{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T20:53:41Z","timestamp":1793912021166,"version":"4.8.0"},"reference-count":81,"publisher":"Informa UK Limited","issue":"1","license":[{"start":{"date-parts":[[2025,9,15]],"date-time":"2025-09-15T00:00:00Z","timestamp":1757894400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIAID of the National Institutes of Health"},{"name":"Gates Foundation","id":[{"id":"https:\/\/ror.org\/0456r8d26","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Achieving Cures Together"},{"DOI":"10.13039\/100021281","name":"Gates Family Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100021281","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health and Care Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.tandfonline.com"],"crossmark-restriction":true},"short-container-title":["Gut Microbes"],"published-print":{"date-parts":[[2025,12,31]]},"DOI":"10.1080\/19490976.2025.2559019","type":"journal-article","created":{"date-parts":[[2025,9,15]],"date-time":"2025-09-15T11:17:45Z","timestamp":1757935065000},"update-policy":"https:\/\/doi.org\/10.1080\/tandf_crossmark_01","source":"Crossref","is-referenced-by-count":9,"title":["Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation"],"prefix":"10.1080","volume":"17","author":[{"given":"Samuel","family":"Bryson","sequence":"first","affiliation":[{"name":"Phase Genomics","place":["Seattle, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary","family":"Sisson","sequence":"additional","affiliation":[{"name":"Phase Genomics","place":["Seattle, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bradley","family":"Nelson","sequence":"additional","affiliation":[{"name":"Phase Genomics","place":["Seattle, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonas","family":"Grove","sequence":"additional","affiliation":[{"name":"Phase Genomics","place":["Seattle, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"Reister","sequence":"additional","affiliation":[{"name":"Phase Genomics","place":["Seattle, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Liachko","sequence":"additional","affiliation":[{"name":"Phase Genomics","place":["Seattle, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Auch","sequence":"additional","affiliation":[{"name":"Phase Genomics","place":["Seattle, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carolyn","family":"Graiziger","sequence":"additional","affiliation":[{"name":"University of Minnesota","place":["Minneapolis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3205-3188","authenticated-orcid":false,"given":"Alexander","family":"Khoruts","sequence":"additional","affiliation":[{"name":"University of Minnesota","place":["Minneapolis, USA"]},{"name":"University of Minnesota","place":["Minneapolis and St. Paul, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"301","published-online":{"date-parts":[[2025,9,15]]},"reference":[{"key":"e_1_3_4_2_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1104816"},{"key":"e_1_3_4_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrgastro.2011.244"},{"key":"e_1_3_4_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(17)30182-4"},{"key":"e_1_3_4_5_1","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2018.20046"},{"key":"e_1_3_4_6_1","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2015.04.001"},{"key":"e_1_3_4_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/S2468-1253(21)00400-3"},{"key":"e_1_3_4_8_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abf3363"},{"key":"e_1_3_4_9_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.abb5920"},{"key":"e_1_3_4_10_1","doi-asserted-by":"publisher","DOI":"10.1016\/S2666-6367(23)00088-X"},{"key":"e_1_3_4_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.eclinm.2023.102111"},{"key":"e_1_3_4_12_1","doi-asserted-by":"publisher","DOI":"10.1002\/hep4.1639"},{"key":"e_1_3_4_13_1","doi-asserted-by":"publisher","DOI":"10.1097\/CLD.0000000000000154"},{"key":"e_1_3_4_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-42183-0"},{"key":"e_1_3_4_15_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41575-020-0350-4"},{"key":"e_1_3_4_16_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0549-6"},{"key":"e_1_3_4_17_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-01964-3"},{"key":"e_1_3_4_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2022.100711"},{"key":"e_1_3_4_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-022-01913-0"},{"key":"e_1_3_4_20_1","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2016.1265196"},{"key":"e_1_3_4_21_1","doi-asserted-by":"publisher","DOI":"10.1136\/gutjnl-2017-313952"},{"key":"e_1_3_4_22_1","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2019.1586037"},{"key":"e_1_3_4_23_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-018-0598-x"},{"key":"e_1_3_4_24_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-025-02046-5"},{"key":"e_1_3_4_25_1","volume-title":"Fecal microbiota for transplantation: safety alert - risk of serious adverse events likely due to transmission of pathogenic organisms","author":"FDA","year":"2020","unstructured":"FDA. Fecal microbiota for transplantation: safety alert - risk of serious adverse events likely due to transmission of pathogenic organisms (Washington DC, US: The US Food and Drug Administration (FDA)). 2020."},{"key":"e_1_3_4_26_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(20)30473-4"},{"key":"e_1_3_4_27_1","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2025.2508950"},{"key":"e_1_3_4_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fuv048"},{"key":"e_1_3_4_29_1","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.02593-20"},{"key":"e_1_3_4_30_1","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.001030"},{"key":"e_1_3_4_31_1","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.415"},{"key":"e_1_3_4_32_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.770323"},{"key":"e_1_3_4_33_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-84152-6"},{"key":"e_1_3_4_34_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0306-2"},{"key":"e_1_3_4_35_1","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2024.2446378"},{"key":"e_1_3_4_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciw390"},{"key":"e_1_3_4_37_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciw185"},{"key":"e_1_3_4_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cix252"},{"key":"e_1_3_4_39_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cix821"},{"key":"e_1_3_4_40_1","doi-asserted-by":"publisher","DOI":"10.3934\/microbiol.2019.1.1"},{"key":"e_1_3_4_41_1","doi-asserted-by":"publisher","DOI":"10.1128\/mSphere.00853-20"},{"key":"e_1_3_4_42_1","doi-asserted-by":"publisher","DOI":"10.1080\/07853890.2021.1927170"},{"key":"e_1_3_4_43_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13756-022-01064-4"},{"key":"e_1_3_4_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cub.2015.04.055"},{"key":"e_1_3_4_45_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-42998-6"},{"key":"e_1_3_4_46_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-024-01306-7"},{"key":"e_1_3_4_47_1","doi-asserted-by":"publisher","DOI":"10.1038\/ajg.2017.6"},{"key":"e_1_3_4_48_1","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2014.30"},{"key":"e_1_3_4_49_1","doi-asserted-by":"publisher","DOI":"10.3390\/v9060141"},{"key":"e_1_3_4_50_1","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2016.11.010"},{"key":"e_1_3_4_51_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms3151"},{"key":"e_1_3_4_52_1","doi-asserted-by":"publisher","DOI":"10.1017\/ice.2016.229"},{"key":"e_1_3_4_53_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jinf.2020.09.003"},{"key":"e_1_3_4_54_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.medmal.2018.11.002"},{"key":"e_1_3_4_55_1","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofw133"},{"key":"e_1_3_4_56_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhin.2018.02.018"},{"key":"e_1_3_4_57_1","doi-asserted-by":"publisher","DOI":"10.4161\/gmic.23571"},{"key":"e_1_3_4_58_1","doi-asserted-by":"publisher","DOI":"10.1152\/ajpgi.00282.2013"},{"key":"e_1_3_4_59_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijantimicag.2018.11.014"},{"key":"e_1_3_4_60_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2018.12.009"},{"key":"e_1_3_4_61_1","doi-asserted-by":"publisher","DOI":"10.1101\/2025.02.12.637985"},{"key":"e_1_3_4_62_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"e_1_3_4_63_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv033"},{"key":"e_1_3_4_64_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"e_1_3_4_65_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu314"},{"key":"e_1_3_4_66_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_3_4_67_1","article-title":"Hi-C deconvolution of a human gut microbiome yields high-quality draft genomes and reveals plasmid-genome interactions","author":"Press WA","year":"2017","unstructured":"Press WA, Kronenberg ZN, Langford KW, Shakya M, Lo C-C, Mueller KA, Sullivan ST, Chain PSG, Liachko I. Hi-C deconvolution of a human gut microbiome yields high-quality draft genomes and reveals plasmid-genome interactions. BioRxiv. 2017.","journal-title":"BioRxiv"},{"key":"e_1_3_4_68_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.186072.114"},{"key":"e_1_3_4_69_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz848"},{"key":"e_1_3_4_70_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-020-00867-0"},{"key":"e_1_3_4_71_1","doi-asserted-by":"publisher","DOI":"10.1101\/2021.06.14.448389"},{"key":"e_1_3_4_72_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-021-91456-0"},{"key":"e_1_3_4_73_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_4_74_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-023-02961-6"},{"key":"e_1_3_4_75_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-020-01626-5"},{"key":"e_1_3_4_76_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-021-00928-6"},{"key":"e_1_3_4_77_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1037"},{"key":"e_1_3_4_78_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421"},{"key":"e_1_3_4_79_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0686-2"},{"key":"e_1_3_4_80_1","doi-asserted-by":"publisher","DOI":"10.25080\/Majora-92bf1922-011"},{"key":"e_1_3_4_81_1","doi-asserted-by":"publisher","DOI":"10.25080\/TCWV9851"},{"key":"e_1_3_4_82_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1239303"}],"container-title":["Gut Microbes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.tandfonline.com\/doi\/pdf\/10.1080\/19490976.2025.2559019","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,19]],"date-time":"2025-12-19T02:43:57Z","timestamp":1766112237000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.tandfonline.com\/doi\/full\/10.1080\/19490976.2025.2559019"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,15]]},"references-count":81,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,12,31]]}},"alternative-id":["10.1080\/19490976.2025.2559019"],"URL":"https:\/\/doi.org\/10.1080\/19490976.2025.2559019","relation":{},"ISSN":["1949-0976","1949-0984"],"issn-type":[{"value":"1949-0976","type":"print"},{"value":"1949-0984","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,9,15]]},"assertion":[{"value":"The publishing and review policy for this title is described in its Aims & Scope.","order":1,"name":"peerreview_statement","label":"Peer Review Statement"},{"value":"http:\/\/www.tandfonline.com\/action\/journalInformation?show=aimsScope&journalCode=kgmi20","URL":"http:\/\/www.tandfonline.com\/action\/journalInformation?show=aimsScope&journalCode=kgmi20","order":2,"name":"aims_and_scope_url","label":"Aim & Scope"},{"value":"2025-01-27","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-07-21","order":1,"name":"revised","label":"Revised","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-09-04","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-09-15","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"2559019"}}