Nature Microbiology, Published online: 19 June 2026; doi:10.1038/s41564-026-02405-4 Prophage FRφ rewires the flagellar apparatus of its Enterobacter sp. host through RNA-guided repression of native flagellin, favouring its own phage-encoded isoform. This enhances host motility and reduces immune recognition, boosting bacterial fitness in mice.