

Researchers have developed a new method that reveals the molecular code governing bacteriophage-bacteria interactions. Bacteriophages (phages) – viruses that infect and kill bacteria – have emerged as a promising new frontier due to potential use in antibacterial therapeutics.

Photo of Vatsan Raman
Assistant Professor Vatsan Raman.

In a paper released March 9 in eLife, Biochemistry Assistant Professor Vatsan Raman and microbiology graduate student Phil Huss present their new method, dubbed ORACLE (Optimized Recombination, Accumulation and Library Expression), for systematically mapping how sequence changes affects the interaction of a phage with its host. Full publication is expected in eLife later this month.

ORACLE is designed as a foundational technology to reveal sequence-function relationships in any phage gene. It creates a library of variants that researchers use to map the phage’s mutational landscape, revealing a comprehensive view of its structure, function, and evolution.

Phil Huss.
Phil Huss.

Researchers utilize this map to identify how alterations to the phage’s sequence and structure influence its interactions with the host bacteria, information that can then be used to create a new, synthetic variant designed for a specific target and function.

In this study, researchers looked at the T7 phage, which infects most strains of E. coli. By comparing which phage mutations did the best after attacking different E. coli, researchers were able to make a map essentially pointing to the best parts of the phage to change.

“It’s really remarkable how variants that are only slightly different can fare so much better or worse on different E. coli,” said Huss. “Mapping all of this information has let us create a very accurate functional profile and I’m excited to use that information as a platform to engineer even better phages.”

Phage and Oracle graphic.The use of natural phages for phage therapy has fundamental limitations in activity, reliability, scalability and speed. Natural phages have lower activity due to evolutionary constraints and provide inconsistent results. Moreover, the discovery of new phages when bacterial resistance arises is a slow and laborious process.

Using ORACLE allows researchers to map phage function and uncover critical variants on an unprecedented scale.

“Compared to traditional phage assays, the scale of ORACLE is 1,000-10,000 times greater,” said Raman. “What this means is we can systematically make and comprehensively cover the mutational landscape of any phage gene, and thus engineer phages with a desired property.”

Once phage variants are created, scaling up ORACLE to investigate numerous hosts is a matter of scaling up sequencing volume, not experimental complexity, making ORACLE a powerful tool for mapping and engineering new phages to attack specific bacteria.

“Recent success stories in the clinic of treating multidrug resistant Acinetobacter and Mycobacterium showcase the enormous potential of phage therapy,” said Raman. “Now the confluence of genome engineering, high-throughput DNA synthesis, and sequencing enabled by ORACLE – together with viral metagenomics – has the potential to transform phage biology.”

Read more from the National Institutes of Health (NIH).