A prophage-encoded sRNA limits phage infection of adherent-invasive E. coli

Prophages are prevalent features of bacterial genomes that can reduce susceptibility to infection by competing phages, yet the mechanisms involved are often elusive. Here, we identify a small RNA (svsR) encoded by the lambdoid prophage NC-SV in adherent-invasive Escherichia coli strain NC101 that limits infection by virulent coliphages. Comparative genomics revealed that NC-SV-like prophages and svsR homologs are broadly conserved across Enterobacteriaceae. Transcriptomic analyses show that svsR represses maltodextrin transport genes, including lamB, which encodes the outer membrane maltoporin LamB, a known receptor for numerous coliphages. Deletion of the lamB gene reveals that while LamB is not required for replication of the virulent phages tested, it contributes to plaque expansion, indicating a role in phage spread but not as an essential receptor. Nutrient supplementation experiments further linked maltodextrin and glucose availability to changes in plaque expansion and phage adsorption. In vivo, we compared wild-type NC101 and a prophage-deletion strain (NC101∆NC-SV) in mice to assess the impact of NC-SV on lytic phage susceptibility. Although intestinal E. coli densities remained stable across groups, animals colonized with NC101 exhibited markedly reduced phage burdens in both the intestinal lumen and mucosa compared to mice colonized with NC101∆NC-SV. This reduced phage pressure was associated with increased dissemination of E. coli to extraintestinal tissues, including the spleen and liver. Together, these findings highlight a nutrient-responsive, prophage-encoded mechanism that protects E. coli from phage predation and may promote bacterial persistence in and dissemination from the mammalian gut.