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This is a limitation of studies on fecal microbiota transplantation (FMT) where bacteriophages likely influence outcome. Here, using metagenomics, we profile phage populations - the phageome - in individuals recruited into two double-blind randomized trials of FMT in ulcerative colitis. We leverage the trial designs to observe that phage populations behave similarly to bacterial populations, showing temporal stability in health, dysbiosis in active disease, modulation by antibiotic treatment and by FMT. We identify a donor bacteriophage putatively associated with disease remission, which on genomic analysis was found integrated in a bacterium classified to\n                    <jats:italic>Oscillospiraceae<\/jats:italic>\n                    , previously isolated from a centenarian and predicted to produce vitamin B complex except B12. Our study provides an in-depth assessment of phage populations during different states and suggests that bacteriophage tracking has utility in identifying determinants of disease activity and resolution.\n                  <\/jats:p>","DOI":"10.1038\/s41467-024-53454-4","type":"journal-article","created":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T15:03:09Z","timestamp":1729177389000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission"],"prefix":"10.1038","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6461-8211","authenticated-orcid":false,"given":"Marwan E.","family":"Majzoub","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sudarshan","family":"Paramsothy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Craig","family":"Haifer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9405-352X","authenticated-orcid":false,"given":"Rohit","family":"Parthasarathy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0519-4698","authenticated-orcid":false,"given":"Thomas J.","family":"Borody","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rupert W.","family":"Leong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael A.","family":"Kamm","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4017-1077","authenticated-orcid":false,"given":"Nadeem O.","family":"Kaakoush","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,10,17]]},"reference":[{"key":"53454_CR1","doi-asserted-by":"publisher","first-page":"724","DOI":"10.1016\/j.chom.2020.08.003","volume":"28","author":"AC Gregory","year":"2020","unstructured":"Gregory, A. C. et al. The gut virome database reveals age-dependent patterns of virome diversity in the human gut. Cell Host Microbe 28, 724\u2013740 (2020).","journal-title":"Cell Host Microbe"},{"key":"53454_CR2","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/j.chom.2019.01.017","volume":"25","author":"AN Shkoporov","year":"2019","unstructured":"Shkoporov, A. N. & Hill, C. Bacteriophages of the human gut: the \u201cKnown Unknown\u201d of the microbiome. Cell Host Microbe 25, 195\u2013209 (2019).","journal-title":"Cell Host Microbe"},{"key":"53454_CR3","doi-asserted-by":"publisher","first-page":"822562","DOI":"10.3389\/fcimb.2021.822562","volume":"11","author":"M Zuppi","year":"2021","unstructured":"Zuppi, M., Hendrickson, H. L., O\u2019Sullivan, J. M. & Vatanen, T. Phages in the gut ecosystem. Front. Cell Infect. Microbiol. 11, 822562 (2021).","journal-title":"Front. Cell Infect. Microbiol."},{"key":"53454_CR4","doi-asserted-by":"crossref","unstructured":"Tiamani, K. et al. 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