Bacteriophage-mediated restoration of epithelial integrity, DNA damage response, and transcriptomic homeostasis in colon organoids exposed to ETBF and <i>pks plus E. coli</i>

Colorectal cancer (CRC)–associated pathobionts such as Enterotoxigenic Bacteroides fragilis (ETBF) and colibactin-producing (pks+) Escherichia coli disrupt epithelial barrier function, promote chronic inflammation, and induce genotoxic stress. To investigate how these pathogenic interactions with the host epithelium can be modulated, we employed patient-derived normal human colon organoids as an ex vivo model. Two lytic bacteriophages, Bac-FRP-3 (targeting ETBF) and Esc-COP-23 (targeting pks + E. coli), were applied to bacterial cultures, and the resulting phage-conditioned supernatants were used to challenge organoids. Exposure to ETBF and pks + E. coli induced strong pro-inflammatory transcriptional responses, DNA damage signaling, and epithelial disruption, whereas phage treatment attenuated these effects. Transcriptomic profiling revealed restoration of inflammatory and DNA damage–related gene expression, while confocal imaging confirmed recovery of epithelial junctional integrity and reduced DNA double-strand breaks. These findings highlight phage-mediated modulation of host–pathobiont interactions and provide mechanistic insight into how targeted viral predation can reshape pathogenic impacts within the human intestinal environment.