{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T15:51:36Z","timestamp":1786117896141,"version":"build-2736575974"},"reference-count":64,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,8,4]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Ruminococcus gnavus<\/jats:italic>\n                      is a prevalent member of human gut microbiota and is associated with inflammatory bowel disease. Phage-based microbiota engineering represents a promising approach for alleviating dysbiosis; however, knowledge regarding\n                      <jats:italic toggle=\"yes\">R. gnavus<\/jats:italic>\n                      phages remains limited. We report the isolation and characterization of 29 novel\n                      <jats:italic toggle=\"yes\">R. gnavus<\/jats:italic>\n                      phages from sewage samples. All isolates exhibited siphovirus morphology, with genome sizes ranging from 32.3 to 46.0 kbp, and represented 18 putative new genera and 24 new species. Whole-proteome clustering tools indicated that\n                      <jats:italic toggle=\"yes\">R. gnavus<\/jats:italic>\n                      phages form a distinct new cluster and are divided into three clusters that could correspond to new subfamilies. Representative phages from each cluster were phenotypically characterized in detail, based on adsorption kinetics, one-step growth, and stress tolerance assays, which revealed diverse infection dynamics and structural features, such as unique globular appendages at distal tail fibers. Collectively, this study established the largest and most diverse\n                      <jats:italic toggle=\"yes\">R. gnavus<\/jats:italic>\n                      phage library to date, providing fundamental insights into phage\u2013host interactions and a valuable resource for the future development of phage-based strategies to modulate\n                      <jats:italic toggle=\"yes\">R. gnavus<\/jats:italic>\n                      in the human gut.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        <jats:italic toggle=\"yes\">Ruminococcus gnavus<\/jats:italic>\n                        is a common gut commensal consistently associated with inflammatory bowel disease (IBD). Phage-based microbiota engineering has emerged as a promising strategy for alleviating dysbiosis. However, progress has been hampered by the limited availability of\n                        <jats:italic toggle=\"yes\">R. gnavus<\/jats:italic>\n                        phages. In this study, we established and characterized a library of 29 novel\n                        <jats:italic toggle=\"yes\">R. gnavus<\/jats:italic>\n                        phages. Whole-genome\/proteome and phenotypic analyses revealed that these phages may represent a new taxonomic lineage and display variation in their infection strategies. This work substantially expands the known repertoire of\n                        <jats:italic toggle=\"yes\">R. gnavus<\/jats:italic>\n                        phages and provides a critical resource for dissecting phage\u2013host interactions in the human gut. Importantly, our findings lay the foundation for the future development of phage-based approaches to selectively modulate\n                        <jats:italic toggle=\"yes\">R. gnavus<\/jats:italic>\n                        populations and inform therapeutic strategies for IBD.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.03672-25","type":"journal-article","created":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T12:00:42Z","timestamp":1782129642000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Extensive library of\n                    <i>Ruminococcus gnavus<\/i>\n                    phages revealing genomic and phenotypic diversity with novel clusters"],"prefix":"10.1128","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3441-7560","authenticated-orcid":true,"given":"Arata","family":"Sakiyama","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/024exxj48","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Phage Biologics, Graduate School of Medicine, Gifu University","place":["Gifu, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5472-5101","authenticated-orcid":false,"given":"Ayaka","family":"Washizaki","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/024exxj48","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Phage Biologics, Graduate School of Medicine, Gifu University","place":["Gifu, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-3417-223X","authenticated-orcid":true,"given":"Keiko","family":"Inaba-Hasegawa","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/024exxj48","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Phage Biologics, Graduate School of Medicine, Gifu University","place":["Gifu, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Most Hushna Ara","family":"Naznin","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/024exxj48","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Phage Biologics, Graduate School of Medicine, Gifu University","place":["Gifu, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keigo","family":"Ide","sequence":"additional","affiliation":[{"name":"R&DX, DigitalX, Astellas Pharma Inc.","place":["Ibaraki, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masayuki","family":"Takase","sequence":"additional","affiliation":[{"name":"Venture Unit Engineered Phage Therapy, Discovery Accelerator, Astellas Pharma Inc","place":["Ibaraki, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoriko","family":"Ibuki","sequence":"additional","affiliation":[{"name":"Venture Unit Engineered Phage Therapy, Discovery Accelerator, Astellas Pharma Inc","place":["Ibaraki, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuichi","family":"Sawaguchi","sequence":"additional","affiliation":[{"name":"Venture Unit Engineered Phage Therapy, Discovery Accelerator, Astellas Pharma Inc","place":["Ibaraki, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shoichi","family":"Mitsunaka","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/024exxj48","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Phage Biologics, Graduate School of Medicine, Gifu University","place":["Gifu, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yutaro","family":"Ono","sequence":"additional","affiliation":[{"name":"Venture Unit Engineered Phage Therapy, Discovery Accelerator, Astellas Pharma Inc","place":["Ibaraki, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Islam Mohammad","family":"Shyful","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/024exxj48","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Phage Biologics, Graduate School of Medicine, Gifu University","place":["Gifu, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1660-7849","authenticated-orcid":true,"given":"Hiroki","family":"Ando","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/024exxj48","id-type":"ROR","asserted-by":"publisher"}],"name":"Laboratory of Phage Biologics, Graduate School of Medicine, Gifu University","place":["Gifu, Japan"]},{"name":"Venture Unit Engineered Phage Therapy, Discovery Accelerator, Astellas Pharma Inc","place":["Ibaraki, Japan"]},{"id":[{"id":"https:\/\/ror.org\/024exxj48","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for One Medicine Innovative Translational Research (COMIT), Institute for Advanced Study, Gifu University","place":["Gifu, Japan"]},{"name":"Arrowsmith Inc.","place":["Ibaraki, Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_4_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/am.27.5.961-979.1974"},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1111\/febs.17327"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-56449-x"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2024.115018"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-02109-8"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1186\/s13073-017-0490-5"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1904099116"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.733992"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2014.02.005"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2007595118"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1006\/tpbi.2002.1590"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2019.01.017"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1080\/14712598.2019.1651287"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.1055427"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2023.2194794"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2025.2597614"},{"key":"e_1_3_4_18_2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI111795"},{"key":"e_1_3_4_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature17645"},{"key":"e_1_3_4_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01915-21"},{"key":"e_1_3_4_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fuad014"},{"key":"e_1_3_4_22_2","doi-asserted-by":"publisher","DOI":"10.1080\/19490976.2016.1186334"},{"key":"e_1_3_4_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-019-0590-7"},{"key":"e_1_3_4_24_2","doi-asserted-by":"publisher","DOI":"10.4161\/bact.1.1.13980"},{"key":"e_1_3_4_25_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2025.04.021"},{"key":"e_1_3_4_26_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biochem.73.011303.073908"},{"key":"e_1_3_4_27_2","doi-asserted-by":"publisher","DOI":"10.3390\/v15041007"},{"key":"e_1_3_4_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.71.8.4872-4874.2005"},{"key":"e_1_3_4_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.23.2.549-552.1979"},{"key":"e_1_3_4_30_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF00211222"},{"key":"e_1_3_4_31_2","doi-asserted-by":"publisher","DOI":"10.1093\/ismejo\/wrae201"},{"key":"e_1_3_4_32_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00726-10"},{"key":"e_1_3_4_33_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0137187"},{"key":"e_1_3_4_34_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2023.11.003"},{"key":"e_1_3_4_35_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-3549-0_9"},{"key":"e_1_3_4_36_2","doi-asserted-by":"publisher","DOI":"10.1099\/acmi.0.000036"},{"key":"e_1_3_4_37_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.5.1503-1517.2004"},{"key":"e_1_3_4_38_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-68389-1"},{"key":"e_1_3_4_39_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002441"},{"key":"e_1_3_4_40_2","doi-asserted-by":"publisher","DOI":"10.1016\/B978-0-12-394621-8.00019-4"},{"key":"e_1_3_4_41_2","doi-asserted-by":"publisher","DOI":"10.3390\/v14091904"},{"key":"e_1_3_4_42_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2018.10.008"},{"key":"e_1_3_4_43_2","doi-asserted-by":"publisher","DOI":"10.3390\/molecules27061857"},{"key":"e_1_3_4_44_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2015.08.013"},{"key":"e_1_3_4_45_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tibtech.2022.08.008"},{"key":"e_1_3_4_46_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2206739119"},{"key":"e_1_3_4_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw387"},{"key":"e_1_3_4_48_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac400"},{"key":"e_1_3_4_49_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_4_50_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac776"},{"key":"e_1_3_4_51_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz265"},{"key":"e_1_3_4_52_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab688"},{"key":"e_1_3_4_53_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh152"},{"key":"e_1_3_4_54_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-8-209"},{"key":"e_1_3_4_55_2","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqab067"},{"key":"e_1_3_4_56_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki008"},{"key":"e_1_3_4_57_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac920"},{"key":"e_1_3_4_58_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3988"},{"key":"e_1_3_4_59_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btad214"},{"key":"e_1_3_4_60_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-022-01488-1"},{"key":"e_1_3_4_61_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01773-0"},{"key":"e_1_3_4_62_2","doi-asserted-by":"publisher","unstructured":"Heinzinger M Weissenow K Sanchez JG Henkel A Mirdita M Steinegger M Rost B. 2023. Bilingual language model for protein sequence and structure. Bioinformatics. doi:10.1101\/2023.07.23.550085","DOI":"10.1101\/2023.07.23.550085"},{"key":"e_1_3_4_63_2","doi-asserted-by":"publisher","DOI":"10.3390\/v12111268"},{"key":"e_1_3_4_64_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx157"},{"key":"e_1_3_4_65_2","doi-asserted-by":"publisher","DOI":"10.1264\/jsme2.ME23061"}],"container-title":["Microbiology Spectrum"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03672-25","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/spectrum.03672-25","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T14:45:29Z","timestamp":1786027529000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/spectrum.03672-25"}},"subtitle":[],"editor":[{"given":"Olaya","family":"Rendueles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,8,4]]},"references-count":64,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2026,8,4]]}},"alternative-id":["10.1128\/spectrum.03672-25"],"URL":"https:\/\/doi.org\/10.1128\/spectrum.03672-25","relation":{},"ISSN":["2165-0497"],"issn-type":[{"value":"2165-0497","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,4]]},"assertion":[{"value":"2025-11-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-05-22","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-06-22","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e03672-25"}}