DNA-damaging bacteriocins from human Escherichia coli intestinal isolates trigger prophage induction and promote lysogeny

Lysogens - bacteria harbouring prophages - are prevalent in the human gut microbiota. Nevertheless, factors triggering induction or repression of prophages remain poorly characterized. Here, we studied the involvement of bacteriocins - antibacterials involved in bacteria-bacteria competition – in prophage induction. We screened a collection of 1,768 fecal Escherichia coli isolates for bacteriocin-producing strains and selected 30 to test their capacity to induce a λ-related coliphage. In these, we identified 74 bacteriocin genes and demonstrate that only those coding a DNA-damaging bacteriocin trigger prophage induction. From one strain co-producing an E-type endonuclease colicin and the Mcc1229 microcin, we demonstrate that these colicins induce a broad panel of temperate phage genera. Assessing bacterial competition by pairwise cocultures between an E-type endonuclease-producing strain and a λ-lysogen revealed enhanced prophage induction and increased emergence of new lysogens among the bacteriocin producers. Remarkably, while the λ-lysogen was outcompeted by the E-type endonuclease colicin producer within 6 hours in vitro , both populations were maintained at comparable levels over 10 days in dixenic mice. This work reveals a dual role for DNA-damaging bacteriocins that kill competitors by prophage induction and propagate lysogeny.