{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T20:24:45Z","timestamp":1778703885635,"version":"3.51.4"},"reference-count":40,"publisher":"The Society for Free Radical Research Japan","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Clin. Biochem. Nutr."],"published-print":{"date-parts":[[2025]]},"DOI":"10.3164\/jcbn.24-173","type":"journal-article","created":{"date-parts":[[2024,11,19]],"date-time":"2024-11-19T22:10:52Z","timestamp":1732054252000},"page":"202-209","source":"Crossref","is-referenced-by-count":1,"title":["Characterization of the gut phageome of Japanese patients with ulcerative colitis under endoscopic remission"],"prefix":"10.3164","volume":"76","author":[{"given":"Akinori","family":"Otsuki","sequence":"first","affiliation":[{"name":"Department of Medicine, Shiga University of Medical Science"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryo","family":"Inoue","sequence":"additional","affiliation":[{"name":"Department of Applied Biological Science, Faculty of Agriculture, Setsunan University"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takayuki","family":"Imai","sequence":"additional","affiliation":[{"name":"Department of Medicine, Shiga University of Medical Science"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroto","family":"Miura","sequence":"additional","affiliation":[{"name":"Department of Applied Biological Science, Faculty of Agriculture, Setsunan University"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Atsushi","family":"Nishida","sequence":"additional","affiliation":[{"name":"Department of Medicine, Shiga University of Medical Science"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Osamu","family":"Inatomi","sequence":"additional","affiliation":[{"name":"Department of Medicine, Shiga University of Medical Science"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akira","family":"Andoh","sequence":"additional","affiliation":[{"name":"Department of Medicine, Shiga University of Medical Science"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1739","reference":[{"key":"1","doi-asserted-by":"crossref","unstructured":"1 Xavier RJ, Podolsky DK. Unravelling the pathogenesis of inflammatory bowel disease. Nature 2007; 448: 427\u2013434.","DOI":"10.1038\/nature06005"},{"key":"2","doi-asserted-by":"crossref","unstructured":"2 Ng SC, Shi HY, Hamidi N, et al. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. Lancet 2017; 390: 2769\u20132778.","DOI":"10.1016\/S0140-6736(17)32448-0"},{"key":"3","doi-asserted-by":"crossref","unstructured":"3 Kaplan GG, Ng SC. Understanding and preventing the global increase of inflammatory bowel disease. Gastroenterology 2017; 152: 313\u2013321.e2.","DOI":"10.1053\/j.gastro.2016.10.020"},{"key":"4","doi-asserted-by":"crossref","unstructured":"4 Jansen D, Matthijnssens J. The emerging role of the gut virome in health and inflammatory bowel disease: challenges, covariates and a viral imbalance. Viruses 2023; 15: 173.","DOI":"10.3390\/v15010173"},{"key":"5","doi-asserted-by":"crossref","unstructured":"5 Andoh A, Nishida A. Alteration of the gut microbiome in inflammatory bowel disease. Digestion 2023; 104: 16\u201323.","DOI":"10.1159\/000525925"},{"key":"6","doi-asserted-by":"crossref","unstructured":"6 Sartor RB, Wu GD. Roles for intestinal bacteria, viruses, and fungi in pathogenesis of inflammatory bowel diseases and therapeutic approaches. Gastroenterology 2017; 152: 327\u2013339.e4.","DOI":"10.1053\/j.gastro.2016.10.012"},{"key":"7","doi-asserted-by":"crossref","unstructured":"7 Nishino K, Nishida A, Inoue R, et al. Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease. J Gastroenterol 2018; 53: 95\u2013106.","DOI":"10.1007\/s00535-017-1384-4"},{"key":"8","doi-asserted-by":"crossref","unstructured":"8 Norman JM, Handley SA, Virgin HW. Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology 2014; 146: 1459\u20131469.","DOI":"10.1053\/j.gastro.2014.02.001"},{"key":"9","doi-asserted-by":"crossref","unstructured":"9 Norman JM, Handley SA, Baldridge MT, et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell 2015; 160: 447\u2013460.","DOI":"10.1016\/j.cell.2015.01.002"},{"key":"10","doi-asserted-by":"crossref","unstructured":"10 Tisza MJ, Buck CB. A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. Proc Natl Acad Sci U S A 2021; 118: e2023202118.","DOI":"10.1073\/pnas.2023202118"},{"key":"11","doi-asserted-by":"crossref","unstructured":"11 Maronek M, Link R, Ambro L, Gardlik R. Phages and their role in gastrointestinal disease: focus on inflammatory bowel disease. Cells 2020; 9: 1013.","DOI":"10.3390\/cells9041013"},{"key":"12","doi-asserted-by":"crossref","unstructured":"12 Wu S, Fang Z, Tan J, et al. DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach. Gigascience 2021; 10: giab056.","DOI":"10.1093\/gigascience\/giab056"},{"key":"13","doi-asserted-by":"crossref","unstructured":"13 Ungaro F, Massimino L, D&apos;Alessio S, Danese S. The gut virome in inflammatory bowel disease pathogenesis: from metagenomics to novel therapeutic approaches. United European Gastroenterol J 2019; 7: 999\u20131007.","DOI":"10.1177\/2050640619876787"},{"key":"14","doi-asserted-by":"crossref","unstructured":"14 Minot S, Bryson A, Chehoud C, Wu GD, Lewis JD, Bushman FD. Rapid evolution of the human gut virome. Proc Natl Acad Sci U S A 2013; 110: 12450\u201312455.","DOI":"10.1073\/pnas.1300833110"},{"key":"15","doi-asserted-by":"crossref","unstructured":"15 Waller AS, Yamada T, Kristensen DM, et al. Classification and quantification of bacteriophage taxa in human gut metagenomes. ISME J 2014; 8: 1391\u20131402.","DOI":"10.1038\/ismej.2014.30"},{"key":"16","doi-asserted-by":"crossref","unstructured":"16 Tun HM, Peng Y, Massimino L, et al. Gut virome in inflammatory bowel disease and beyond. Gut 2024; 73: 350\u2013360.","DOI":"10.1136\/gutjnl-2023-330001"},{"key":"17","doi-asserted-by":"crossref","unstructured":"17 Matsumoto M, Inoue R, Tsuruta T, Hara H, Yajima T. Long-term oral administration of cows\u2019 milk improves insulin sensitivity in rats fed a high-sucrose diet. Br J Nutr 2009; 102: 1324\u20131333.","DOI":"10.1017\/S0007114509990365"},{"key":"18","doi-asserted-by":"crossref","unstructured":"18 Inoue R, Sakaue Y, Sawai C, et al. A preliminary investigation on the relationship between gut microbiota and gene expressions in peripheral mononuclear cells of infants with autism spectrum disorders. Biosci Biotechnol Biochem 2016; 80: 2450\u20132458.","DOI":"10.1080\/09168451.2016.1222267"},{"key":"19","doi-asserted-by":"crossref","unstructured":"19 Bolyen E, Rideout JR, Dillon MR, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 2019; 37: 852\u2013857.","DOI":"10.1038\/s41587-019-0209-9"},{"key":"20","doi-asserted-by":"crossref","unstructured":"20 Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 2016; 13: 581\u2013583.","DOI":"10.1038\/nmeth.3869"},{"key":"21","doi-asserted-by":"crossref","unstructured":"21 Imai T, Inoue R, Nishida A, et al. Features of the gut prokaryotic virome of Japanese patients with Crohn\u2019s disease. J Gastroenterol 2022; 57: 559\u2013570.","DOI":"10.1007\/s00535-022-01882-8"},{"key":"22","doi-asserted-by":"crossref","unstructured":"22 Tamames J, Puente-S\u00e1nchez F. SqueezeMeta, a highly portable, fully automatic metagenomic analysis pipeline. Front Microbiol 2018; 9: 3349.","DOI":"10.3389\/fmicb.2018.03349"},{"key":"23","doi-asserted-by":"crossref","unstructured":"23 Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res 2017; 27: 824\u2013834.","DOI":"10.1101\/gr.213959.116"},{"key":"24","doi-asserted-by":"crossref","unstructured":"24 Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11: 119.","DOI":"10.1186\/1471-2105-11-119"},{"key":"25","doi-asserted-by":"crossref","unstructured":"25 Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods 2015; 12: 59\u201360.","DOI":"10.1038\/nmeth.3176"},{"key":"26","doi-asserted-by":"crossref","unstructured":"26 Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9: 357\u2013359.","DOI":"10.1038\/nmeth.1923"},{"key":"27","doi-asserted-by":"crossref","unstructured":"27 Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010; 26: 841\u2013842.","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"28","doi-asserted-by":"crossref","unstructured":"28 Shang J, Peng C, Liao H, Tang X, Sun Y. PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic data. Bioinform Adv 2023; 3: vbad101.","DOI":"10.1093\/bioadv\/vbad101"},{"key":"29","doi-asserted-by":"crossref","unstructured":"29 McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 2013; 8: e61217.","DOI":"10.1371\/journal.pone.0061217"},{"key":"30","doi-asserted-by":"crossref","unstructured":"30 Mallick H, Rahnavard A, McIver LJ, et al. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput Biol 2021; 17: e1009442.","DOI":"10.1371\/journal.pcbi.1009442"},{"key":"31","doi-asserted-by":"crossref","unstructured":"31 Kauffman KM, Hussain FA, Yang J, et al. A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Nature 2018; 554: 118\u2013122.","DOI":"10.1038\/nature25474"},{"key":"32","doi-asserted-by":"crossref","unstructured":"32 Imai T, Inoue R, Kawada Y, et al. Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease. J Gastroenterol 2019; 54: 149\u2013159.","DOI":"10.1007\/s00535-018-1530-7"},{"key":"33","doi-asserted-by":"crossref","unstructured":"33 Clooney AG, Sutton TDS, Shkoporov AN, et al. Whole-virome analysis sheds light on viral dark matter in inflammatory bowel disease. Cell Host Microbe 2019; 26: 764\u2013778.e5.","DOI":"10.1016\/j.chom.2019.10.009"},{"key":"34","doi-asserted-by":"crossref","unstructured":"34 Nishijima S, Suda W, Oshima K, et al. The gut microbiome of healthy Japanese and its microbial and functional uniqueness. DNA Res 2016; 23: 125\u2013133.","DOI":"10.1093\/dnares\/dsw002"},{"key":"35","doi-asserted-by":"crossref","unstructured":"35 Reyes A, Haynes M, Hanson N, et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010; 466: 334\u2013338.","DOI":"10.1038\/nature09199"},{"key":"36","doi-asserted-by":"crossref","unstructured":"36 P\u00e9rez-Brocal V, Garc\u00eda-L\u00f3pez R, Nos P, Beltr\u00e1n B, Moret I, Moya A. Metagenomic analysis of Crohn\u2019s disease patients identifies changes in the virome and microbiome related to disease status and therapy, and detects potential interactions and biomarkers. Inflamm Bowel Dis 2015; 21: 2515\u20132532.","DOI":"10.1097\/MIB.0000000000000549"},{"key":"37","doi-asserted-by":"crossref","unstructured":"37 Zuo T, Lu XJ, Zhang Y, et al. Gut mucosal virome alterations in ulcerative colitis. Gut 2019; 68: 1169\u20131179.","DOI":"10.1136\/gutjnl-2018-318131"},{"key":"38","doi-asserted-by":"crossref","unstructured":"38 Gogokhia L, Round JL. Immune-bacteriophage interactions in inflammatory bowel diseases. Curr Opin Virol 2021; 49: 30\u201335.","DOI":"10.1016\/j.coviro.2021.04.010"},{"key":"39","doi-asserted-by":"crossref","unstructured":"39 Xing C, Wang M, Ajibade AA, et al. Microbiota regulate innate immune signaling and protective immunity against cancer. Cell Host Microbe 2021; 29: 959\u2013974.e7.","DOI":"10.1016\/j.chom.2021.03.016"},{"key":"40","doi-asserted-by":"crossref","unstructured":"40 Buttimer C, Khokhlova EV, Stein L, et al. Temperate bacteriophages infecting the mucin-degrading bacterium <i>Ruminococcus gnavus<\/i> from the human gut. Gut Microbes 2023; 15: 2194794.","DOI":"10.1080\/19490976.2023.2194794"}],"container-title":["Journal of Clinical Biochemistry and Nutrition"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.jstage.jst.go.jp\/article\/jcbn\/76\/2\/76_24-173\/_pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,3,1]],"date-time":"2025-03-01T03:48:12Z","timestamp":1740800892000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.jstage.jst.go.jp\/article\/jcbn\/76\/2\/76_24-173\/_article"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":40,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2025]]}},"URL":"https:\/\/doi.org\/10.3164\/jcbn.24-173","relation":{},"ISSN":["0912-0009","1880-5086"],"issn-type":[{"value":"0912-0009","type":"print"},{"value":"1880-5086","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025]]},"article-number":"24-173"}}