A third of the prophages predicted in Bacillus subtilis strains are SPbetaviruses. SPß-like prophages have large genomes, around 130,000 bp and integrate into host functional genes such as spsM. Because they feature a reversible active lysogenic lifestyle, meaning they can actively switch between intra and extrachromosomal stages without lysing their host, they affect their host behaviour switching on and off those particular genes. However, little is known about the triggers and the manner they alter their host behaviour and a majority of SPß gene functions are still unknown. To gain insight into prophage-host interactions, we first developed a bioinformatic pipeline to generate a graphical synteny between a group of SPbeta-like prophages, identifying that circa 25% of SPß genes or gene clusters are conserved among the group. Another 25% of SPß genome appear unique to SPß phage, including genes associated with cell lysis and sublancin production. We then used publicly available transcriptomic data to assess what genes are potentially involved in the prophage excision under particular conditions. We noticed that conserved genes globally present low expression variation over the different conditions, although most of them show an increased expression under certain stress conditions. In addition, this analysis allowed us to establish potential correlation between genes or between genes and conditions, based on their expression pattern, indicating their potential role during those processes. Taken together those data show which conditions influence the prophage gene expression profile and whether this behaviour is to be expected in other related prophages, highlighting the relation between prophage genes, their function and their effect on its host.