A "Microbiome" paper describes how the Sunagawa lab developed and experimentally tested an analytical framework to (i) use DNA sequencing to exactly locate inducible prophages in bacterial genomes and (ii) quantify their activity in vitro and ex vivo in bacterial strains and communities.
Many gut bacteria are lysogens hosting a prophage that upon induction produce virions to infect and kill bacteria. Although phages are recognized as microbiome modulators, challenges in locating inducible prophages in host genomes and quantifying their activity have limited our understanding of prophage-host interactions. Since gut bacterial composition is closely linked to human health, improved insight on how prophages shape the bacterial gut community is curial. The development and experimental validation of the analytical framework for DNA sequencing data enabled the Sunagawa lab to exactly locate and quantify in vitro and ex vivo induced prophages in murine gut model strains (Oligo-MM12). The study estimates the activity of induced prophages by determining phage-to-host ratios and revealed signatures of lateral transduction. Notably, the results reveal that DNA sequencing data allow exact de novo localization of prophages, even in strains with relative abundances in communities below 1%.
Link to the paper in Microbiome.
Link to the video abstract.
