{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T04:58:08Z","timestamp":1793163488375,"version":"4.5.0"},"reference-count":87,"publisher":"American Society for Microbiology","issue":"1","license":[{"start":{"date-parts":[[2022,2,22]],"date-time":"2022-02-22T00:00:00Z","timestamp":1645488000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2022,2,22]],"date-time":"2022-02-22T00:00:00Z","timestamp":1645488000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100000024","name":"Gouvernement du Canada | Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["MOP 142347"],"award-info":[{"award-number":["MOP 142347"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN 238422"],"award-info":[{"award-number":["RGPIN 238422"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Alberta Innovates Major Innovation Fund","award":["MIF03"],"award-info":[{"award-number":["MIF03"]}]},{"DOI":"10.13039\/501100001804","name":"Canada Research Chairs","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001804","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mBio"],"published-print":{"date-parts":[[2022,2,22]]},"abstract":"<jats:p>Although research exploring the microbiome has exploded in recent years, our understanding of the viral component of the microbiome is lagging far behind our understanding of the bacterial component. The vast majority of intestinal bacteria carry prophages integrated into their chromosomes, but most of these bacteriophages remain uncharacterized and unexplored.<\/jats:p>","DOI":"10.1128\/mbio.02085-21","type":"journal-article","created":{"date-parts":[[2022,1,25]],"date-time":"2022-01-25T04:30:51Z","timestamp":1643085051000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":17,"title":["Isolation and Characterization of a Novel Temperate Escherichia coli Bacteriophage, Kapi1, Which Modifies the O-Antigen and Contributes to the Competitiveness of Its Host during Colonization of the Murine Gastrointestinal Tract"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7291-5440","authenticated-orcid":true,"given":"Kat","family":"Pick","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Ju","sequence":"additional","affiliation":[{"name":"Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin P.","family":"Willing","sequence":"additional","affiliation":[{"name":"Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4450-1352","authenticated-orcid":true,"given":"Tracy L.","family":"Raivio","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro2298"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2017.16"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2016.47"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41396-018-0061-9"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2019.05.001"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1906958116"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1093\/femsle\/fnw015"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.3390\/v11010010"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1016\/s0966-842x(99)01646-7"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2020.09.008"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01296-13"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw387"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr485"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baaa062"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01107-17"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.33.3.933-938.1981"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01238-08"},{"key":"e_1_3_2_19_2","first-page":"29","article-title":"Die antagonistische Behandlung chronischer Darmst\u00f6rungen mit Colibakterien","author":"Nissle A","year":"1918","unstructured":"Nissle A. 1918. Die antagonistische Behandlung chronischer Darmst\u00f6rungen mit Colibakterien. Med Klin 29\u201330.","journal-title":"Med Klin"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-14042-z"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.3390\/v9040070"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0100-8"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.175.21.7115-7118.1993"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-15-742"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2001.4868"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00253-010-2638-8"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/jb.153.2.872-877.1983"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01172-06"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/17.5.1907"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2004.03.068"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M701827200"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1093\/femsle\/fnw002"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1574-6968.1998.tb12938.x"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.carres.2003.07.009"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.273.15.8849"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1432-1327.2000.01754.x"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1002\/jobm.201600065"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-40598-8_16-1"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.1991.tb01827.x"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.182.22.6472-6481.2000"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(88)90440-4"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2958.2001.02311.x"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1016\/0378-1119(83)90040-9"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00621-10"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/s0378-1119(97)00619-7"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.13729"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.75.10.4714"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.77.6.3225"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1111\/1574-6976.12077"},{"key":"e_1_3_2_51_2","first-page":"149","article-title":"Gastrointestinal survival of bacteria in commercial probiotic products","volume":"8","author":"Millette M","year":"2013","unstructured":"Millette M, Nguyen A, Amine KM, Lacroix M. 2013. Gastrointestinal survival of bacteria in commercial probiotic products. Int J Probiotics Prebiotics 8:149\u2013156.","journal-title":"Int J Probiotics Prebiotics"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2005.02.001"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.00798-08"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms1146"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005861"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2018.11.016"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01922-19"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-019-5674-5"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.2019"},{"key":"e_1_3_2_60_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky379"},{"key":"e_1_3_2_61_2","unstructured":"Babraham Bioinformatics. 2012. Trim Galore! A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. https:\/\/www.bioinformatics.babraham.ac.uk\/projects\/trim_galore\/."},{"key":"e_1_3_2_62_2","unstructured":"Babraham Bioinformatics. 2010. FastQC: a quality control tool for high throughput sequence data. http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/."},{"key":"e_1_3_2_63_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw354"},{"key":"e_1_3_2_64_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595"},{"key":"e_1_3_2_65_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_2_66_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty266"},{"key":"e_1_3_2_67_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"e_1_3_2_68_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu135"},{"key":"e_1_3_2_69_2","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20143391"},{"key":"e_1_3_2_70_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/29.12.2607"},{"key":"e_1_3_2_71_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm009"},{"key":"e_1_3_2_72_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkq1189"},{"key":"e_1_3_2_73_2","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1239303"},{"key":"e_1_3_2_74_2","doi-asserted-by":"publisher","DOI":"10.1128\/iai.46.1.202-212.1984"},{"key":"e_1_3_2_75_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-39590-8"},{"key":"e_1_3_2_76_2","doi-asserted-by":"publisher","DOI":"10.1016\/0003-2697(82)90673-X"},{"key":"e_1_3_2_77_2","doi-asserted-by":"publisher","DOI":"10.3791\/3916"},{"key":"e_1_3_2_78_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-0554-6_12"},{"key":"e_1_3_2_79_2","unstructured":"Seemann T. 2015. snippy: fast bacterial variant calling from NGS reads. https:\/\/github.com\/tseemann\/snippy."},{"key":"e_1_3_2_80_2","volume-title":"Molecular cloning: a laboratory manual","author":"Sambrook J","year":"2001","unstructured":"Sambrook J, Russell DW. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.","edition":"3"},{"key":"e_1_3_2_81_2","volume-title":"Experiments with gene fusions","author":"Silhavy TJ","year":"1984","unstructured":"Silhavy TJ, Berman ML, Enquist LW. 1984. Experiments with gene fusions. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY."},{"key":"e_1_3_2_82_2","doi-asserted-by":"publisher","DOI":"10.1038\/msb4100050"},{"key":"e_1_3_2_83_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.120163297"},{"key":"e_1_3_2_84_2","doi-asserted-by":"publisher","DOI":"10.1111\/mmi.14182"},{"key":"e_1_3_2_85_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/38.1.51"},{"key":"e_1_3_2_86_2","unstructured":"GraphPad Software. GraphPad Prism. www.graphpad.com."},{"key":"e_1_3_2_87_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu808"},{"key":"e_1_3_2_88_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-60327-164-6_15"}],"container-title":["mBio"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.02085-21","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mbio.02085-21","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T23:02:07Z","timestamp":1646694127000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mbio.02085-21"}},"subtitle":[],"editor":[{"given":"Matthew R.","family":"Chapman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,2,22]]},"references-count":87,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,2,22]]}},"alternative-id":["10.1128\/mbio.02085-21"],"URL":"https:\/\/doi.org\/10.1128\/mbio.02085-21","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.11.03.467220","asserted-by":"object"}]},"ISSN":["2150-7511"],"issn-type":[{"value":"2150-7511","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,2,22]]},"assertion":[{"value":"2021-11-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-12-23","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-01-25","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e02085-21"}}