Predictable induction responses of gut prophages

Temperate bacteriophages are dominant members of the human gut microbiome that can infect and lyse their bacterial hosts or integrate as prophages. During this integrated state, prophages exhibit extensive control over host physiology and lysis via induction. Here, we studied a diverse collection of Bacteroidales isolates, which are amongst the most abundant bacterial orders within the human gut, identifying 902 high-quality prophage genomes present within 305 isolates, 240 of which were poly-lysogens. Despite their prevalence, our understanding of the function and induction triggers of prophages is limited. To predict prophage induction, we employed an iterative profile Hidden Markov Model search across divergent bacterial hosts to identify prophage regulatory components. We found 197 Bacteroidales prophages encoding complete CI-like repressor proteins, which initiate induction upon DNA damage. We selected Bacteroides thetaiotaomicron strain Bt_806 to characterise further as it harboured six diverse prophages, including the prevalent and abundant prophage LoVE, which was the only integrated prophage encoding a complete CI-like repressor. Transcriptomics revealed phage LoVE was routinely induced upon DNA damage, while the five co-habiting prophages remained stably integrated yet exhibited transcriptionally active genes associated with regulation, prophage maintenance, and uncharacterised functions. Finally, we selected an additional eleven Bacteroidales poly-lysogens, confirming that integrated prophages encoding complete CI-like repressors were reliably induced upon DNA damage. Together, we demonstrate that mechanistic understanding of prophage induction linked with identification of regulatory genes enables selective and predictable induction of gut prophage species as a potential tool to modulate the microbiome.