PHASTEST-Based Prophage Mapping and Functional Analysis of Lactiplantibacillus plantarum WCFS1

The aim in this study was identify prophage and cryptic prophage elements in the complete genome of Lactiplantibacillus plantarum WCFS1. phage search tool with enhanced sequence translation (PHASTEST) was used for predicting prophages, and Prokka and Bakta were used for comparative annotation. Three prophage regions were detected, two of which were classified as intact and one as incomplete based on their completeness scores. Comparative annotation showed that the intact regions contained structural and regulatory genes responsible for phage assembly and lysogenic-lytic control. The incomplete region lacked structural modules but retained the integrase and recombinase functions and genes related to exopolysaccharide biosynthesis. This incomplete-metabolism-associated cryptic prophage appears to contribute to modifying the host surface and maintaining genomic plasticity rather than lytic induction. Overall, the prophage regions identified in L. plantarum WCFS1 are not only inactive genetic remnants but also functional genomic modules that may support host genomic stability and adaptability under stress. These findings highlight the need to evaluate the prophage and cryptic prophage content when assessing the safety and stability of lactic acid bacteria starter cultures in industrial fermentation.