Gut virome orchestrates nitrogen partitioning between the host and microbiome

Abstract Dietary protein is essential for host growth and nitrogen homeostasis. How dietary protein shapes intestinal phage–bacteria interactions and influences the translation of dietary cues into host physiological outcomes remains poorly understood. We show that low‐protein diet (LPD) substantially remodels the murine gut virome by altering phage–bacteria dynamics. Under LPD, nutritional stress suppresses bacterial phage release without altering the predicted proportion of lysogenic phages, leading to reduced free phage abundance and weaker bacterial lysis. Lysogenic phages carrying carbohydrate‐related auxiliary metabolic genes (AMGs) may promote expansion of the bacterial host population while suppressing urease‐mediated nitrogen recycling. High bacterial load coupled with low free phage availability creates a nitrogen trap that both sequesters host‐accessible nitrogen and accelerates urea loss, thereby constraining host growth. Both the normal diet (ND) virome, defined by its high free phage abundance and lytic potential, and an equivalently sized LPD phage pool partially rescued nitrogen flow in mice fed a LPD. These results reveal a previously unrecognized gut “viral shunt,” in which balanced phage–bacteria interactions redistribute nitrogen within the gut. Together, this study highlights the ecological significance of phage–bacteria interactions in host nutritional adaptation and suggests that targeted viral manipulation may offer a potential therapeutic strategy for protein‐deficiency‐related disorders.