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Despite their potential, the effect of phage therapy on gut microbiota remains insufficiently explored. This study investigated the impacts of recurrent phage administration on the gut microbiota of chickens challenged with\n                    <jats:italic>Salmonella<\/jats:italic>\n                    Enteritidis. Eighty chicks were infected at 7 days of age and either treated with a cocktail of six lytic phages of\n                    <jats:italic>Salmonella<\/jats:italic>\n                    via drinking water for 21 days before and after infection, or left untreated. Surprisingly, continuous high-dose phage treatment led to higher\n                    <jats:italic>Salmonella<\/jats:italic>\n                    colonization levels than short-term pre-infection exposure. Through fecal and cecal microbiota analysis, we found that phage treatment significantly influenced alpha and beta diversities as well as microbiota development, with the most significant changes occurring prior to\n                    <jats:italic>Salmonella<\/jats:italic>\n                    infection, and gradually diminishing over time. Furthermore, phage treatment transiently altered predicted microbiota functions, promoting an oxygen-utilizing microbial community that may have counteracted the protective effects of phages. These findings demonstrate that phages can induce time-dependent modifications in both the composition and functional profile of the gut microbiota, emphasizing the importance of considering these dynamic interactions when developing phage-based strategies against enteric pathogens.\n                  <\/jats:p>","DOI":"10.1186\/s13567-025-01708-4","type":"journal-article","created":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T15:45:59Z","timestamp":1773503159000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Recurrent phage treatment of Salmonella-infected chickens transiently reshapes gut microbiota composition and function"],"prefix":"10.1186","volume":"57","author":[{"given":"Lorna","family":"Agap\u00e9","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florent","family":"Kempf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierrette","family":"Menanteau","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Madeline","family":"Morinet","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Catherine","family":"Schouler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Boulesteix","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Micka\u00ebl","family":"Riou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Isabelle","family":"Virlogeux-Payant","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philippe","family":"Velge","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2026,3,14]]},"reference":[{"key":"1708_CR1","doi-asserted-by":"publisher","first-page":"162","DOI":"10.4292\/wjgpt.v8.i3.162","volume":"8","author":"DM Lin","year":"2017","unstructured":"Lin DM, Koskella B, Lin HC (2017) Phage therapy: an alternative to antibiotics in the age of multi-drug resistance. 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However, the company had no involvement in the design or execution of the experiments, the analysis of the results, or the preparation of the manuscript.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"54"}}