Phage find clever ways to infiltrate resistant bacteria and shuttle DNA between strains

In the gut, in the soil, and myriad other spots, bacteria reign, forming complex communities—but not in isolation. They’re often influenced by bacteria-killing viruses known as bacteriophages. A recent study in Cell now shows how such viruses can infect bystander, virus-resistant bacteria and transfer bits of DNA to them.

Phage are known to facilitate horizontal gene transfer, a movement of DNA between organisms that helps drive evolution in bacteria. But most types of phage only infect a limited range of bacteria, potentially limiting any DNA exchange.

The new data show how phage can expand their influence, highlighting a previously-unexplored route for horizontal gene transfer. “The implications, if the findings hold true, are great,” says Vincent Fischetti, at the Laboratory of Bacterial Pathogenesis and Immunology at Rockefeller University, who was not involved in the study.

Bacterial populations usually consist of mixtures of bacteria sensitive to phages and those resistant to them. When cultured in isolation, resistant strains are left unscathed by phage. But when incubated with sensitive strains, some of them succumb, an understudied phenomenon that the researchers were keen to explore.

They added phage that targets Bacillus subtilis to a culture of the soil bacterium that contained both phage-sensitive and phage-resistant strains. The result: massive die-off of resistant cells, more than half in some culture conditions. “We did not expect the effect to be so strong,” says co-author Sigal Ben-Yehuda, leader of the group at The Hebrew University, Institute for Medical Research-Israel Canada, in Jerusalem, whose group observed the effect with three distinct phage types. “Why would the resistant ones die so efficiently?”

The researchers found that lysins, cell-popping phage proteins released by dying infected bacteria, were able to also kill resistant bacteria. More surprisingly, they observed that the resistant strains also sometimes temporarily acquired a phage-binding receptor on their surface, obtained from the sensitive strains. This cargo was delivered via tiny membrane vesicles that bud off of bacterial surfaces; the vesicles can transfer material between them, a process hastened when phage pop open and destroy bacteria. With the receptor on their surface, previously-impermeable bacteria became susceptible to attachment and invasion by the phage.

These phage also served as DNA shuttles. With low frequency, the phage could permanently pass on bits of DNA to the phage-resistant strains, a feat the researchers demonstrated by transferring an antibiotic resistance gene and bacterial genomic DNA.

“You can imagine that many genes could be transferred in such a way,” says Ben-Yehuda. Her group’s findings show that this process occurs between closely related strains, but she speculates that it could also account for DNA transfer between more distantly related species. Supporting this notion, the researchers found that phage receptor molecules could transfer between B. subtilius and a distinct species called Bacillus cereus.

Fischetti wonders whether this phenomenon is widespread, perhaps affecting other virus-host systems. “Any organism could potentially pick up vesicles like these,” he speculates.

The newly-discovered system, notes Fischetti, is a “win-win situation” for both phage and bacteria. It allows phage to infect new bacterial hosts, while allowing bacteria to acquire new genes to help them adapt, hence crafting a hardier microbial community.

Ben-Yehuda says that her findings also sound a note of caution for “phage therapies” intended to attack specific bacteria, a focus of several biotechnology companies and clinical trials. Off-target effects of such therapies—the killing of beneficial bacteria, for instance—might be more common than previously thought.

Her group is now investigating what happens when they mix different phage types and bacterial species together. “We want to understand more complex communities,” more akin to those found in nature, she says.