The gut microbiome comprises a diverse range of eukaryotic microorganisms, archaea, bacteria, and viruses that influence our health and wellness. The most abundant type of microbe in the gut – viruses that infect bacteria, called phages – are highly diverse, individual-specific, and stable over time. Phages have gained attention recently as modulators of the gut microbiome and health, but inducible prophages are difficult to identify in bacterial genomes, making them challenging to study. A new study presents a method for using high-throughput sequencing data to locate inducible prophages. Researchers used a well-established model system to validate their methods, including phage-to-host ratios and phage location in the reference genome. After validation, they expanded their methods to a murine gut model microbiota and were able to locate five novel inducible prophages, quantify their activity, and show signatures of lateral transduction potential. The methods were also applicable to metagenomes from fecal samples obtained from mice, including for low-abundance strains. This study demonstrates that integrating experimental induction and bioinformatics analysis can be a powerful approach, helping researchers gain insight into the factors that determine phage activity and how prophage-bacteria interactions influence our microbiome and health.