Entry exclusion enables selective conjugative DNA delivery in synthetic bacterial communities.

Abstract

Selective DNA delivery to specific members of assembled bacterial communities remains challenging. Bacterial conjugation enables efficient DNA delivery, but transfer to non-target recipients limits its specificity within mixed communities. Here, we repurpose plasmid entry exclusion (Eex) as a recipient-side gate to control conjugative DNA delivery. We demonstrate selective plasmid delivery to Eex-negative recipients within populations containing both Eex-expressing and Eex-negative cells. This recipient selectivity was maintained at increased cell densities and during prolonged mating. By combining RP4-type and F-type conjugation systems with their corresponding exclusion modules, we further directed DNA delivery from distinct donors to defined recipient populations. RP4-derived Eex also functioned in environmental bacteria, including Pseudomonas putida and Sphingobium japonicum, enabling recipient-specific exclusion within a multispecies mixture. Furthermore, repeated cycles of Eex-guided conjugation and selection altered community composition after assembly. These results establish entry exclusion as a recipient-side strategy for selective conjugative DNA delivery and, when combined with selection, for controlling the composition of assembled bacterial communities.