{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T04:33:35Z","timestamp":1783571615325,"version":"3.55.0"},"reference-count":81,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,12,20]],"date-time":"2024-12-20T00:00:00Z","timestamp":1734652800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"publisher","award":["DNRF137"],"award-info":[{"award-number":["DNRF137"]}],"id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","award":["460129525"],"award-info":[{"award-number":["460129525"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["BAA 75D301-21-C-12111"],"award-info":[{"award-number":["BAA 75D301-21-C-12111"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019180","name":"HORIZON EUROPE European Research Council","doi-asserted-by":"publisher","award":["101041421"],"award-info":[{"award-number":["101041421"]}],"id":[{"id":"10.13039\/100019180","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"publisher","award":["BI-US\/22-24-161"],"award-info":[{"award-number":["BI-US\/22-24-161"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"publisher","award":["P4-0116"],"award-info":[{"award-number":["P4-0116"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"publisher","award":["J1-4411"],"award-info":[{"award-number":["J1-4411"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"publisher","award":["J4-4550"],"award-info":[{"award-number":["J4-4550"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["7005519"],"award-info":[{"award-number":["7005519"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["PEN04853"],"award-info":[{"award-number":["PEN04853"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports"],"published-print":{"date-parts":[[2025,1]]},"DOI":"10.1016\/j.celrep.2024.115197","type":"journal-article","created":{"date-parts":[[2025,1,10]],"date-time":"2025-01-10T08:10:29Z","timestamp":1736496629000},"page":"115197","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":8,"title":["Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales"],"prefix":"10.1016","volume":"44","author":[{"given":"Polonca","family":"Stefanic","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eva","family":"Stare","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Valentina A.","family":"Floccari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jasna","family":"Kovac","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Hertel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ulisses","family":"Rocha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c1kos T.","family":"Kov\u00e1cs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ines","family":"Mandi\u0107-Mulec","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mikael Lenz","family":"Strube","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4136-986X","authenticated-orcid":false,"given":"Anna","family":"Drago\u0161","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.celrep.2024.115197_bib1","doi-asserted-by":"crossref","first-page":"31","DOI":"10.4161\/bact.1.1.14942","article-title":"Phages in nature","volume":"1","author":"Clokie","year":"2011","journal-title":"Bacteriophage"},{"key":"10.1016\/j.celrep.2024.115197_bib2","doi-asserted-by":"crossref","first-page":"9973","DOI":"10.1038\/s41598-018-28326-9","article-title":"Widespread distribution of prophage-encoded virulence factors in marine Vibrio communities","volume":"8","author":"Castillo","year":"2018","journal-title":"Sci. Rep."},{"key":"10.1016\/j.celrep.2024.115197_bib3","doi-asserted-by":"crossref","first-page":"404","DOI":"10.3390\/pathogens10040404","article-title":"Bacteriophages of Shiga toxin-producing Escherichia coli and their contribution to pathogenicity","volume":"10","author":"Rodr\u00edguez-Rubio","year":"2021","journal-title":"Pathogens"},{"key":"10.1016\/j.celrep.2024.115197_bib4","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1016\/j.tim.2022.11.009","article-title":"Unique relationships between phages and endospore-forming hosts","volume":"31","author":"Butala","year":"2022","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.celrep.2024.115197_bib5","doi-asserted-by":"crossref","first-page":"3479","DOI":"10.1016\/j.cub.2021.05.046","article-title":"Phages carry interbacterial weapons encoded by biosynthetic gene clusters","volume":"31","author":"Drago\u0161","year":"2021","journal-title":"Curr. Biol."},{"key":"10.1016\/j.celrep.2024.115197_bib6","doi-asserted-by":"crossref","first-page":"1620","DOI":"10.1016\/j.chom.2021.09.002","article-title":"Prophages encode phage-defense systems with cognate self-immunity","volume":"29","author":"Owen","year":"2021","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2024.115197_bib7","doi-asserted-by":"crossref","DOI":"10.3390\/microorganisms8040480","article-title":"Bacteriophages promote metabolic changes in bacteria biofilm","volume":"8","author":"Papaianni","year":"2020","journal-title":"Microorganisms"},{"key":"10.1016\/j.celrep.2024.115197_bib8","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.1038\/ismej.2016.3","article-title":"High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection","volume":"10","author":"De Smet","year":"2016","journal-title":"ISME J."},{"key":"10.1016\/j.celrep.2024.115197_bib9","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1038\/nature21049","article-title":"Communication between viruses guides lysis-lysogeny decisions","volume":"541","author":"Erez","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2024.115197_bib10","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/s41396-020-00795-9","article-title":"Beyond arbitrium: identification of a second communication system in Bacillus phage phi3T that may regulate host defense mechanisms","volume":"15","author":"Bernard","year":"2021","journal-title":"ISME J."},{"key":"10.1016\/j.celrep.2024.115197_bib11","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1038\/s41564-021-01008-5","article-title":"Dormant phages communicate via arbitrium to control exit from lysogeny","volume":"7","author":"Aframian","year":"2021","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.celrep.2024.115197_bib12","series-title":"Bacteriophage Ecology: Population Growth, Evolution, and Impact of Bacterial Viruses","author":"Abedon","year":"2008"},{"key":"10.1016\/j.celrep.2024.115197_bib13","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/j.jmii.2011.07.001","article-title":"A new health threat in Europe: Shiga toxin\u2013producing Escherichia coli O104:H4 infections","volume":"44","author":"Wu","year":"2011","journal-title":"J.\u00a0Microbiol. Immunol. Infect."},{"key":"10.1016\/j.celrep.2024.115197_bib14","doi-asserted-by":"crossref","first-page":"ftw037","DOI":"10.1093\/femspd\/ftw037","article-title":"Phage-mediated Shiga toxin (Stx) horizontal gene transfer and expression in non-Shiga toxigenic Enterobacter and Escherichia coli strains","volume":"74","author":"Khalil","year":"2016","journal-title":"Pathog. Dis."},{"key":"10.1016\/j.celrep.2024.115197_bib15","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1038\/nature21391","article-title":"Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility","volume":"543","author":"Le Page","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2024.115197_bib16","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00326-22","article-title":"Mining of thousands of prokaryotic genomes reveals high abundance of prophages with a strictly narrow host range","volume":"7","author":"L\u00f3pez-Leal","year":"2022","journal-title":"mSystems"},{"key":"10.1016\/j.celrep.2024.115197_bib17","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1038\/s41396-018-0061-9","article-title":"Lysogeny is prevalent and widely distributed in the murine gut microbiota","volume":"12","author":"Kim","year":"2018","journal-title":"ISME J."},{"key":"10.1016\/j.celrep.2024.115197_bib18","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1093\/molbev\/mss279","article-title":"The adaptation of temperate bacteriophages to their host genomes","volume":"30","author":"Bobay","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.celrep.2024.115197_bib19","doi-asserted-by":"crossref","DOI":"10.3390\/v11110983","article-title":"Large phenotypic and genetic diversity of prophages induced from the fish pathogen vibrio anguillarum","volume":"11","author":"Castillo","year":"2019","journal-title":"Viruses"},{"key":"10.1016\/j.celrep.2024.115197_bib20","doi-asserted-by":"crossref","first-page":"2027","DOI":"10.1128\/JB.01542-10","article-title":"Tracing the domestication of a biofilm-forming bacterium","volume":"193","author":"McLoon","year":"2011","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.celrep.2024.115197_bib21","doi-asserted-by":"crossref","first-page":"1922","DOI":"10.1099\/mic.0.000371","article-title":"Specific Bacillus subtilis 168 variants form biofilms on nutrient-rich medium","volume":"162","author":"Gallegos-Monterrosa","year":"2016","journal-title":"Microbiology"},{"key":"10.1016\/j.celrep.2024.115197_bib22","article-title":"Laboratory strains of Escherichia coli K-12: things are seldom what they seem","volume":"9","author":"Browning","year":"2023","journal-title":"Microb. Genom."},{"key":"10.1016\/j.celrep.2024.115197_bib23","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1128\/JB.01515-09","article-title":"Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strains","volume":"192","author":"Klockgether","year":"2010","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.celrep.2024.115197_bib24","first-page":"221","article-title":"Host Organisms: Bacillus subtilis","volume":"1","author":"Hohmann","year":"2017","journal-title":"Ind. Biotechnol."},{"key":"10.1016\/j.celrep.2024.115197_bib25","series-title":"Molecular Aspects of Plant Growth Promotion and Protection by Bacillus Subtilis","author":"Blake","year":"2021"},{"key":"10.1016\/j.celrep.2024.115197_bib26","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.02955-20","article-title":"Bacillaene mediates the inhibitory effect of Bacillus subtilis on Campylobacter jejuni biofilms","volume":"87","author":"Erega","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.celrep.2024.115197_bib27","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.01836-22","article-title":"Nutrient availability and biofilm polysaccharide shape the bacillaene-dependent antagonism of Bacillus subtilis against Salmonella Typhimurium","volume":"10","author":"Podnar","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"10.1016\/j.celrep.2024.115197_bib28","doi-asserted-by":"crossref","first-page":"289","DOI":"10.3390\/microorganisms10020289","article-title":"Bacillus subtilis PS-216 antagonistic activities against Campylobacter jejuni NCTC 11168 are modulated by temperature, oxygen, and growth medium","volume":"10","author":"\u0160imunovi\u0107","year":"2022","journal-title":"Microorganisms"},{"key":"10.1016\/j.celrep.2024.115197_bib29","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2017.00354","article-title":"Bacillus subtilis improves immunity and disease resistance in rabbits","volume":"8","author":"Guo","year":"2017","journal-title":"Front. Immunol."},{"key":"10.1016\/j.celrep.2024.115197_bib30","doi-asserted-by":"crossref","first-page":"4813","DOI":"10.4049\/jimmunol.1303369","article-title":"Protection from intestinal inflammation by bacterial exopolysaccharides","volume":"192","author":"Jones","year":"2014","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.celrep.2024.115197_bib31","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms14332","article-title":"Bacillus subtilis biofilm extends Caenorhabditis elegans longevity through downregulation of the insulin-like signalling pathway","volume":"8","author":"Donato","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.115197_bib32","doi-asserted-by":"crossref","first-page":"3967","DOI":"10.3382\/ps\/pey265","article-title":"Bacillus subtilis in broiler diets with different levels of energy and protein","volume":"97","author":"Goodarzi Boroojeni","year":"2018","journal-title":"Poultry Sci."},{"key":"10.1016\/j.celrep.2024.115197_bib33","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1111\/j.1365-2672.2005.02736.x","article-title":"Spores of Bacillus subtilis: Their resistance to and killing by radiation, heat and chemicals","volume":"101","author":"Setlow","year":"2006","journal-title":"J.\u00a0Appl. Microbiol."},{"key":"10.1016\/j.celrep.2024.115197_bib34","doi-asserted-by":"crossref","first-page":"638","DOI":"10.1016\/j.tree.2006.07.004","article-title":"Aerobiology and the global transport of desert dust","volume":"21","author":"Kellogg","year":"2006","journal-title":"Trends Ecol. Evol."},{"key":"10.1016\/j.celrep.2024.115197_bib35","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1128\/CMR.00039-06","article-title":"Atmospheric movement of microorganisms in clouds of desert dust and implications for human health","volume":"20","author":"Griffin","year":"2007","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.celrep.2024.115197_bib36","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1007\/s00248-019-01455-y","article-title":"Environment Shapes the Intra-species Diversity of Bacillus subtilis Isolates","volume":"79","author":"\u0160tefani\u010d","year":"2020","journal-title":"Microb. Ecol."},{"key":"10.1016\/j.celrep.2024.115197_bib37","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms15127","article-title":"De novo evolved interference competition promotes the spread of biofilm defectors","volume":"8","author":"Martin","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.115197_bib38","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1128\/AEM.02473-14","article-title":"Identification of ypqP as a new Bacillus subtilis biofilm determinant that mediates the protection of Staphylococcus aureus against antimicrobial agents in mixed-species communities","volume":"81","author":"Sanchez-Vizuete","year":"2015","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.celrep.2024.115197_bib39","first-page":"1","article-title":"Pervasive prophage recombination occurs during evolution of spore-forming Bacilli","author":"Drago\u0161","year":"2020","journal-title":"ISME J."},{"key":"10.1016\/j.celrep.2024.115197_bib40","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1010065","article-title":"Interactions between mobile genetic elements: An anti-phage gene in an integrative and conjugative element protects host cells from predation by a temperate bacteriophage","volume":"18","author":"Johnson","year":"2022","journal-title":"PLoS Genet."},{"key":"10.1016\/j.celrep.2024.115197_bib41","doi-asserted-by":"crossref","first-page":"4085","DOI":"10.1128\/JB.00696-13","article-title":"Plasmid-encoded ComI inhibits competence in the ancestral 3610 strain of Bacillus subtilis","volume":"195","author":"Konkol","year":"2013","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.celrep.2024.115197_bib42","doi-asserted-by":"crossref","first-page":"3399","DOI":"10.1128\/jb.178.11.3399-3401.1996","article-title":"Phenotypic differentiation of \u201csmart\u201d versus \u201cnaive\u201d bacteriophages of Bacillus subtilis","volume":"178","author":"Mcveigh","year":"1996","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.celrep.2024.115197_bib43","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1128\/jvi.54.3.773-780.1985","article-title":"DNA packaging by the Bacillus subtilis defective bacteriophage PBSX","volume":"54","author":"Anderson","year":"1985","journal-title":"J.\u00a0Virol."},{"key":"10.1016\/j.celrep.2024.115197_bib44","doi-asserted-by":"crossref","first-page":"6209","DOI":"10.1128\/JB.00625-10","article-title":"Repression of sigK intervening (skin) element gene expression by the CI-like protein SknR and effect of SknR depletion on growth of Bacillus subtilis cells","volume":"192","author":"Kimura","year":"2010","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.celrep.2024.115197_bib45","doi-asserted-by":"crossref","first-page":"1756","DOI":"10.1128\/JB.01290-08","article-title":"Social interactions and distribution of Bacillus subtilis pherotypes at microscale","volume":"191","author":"\u0160tefani\u010d","year":"2009","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.celrep.2024.115197_bib46","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1038\/s41587-019-0100-8","article-title":"Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks","volume":"37","author":"Bin Jang","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2024.115197_bib47","first-page":"214","article-title":"INfrastructure for a PHAge REference Database: Identification of large-scale biases in the current collection of cultured phage genomes","volume":"2","author":"Cook","year":"2021","journal-title":"PHAGE (New Rochelle, N.Y.)"},{"key":"10.1016\/j.celrep.2024.115197_bib48","article-title":"Temperate gut phages are prevalent, diverse, and predominantly inactive","author":"Dahlman","year":"2023","journal-title":"bioRxiv"},{"key":"10.1016\/j.celrep.2024.115197_bib49","doi-asserted-by":"crossref","DOI":"10.3390\/v14030483","article-title":"Prevalence, diversity and UV-light inducibility potential of prophages in Bacillus subtilis and their possible roles in host properties","volume":"14","author":"Abraha","year":"2022","journal-title":"Viruses"},{"key":"10.1016\/j.celrep.2024.115197_bib50","doi-asserted-by":"crossref","first-page":"17906","DOI":"10.1073\/pnas.1906958116","article-title":"Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut","volume":"116","author":"Fraz\u00e3o","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2024.115197_bib51","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1007\/s00239-020-09951-3","article-title":"Spatial patterns of gene expression in bacterial genomes","volume":"88","author":"Lato","year":"2020","journal-title":"J.\u00a0Mol. Evol."},{"key":"10.1016\/j.celrep.2024.115197_bib52","doi-asserted-by":"crossref","first-page":"12127","DOI":"10.1073\/pnas.1405336111","article-title":"Pervasive domestication of defective prophages by bacteria","volume":"111","author":"Bobay","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2024.115197_bib53","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1093\/molbev\/msg219","article-title":"Genome engineering reveals large dispensable regions in Bacillus subtilis","volume":"20","author":"Westers","year":"2003","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.celrep.2024.115197_bib54","first-page":"1","article-title":"Prophage-triggered membrane vesicle formation through peptidoglycan damage in Bacillus subtilis","volume":"81","author":"Toyofuku","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.115197_bib55","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1139\/w03-041","article-title":"Chromosome DNA fragmentation and excretion caused by defective prophage gene expression in the early-exponential-phase culture of Bacillus subtilis","volume":"49","author":"Shingaki","year":"2003","journal-title":"Can. J. Microbiol."},{"key":"10.1016\/j.celrep.2024.115197_bib56","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1038\/ismej.2011.30","article-title":"Within-host competition determines reproductive success of temperate bacteriophages","volume":"5","author":"Refardt","year":"2011","journal-title":"ISME J."},{"key":"10.1016\/j.celrep.2024.115197_bib57","doi-asserted-by":"crossref","DOI":"10.1016\/j.mib.2023.102321","article-title":"Prophages provide a rich source of antiphage defense systems","volume":"73","author":"Patel","year":"2023","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.celrep.2024.115197_bib58","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.chom.2022.12.008","article-title":"PICI thieves: Molecular piracy and cooperation","volume":"31","author":"Schmidt","year":"2023","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2024.115197_bib59","article-title":"An integrative and conjugative element encodes an abortive infection system to protect host cells from predation by a bacteriophage","author":"Johnson","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.celrep.2024.115197_bib60","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1080\/19490976.2019.1701353","article-title":"Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome","volume":"11","author":"Boling","year":"2020","journal-title":"Gut Microb."},{"key":"10.1016\/j.celrep.2024.115197_bib61","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.celrep.2024.115197_bib62","article-title":"Completing bacterial genome assemblies with multiplex MinION sequencing","volume":"3","author":"Wick","year":"2017","journal-title":"Microb. Genom."},{"key":"10.1016\/j.celrep.2024.115197_bib63","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: a better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2024.115197_bib64","doi-asserted-by":"crossref","first-page":"W347","DOI":"10.1093\/nar\/gkr485","article-title":"PHAST: A Fast Phage Search Tool","volume":"39","author":"Zhou","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2024.115197_bib65","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.3243","article-title":"vConTACT: An iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria","volume":"5","author":"Bolduc","year":"2017","journal-title":"PeerJ"},{"key":"10.1016\/j.celrep.2024.115197_bib66","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: Prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.celrep.2024.115197_bib67","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1038\/nmeth.1938","article-title":"Detecting overlapping protein complexes in protein-protein interaction networks","volume":"9","author":"Nepusz","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2024.115197_bib68","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2024.115197_bib69","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2024.115197_bib70","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/molbev\/msp077","article-title":"FastTree: Computing large minimum evolution trees with profiles instead of a distance matrix","volume":"26","author":"Price","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.celrep.2024.115197_bib71","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: Improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.celrep.2024.115197_bib72","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2024.115197_bib73","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/36786","article-title":"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis","volume":"390","author":"Kunst","year":"1997","journal-title":"Nature (London, U. K.)"},{"key":"10.1016\/j.celrep.2024.115197_bib74","doi-asserted-by":"crossref","first-page":"12554","DOI":"10.1073\/pnas.0505835102","article-title":"Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response","volume":"102","author":"Auchtung","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2024.115197_bib75","doi-asserted-by":"crossref","first-page":"2667","DOI":"10.1128\/jb.172.5.2667-2674.1990","article-title":"Characterization of PBSX, a defective prophage of Bacillus subtilis","volume":"172","author":"Wood","year":"1990","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.celrep.2024.115197_bib76","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1101\/gad.4.4.525","article-title":"The Bacillus subtilis gene for the developmental transcription factor \u03c3(K) is generated by excision of a dispensable DNA element containing a sporulation recombinase gene","volume":"4","author":"Kunkel","year":"1990","journal-title":"Genes Dev."},{"key":"10.1016\/j.celrep.2024.115197_bib77","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1004636","article-title":"Developmentally-regulated excision of the SP\u03b2 prophage reconstitutes a gene required for spore envelope maturation in Bacillus subtilis","volume":"10","author":"Abe","year":"2014","journal-title":"PLoS Genet."},{"key":"10.1016\/j.celrep.2024.115197_bib78","doi-asserted-by":"crossref","DOI":"10.1128\/JB.00290-20","article-title":"The large pBS32\/pLS32 plasmid of ancestral Bacillus subtilis","volume":"202","author":"Burton","year":"2020","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.celrep.2024.115197_bib79","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1128\/genomeA.00641-13","article-title":"Complete genome sequence of Bacillus subtilis phage \u03d5105","volume":"1","author":"Zeigler","year":"2013","journal-title":"Genome Announc."},{"key":"10.1016\/j.celrep.2024.115197_bib80","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1111\/j.1462-2920.2012.02717.x","article-title":"The quorum sensing diversity within and between ecotypes of Bacillus subtilis","volume":"14","author":"Stefanic","year":"2012","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.celrep.2024.115197_bib81","doi-asserted-by":"crossref","first-page":"14042","DOI":"10.1073\/pnas.1512671112","article-title":"Kin discrimination between sympatric Bacillus subtilis isolates","volume":"112","author":"Stefanic","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124724015481?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124724015481?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T20:42:31Z","timestamp":1781556151000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2211124724015481"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1]]},"references-count":81,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1]]}},"alternative-id":["S2211124724015481"],"URL":"https:\/\/doi.org\/10.1016\/j.celrep.2024.115197","relation":{},"ISSN":["2211-1247"],"issn-type":[{"value":"2211-1247","type":"print"}],"subject":[],"published":{"date-parts":[[2025,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scales","name":"articletitle","label":"Article Title"},{"value":"Cell Reports","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2024.115197","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"115197"}}