For decades, the ability to precisely rewrite bacterial genomes has been largely confined to a single workhorse organism: Escherichia coli. That limitation has slowed efforts to study pathogens, engineer sustainable biomanufacturing strains, and probe how microbes influence human health. While genome editing tools have transformed eukaryotic biology, most high‑efficiency bacterial editors simply haven’t worked outside E. coli.
A new study from the Gladstone Institutes aims to change that. In a large, nine‑lab collaboration, researchers have translated a retron‑based DNA editing system from E. coli into 14 additional bacterial species spanning three major phyla. The work, published in Nature Biotechnology and titled “Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering,” demonstrates that retrons, bacterial immune elements that continuously produce short DNA strands, can be engineered into portable genome editing modules the authors call recombitrons. “Recombitrons—a genome editing tool created by pairing modified, donor-producing bacterial retrons with single-stranded binding and annealing proteins—have increased the efficiency of recombineering to install flexible, precise edits in the prokaryotic chromosome,” the authors wrote.
Retrons normally function as part of a viral defense system, generating DNA fragments that help bacteria detect and respond to infection. Seth Shipman, PhD, a Gladstone Investigator and senior author of the study, has spent years repurposing this machinery. “We’ve been easily editing E. coli genomes using retrons for years now, which has substantially increased the pace of our fundamental biology and our molecular technology development,” he said. “But we kept hearing from the broader field, asking when there would be a version of this technology that could be put to work in other bacterial species that matter for the environment, industrial processes, or human health.”
Shipman’s lab previously showed that retrons can act as cellular DNA-making factories, generating the donor strands needed for genome editing. In bacteria, the resulting editing tool built by pairing modified retrons with single‑stranded DNA–binding and annealing proteins is known as a recombitron. Until now, however, functional recombitrons existed only in E. coli.
To test whether the architecture could travel, the team designed a panel of 10 retron-based editing systems and partnered with other labs specializing in diverse bacterial species. “We designed all the molecular parts at Gladstone, then sent them to the collaborators, where they ran the experiment in their labs,” said first author Alejandro González‑Delgado, PhD. Samples were then returned to Gladstone for centralized analysis.
The results show broad functionality. The recombitrons worked in all 15 species tested, including clinically relevant pathogens such as Klebsiella pneumoniae and Pseudomonas aeruginosa, as well as fast‑growing biotechnology strains like Vibrio natriegens and Pseudomonas putida. Editing efficiencies varied widely—from fractions of a percent to more than 90%—but the team demonstrated that modifying retron structure or other system components could boost performance in lower‑efficiency hosts.
“Each retron worked differently in different bacteria,” González‑Delgado noted. “This reinforces why it’s important to have lots of different retrons, so scientists can choose the ones best suited to their favorite bacterial species.”
The study provides a roadmap for expanding genome editing into species that have historically been difficult to engineer. Researchers studying microbial pathogenesis, gut ecology, or industrial bioproduction can now match retron systems to their organism of interest.
“My lab builds molecular technology, and we want these technologies to be used as broadly as possible to uncover new biology and intervene in disease,” Shipman said. “We hope it will continue to spread from here.”
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