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How dietary protein shapes intestinal phage\u2013bacteria interactions and influences the translation of dietary cues into host physiological outcomes remains poorly understood. We show that low\u2010protein diet (LPD) substantially remodels the murine gut virome by altering phage\u2013bacteria 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\u2010related auxiliary metabolic genes (AMGs) may promote expansion of the bacterial host population while suppressing urease\u2010mediated nitrogen recycling. High bacterial load coupled with low free phage availability creates a nitrogen trap that both sequesters host\u2010accessible 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 \u201cviral shunt,\u201d in which balanced phage\u2013bacteria interactions redistribute nitrogen within the gut. Together, this study highlights the ecological significance of phage\u2013bacteria interactions in host nutritional adaptation and suggests that targeted viral manipulation may offer a potential therapeutic strategy for protein\u2010deficiency\u2010related disorders.<\/jats:p>","DOI":"10.1002\/imt2.70177","type":"journal-article","created":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T06:45:09Z","timestamp":1791182709000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Gut virome orchestrates nitrogen partitioning between the host and microbiome"],"prefix":"10.1002","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-3095-4283","authenticated-orcid":false,"given":"Shujie","family":"Xu","sequence":"first","affiliation":[{"name":"Zhejiang Key Laboratory of nutrition and breeding for high\u2010quality animal products, College of Animal Sciences Zhejiang University Hangzhou 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