{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T20:53:20Z","timestamp":1791579200714,"version":"4.3.4"},"reference-count":91,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100002112","name":"A P Giannini Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100002112","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["222528\/Z\/21\/Z"],"award-info":[{"award-number":["222528\/Z\/21\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"National Institute of Allergy and Infectious Diseases Division of Intramural Research","doi-asserted-by":"publisher","award":["K99-AI190131"],"award-info":[{"award-number":["K99-AI190131"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"National Institute of Allergy and Infectious Diseases Division of Intramural Research","doi-asserted-by":"publisher","award":["R01-AI183463"],"award-info":[{"award-number":["R01-AI183463"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005643","name":"Baxter International Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005643","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000952","name":"Allen Family Philanthropies","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000952","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Host &amp; Microbe"],"published-print":{"date-parts":[[2026,10]]},"DOI":"10.1016\/j.chom.2026.09.009","type":"journal-article","created":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T14:50:03Z","timestamp":1791471003000},"update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Native pathogen-phage networks reveal multilayered defense and gut-active anti-phage immunity"],"prefix":"10.1016","author":[{"given":"Benjamin X.","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramya","family":"Narasimhan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aisling","family":"Brady","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Wenner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Blanca","family":"Perez Sepulveda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly","family":"Hughes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yogesh","family":"Hooda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Senjuti","family":"Saha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jay C.D.","family":"Hinton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3804-2209","authenticated-orcid":false,"given":"Denise M.","family":"Monack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.chom.2026.09.009_bib1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41538-023-00245-8","article-title":"Positive and negative aspects of bacteriophages and their immense role in the food chain","volume":"8","author":"Ranveer","year":"2024","journal-title":"NPJ Sci. Food"},{"key":"10.1016\/j.chom.2026.09.009_bib2","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1002\/bies.201400152","article-title":"A century of phage research: Bacteriophages and the shaping of modern biology","volume":"37","author":"Keen","year":"2015","journal-title":"BioEssays"},{"key":"10.1016\/j.chom.2026.09.009_bib3","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1007\/s12551-017-0382-3","article-title":"Review of the nature, diversity and structure of bacteriophage receptor binding proteins that target Gram-positive bacteria","volume":"10","author":"Dowah","year":"2018","journal-title":"Biophys. Rev."},{"key":"10.1016\/j.chom.2026.09.009_bib4","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/s41579-019-0311-5","article-title":"Phage diversity, genomics and phylogeny","volume":"18","author":"Dion","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib5","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1038\/s41564-020-0746-5","article-title":"Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron","volume":"5","author":"Porter","year":"2020","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib6","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2322371121","article-title":"Evolution of a bistable genetic system in fluctuating and nonfluctuating environments","volume":"121","author":"Fern\u00e1ndez-Fern\u00e1ndez","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2026.09.009_bib7","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1146\/annurev-micro-020722-013730","article-title":"Toxin-Antitoxin Systems as Phage Defense Elements","volume":"76","author":"LeRoux","year":"2022","journal-title":"Annu. Rev. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib8","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1146\/annurev-genet-022120-112523","article-title":"Molecular Mechanisms of CRISPR-Cas Immunity in Bacteria","volume":"54","author":"Nussenzweig","year":"2020","journal-title":"Annu. Rev. Genet."},{"key":"10.1016\/j.chom.2026.09.009_bib9","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1128\/MMBR.00044-12","article-title":"Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense","volume":"77","author":"Vasu","year":"2013","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.chom.2026.09.009_bib10","doi-asserted-by":"crossref","DOI":"10.1126\/science.aar4120","article-title":"Systematic discovery of antiphage defense systems in the microbial pangenome","volume":"359","author":"Doron","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.chom.2026.09.009_bib11","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adj0341","article-title":"Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa","volume":"10","author":"Costa","year":"2024","journal-title":"Sci. Adv."},{"key":"10.1016\/j.chom.2026.09.009_bib12","doi-asserted-by":"crossref","first-page":"1568","DOI":"10.1038\/s41564-022-01219-4","article-title":"A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome","volume":"7","author":"Vassallo","year":"2022","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib13","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-022-30269-9","article-title":"Systematic and quantitative view of the antiviral arsenal of prokaryotes","volume":"13","author":"Tesson","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2026.09.009_bib14","doi-asserted-by":"crossref","first-page":"W541","DOI":"10.1093\/nar\/gkac400","article-title":"PADLOC: a web server for the identification of antiviral defence systems in microbial genomes","volume":"50","author":"Payne","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2026.09.009_bib15","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1038\/s41586-024-08493-8","article-title":"Structure and mechanism of the Zorya anti-phage defence system","volume":"639","author":"Hu","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.chom.2026.09.009_bib16","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-16703-w","article-title":"Structural and functional evidence of bacterial antiphage protection by Thoeris defense system via NAD+ degradation","volume":"11","author":"Ka","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2026.09.009_bib17","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1038\/s41586-023-06743-9","article-title":"Bacterial cGAS senses a viral RNA to initiate immunity","volume":"623","author":"Banh","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.chom.2026.09.009_bib18","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1038\/s41586-022-05444-z","article-title":"Direct activation of a bacterial innate immune system by a viral capsid protein","volume":"612","author":"Zhang","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.chom.2026.09.009_bib19","doi-asserted-by":"crossref","DOI":"10.1126\/science.abm4096","article-title":"Prokaryotic innate immunity through pattern recognition of conserved viral proteins","volume":"377","author":"Gao","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.chom.2026.09.009_bib20","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2024.0067","article-title":"Systematic functional assessment of anti-phage systems in their native host","volume":"380","author":"David","year":"2025","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"10.1016\/j.chom.2026.09.009_bib21","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.chom.2026.09.009_bib22","doi-asserted-by":"crossref","DOI":"10.1016\/j.mib.2022.102225","article-title":"Toothpicks, logic, and next-generation sequencing: systematic investigation of bacteriophage-host interactions","volume":"70","author":"Shaidullina","year":"2022","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib23","doi-asserted-by":"crossref","DOI":"10.1016\/j.mib.2022.102262","article-title":"One species, different diseases: the unique molecular mechanisms that underlie the pathogenesis of typhoidal Salmonella infections","volume":"72","author":"Wang","year":"2023","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1574-6968.2010.01904.x","article-title":"So similar, yet so different: uncovering distinctive features in the genomes of Salmonella enterica serovars Typhimurium and Typhi","volume":"305","author":"Sabbagh","year":"2010","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.chom.2026.09.009_bib25","doi-asserted-by":"crossref","DOI":"10.1080\/21505594.2025.2504658","article-title":"Comparative genomics of Salmonella enterica serovars Paratyphi A, Typhi and Typhimurium reveals distinct profiles of their pangenome, mobile genetic elements, antimicrobial resistance and defense systems repertoire","volume":"16","author":"Coluzzi","year":"2025","journal-title":"Virulence"},{"key":"10.1016\/j.chom.2026.09.009_bib26","doi-asserted-by":"crossref","first-page":"e01985-19","DOI":"10.1128\/AEM.01985-19","article-title":"Implications of Mobile Genetic Elements for Salmonella enterica Single-Nucleotide Polymorphism Subtyping and Source Tracking Investigations","volume":"85","author":"Li","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib27","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1010694","article-title":"The defense island repertoire of the Escherichia coli pan-genome","volume":"19","author":"Hochhauser","year":"2023","journal-title":"PLoS Genet."},{"key":"10.1016\/j.chom.2026.09.009_bib28","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1016\/j.chom.2025.04.021","article-title":"E. coli prophages encode an arsenal of defense systems to protect against temperate phages","volume":"33","author":"Brenes","year":"2025","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2026.09.009_bib29","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.chom.2026.09.009_bib30","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1016\/j.chom.2024.05.017","article-title":"Going viral: The role of mobile genetic elements in bacterial immunity","volume":"32","author":"Beamud","year":"2024","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2026.09.009_bib31","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1073\/pnas.1416707112","article-title":"Patterns of genome evolution that have accompanied host adaptation in Salmonella","volume":"112","author":"Langridge","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2026.09.009_bib32","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.mib.2021.05.013","article-title":"Salmonella pathogenesis and host-adaptation in farmed animals","volume":"63","author":"Stevens","year":"2021","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib33","doi-asserted-by":"crossref","first-page":"4579","DOI":"10.1128\/IAI.66.10.4579-4587.1998","article-title":"Evolution of Host Adaptation in Salmonella enterica","volume":"66","author":"B\u00e4umler","year":"1998","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2026.09.009_bib34","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-022-29597-7","article-title":"Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium","volume":"13","author":"Bakkeren","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2026.09.009_bib35","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00883-23","article-title":"Mobilome-driven partitions of the resistome in Salmonella","volume":"8","author":"Jia","year":"2023","journal-title":"mSystems"},{"key":"10.1016\/j.chom.2026.09.009_bib36","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.chom.2017.01.009","article-title":"Pseudogenization of the Secreted Effector Gene sseI Confers Rapid Systemic Dissemination of S. Typhimurium ST313 within Migratory Dendritic Cells","volume":"21","author":"Carden","year":"2017","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2026.09.009_bib37","doi-asserted-by":"crossref","first-page":"1288","DOI":"10.1038\/s41588-024-01779-7","article-title":"High-throughput fitness experiments reveal specific vulnerabilities of human-adapted Salmonella during stress and infection","volume":"56","author":"Wang","year":"2024","journal-title":"Nat. Genet."},{"key":"10.1016\/j.chom.2026.09.009_bib38","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1038\/s41564-025-01953-5","article-title":"Profiling Salmonella transcriptional dynamics during macrophage infection using a comprehensive reporter library","volume":"10","author":"Nguyen","year":"2025","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib39","doi-asserted-by":"crossref","first-page":"478","DOI":"10.3390\/v13030478","article-title":"Isolation and Characterisation of Bacteriophages with Activity against Invasive Non-Typhoidal Salmonella Causing Bloodstream Infection in Malawi","volume":"13","author":"Rodwell","year":"2021","journal-title":"Viruses"},{"key":"10.1016\/j.chom.2026.09.009_bib40","doi-asserted-by":"crossref","DOI":"10.1128\/mra.00447-24","article-title":"Genome sequences of bacteriophages that infect Salmonella Typhi from Bangladesh","volume":"14","author":"Islam","year":"2025","journal-title":"Microbiol. Resour. Announc."},{"key":"10.1016\/j.chom.2026.09.009_bib41","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/s41564-020-00836-1","article-title":"Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa","volume":"6","author":"Pulford","year":"2020","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib42","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3000059","article-title":"Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580","volume":"17","author":"Canals","year":"2019","journal-title":"PLoS Biol."},{"key":"10.1016\/j.chom.2026.09.009_bib43","article-title":"Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis","volume":"9","author":"Fong","year":"2023","journal-title":"Microb. Genom."},{"key":"10.1016\/j.chom.2026.09.009_bib44","doi-asserted-by":"crossref","DOI":"10.1099\/mic.0.001521","article-title":"Microbe Profile: Salmonella Typhimurium: the master of the art of adaptation","volume":"171","author":"Perez-Sepulveda","year":"2025","journal-title":"Microbiology (Reading)"},{"key":"10.1016\/j.chom.2026.09.009_bib45","doi-asserted-by":"crossref","first-page":"e02112-18","DOI":"10.1128\/mBio.02112-18","article-title":"Salmonella enterica Serovar Typhi in Bangladesh: Exploration of Genomic Diversity and Antimicrobial Resistance","volume":"9","author":"Tanmoy","year":"2018","journal-title":"mBio"},{"key":"10.1016\/j.chom.2026.09.009_bib46","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0011822","article-title":"Old tools, new applications: Use of environmental bacteriophages for typhoid surveillance and evaluating vaccine impact","volume":"18","author":"Hooda","year":"2024","journal-title":"PLOS Negl. Trop. Dis."},{"key":"10.1016\/j.chom.2026.09.009_bib47","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1038\/s41564-024-01832-5","article-title":"Prediction of strain level phage\u2013host interactions across the Escherichia genus using only genomic information","volume":"9","author":"Gaborieau","year":"2024","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib48","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-022-30967-4","article-title":"A genome-wide atlas of antibiotic susceptibility targets and pathways to tolerance","volume":"13","author":"Leshchiner","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2026.09.009_bib49","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1128\/jb.178.6.1691-1698.1996","article-title":"Characterization of the rcsA and rcsB genes from Salmonella typhi: rcsB through tviA is involved in regulation of Vi antigen synthesis","volume":"178","author":"Virlogeux","year":"1996","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2026.09.009_bib50","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.micpath.2018.08.050","article-title":"OxyR positively and directly regulates Vi polysaccharide capsular antigen in Salmonella enterica serovar Typhi","volume":"124","author":"Zhang","year":"2018","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.chom.2026.09.009_bib51","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1093\/genetics\/162.4.1513","article-title":"Regulation of capsule synthesis and cell motility in Salmonella enterica by the essential gene igaA","volume":"162","author":"Cano","year":"2002","journal-title":"Genetics"},{"key":"10.1016\/j.chom.2026.09.009_bib52","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.tim.2012.11.003","article-title":"Phage\u2013bacteria infection networks","volume":"21","author":"Weitz","year":"2013","journal-title":"Trends Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib53","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1003568","article-title":"Horizontally Acquired Glycosyltransferase Operons Drive Salmonellae Lipopolysaccharide Diversity","volume":"9","author":"Davies","year":"2013","journal-title":"PLoS Genet."},{"key":"10.1016\/j.chom.2026.09.009_bib54","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1005667","article-title":"Epigenetic Control of Salmonella enterica O-Antigen Chain Length: A Tradeoff between Virulence and Bacteriophage Resistance","volume":"11","author":"Cota","year":"2015","journal-title":"PLoS Genet."},{"key":"10.1016\/j.chom.2026.09.009_bib55","doi-asserted-by":"crossref","first-page":"3567","DOI":"10.1128\/JB.185.12.3567-3574.2003","article-title":"Flagellar Phase Variation in Salmonella enterica Is Mediated by a Posttranscriptional Control Mechanism","volume":"185","author":"Bonifield","year":"2003","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2026.09.009_bib56","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1002\/path.1700250411","article-title":"Studies in group-agglutination I. The salmonella group and its antigenic structure","volume":"25","author":"Andrewes","year":"1922","journal-title":"J. Pathol."},{"key":"10.1016\/j.chom.2026.09.009_bib57","doi-asserted-by":"crossref","DOI":"10.1111\/cmi.12739","article-title":"Flagellin phase-dependent swimming on epithelial cell surfaces contributes to productive Salmonella gut colonisation","volume":"19","author":"Horstmann","year":"2017","journal-title":"Cell. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib58","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-15738-3","article-title":"Methylation of Salmonella Typhimurium flagella promotes bacterial adhesion and host cell invasion","volume":"11","author":"Horstmann","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2026.09.009_bib59","doi-asserted-by":"crossref","first-page":"3021","DOI":"10.1128\/IAI.69.5.3021-3030.2001","article-title":"Flagellar Phase Variation of Salmonella enterica Serovar Typhimurium Contributes to Virulence in the Murine Typhoid Infection Model but Does Not Influence Salmonella-Induced Enteropathogenesis","volume":"69","author":"Ikeda","year":"2001","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2026.09.009_bib60","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1128\/iai.58.1.137-143.1990","article-title":"Salmonella typhimurium mutants lacking flagella or motility remain virulent in BALB\/c mice","volume":"58","author":"Lockman","year":"1990","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2026.09.009_bib61","doi-asserted-by":"crossref","first-page":"10232","DOI":"10.1073\/pnas.1705437114","article-title":"A trans-acting leader RNA from a Salmonella virulence gene","volume":"114","author":"Choi","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2026.09.009_bib62","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1128\/jb.173.7.2301-2310.1991","article-title":"Negative regulatory loci coupling flagellin synthesis to flagellar assembly in Salmonella typhimurium","volume":"173","author":"Gillen","year":"1991","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2026.09.009_bib63","doi-asserted-by":"crossref","first-page":"65","DOI":"10.3389\/fgene.2019.00065","article-title":"Bacterial \u2018Grounded\u2019 Prophages: Hotspots for Genetic Renovation and Innovation","volume":"10","author":"Ramisetty","year":"2019","journal-title":"Front. Genet."},{"key":"10.1016\/j.chom.2026.09.009_bib64","doi-asserted-by":"crossref","first-page":"6857","DOI":"10.1128\/JB.00769-08","article-title":"A Singular Case of Prophage Complementation in Mutational Activation of recET Orthologs in Salmonella enterica Serovar Typhimurium","volume":"190","author":"Lemire","year":"2008","journal-title":"J. Bacteriol."},{"key":"10.1016\/j.chom.2026.09.009_bib65","doi-asserted-by":"crossref","first-page":"235","DOI":"10.3389\/fmicb.2017.00235","article-title":"Characterization of the Prophage Repertoire of African Salmonella Typhimurium ST313 Reveals High Levels of Spontaneous Induction of Novel Phage BTP1","volume":"8","author":"Owen","year":"2017","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib66","doi-asserted-by":"crossref","first-page":"3652","DOI":"10.1073\/pnas.74.9.3652","article-title":"DNA packaging and the pathway of bacteriophage T4 head assembly","volume":"74","author":"Hsiao","year":"1977","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2026.09.009_bib67","doi-asserted-by":"crossref","first-page":"8719","DOI":"10.1093\/nar\/gkac647","article-title":"Structural basis of DNA packaging by a ring-type ATPase from an archetypal viral system","volume":"50","author":"Fung","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2026.09.009_bib68","doi-asserted-by":"crossref","first-page":"10431","DOI":"10.1093\/nar\/gkae675","article-title":"A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread","volume":"52","author":"Boyd","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2026.09.009_bib69","doi-asserted-by":"crossref","first-page":"3285","DOI":"10.1016\/j.jmb.2015.08.013","article-title":"Architecture of the Complex Formed by Large and Small Terminase Subunits from Bacteriophage P22","volume":"427","author":"McNulty","year":"2015","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.chom.2026.09.009_bib92","doi-asserted-by":"crossref","unstructured":"Rodrigues, C.H.M., Myung, Y., Pires, D.E. V, and Ascher, D.B. (2019). mCSM-PPI2: predicting the effects of mutations on protein\u2013protein interactions. Nucleic Acids Res. 47, W338\u2013W344. https:\/\/doi.org\/10.1093\/nar\/gkz383.","DOI":"10.1093\/nar\/gkz383"},{"key":"10.1016\/j.chom.2026.09.009_bib70","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1073\/pnas.1110224109","article-title":"Structure and function of the small terminase component of the DNA packaging machine in T4-like bacteriophages","volume":"109","author":"Sun","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2026.09.009_bib71","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1016\/j.chom.2013.11.010","article-title":"An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium","volume":"14","author":"Kr\u00f6ger","year":"2013","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2026.09.009_bib72","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1038\/s42003-025-07687-8","article-title":"Capsule mutations serve as a key strategy of phage resistance evolution of K54 hypervirulent Klebsiella pneumoniae","volume":"8","author":"Fu","year":"2025","journal-title":"Commun. Biol."},{"key":"10.1016\/j.chom.2026.09.009_bib73","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1111\/j.1365-2958.2012.08202.x","article-title":"Spontaneous and transient defence against bacteriophage by phase-variable glucosylation of O-antigen in Salmonella enterica serovar Typhimurium","volume":"86","author":"Kim","year":"2012","journal-title":"Mol. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib74","doi-asserted-by":"crossref","first-page":"1049","DOI":"10.1038\/s41586-025-09260-z","article-title":"Prophages block cell surface receptors to preserve their viral progeny","volume":"644","author":"Taylor","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.chom.2026.09.009_bib75","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2507909122","article-title":"The intestinal environment potentiates bacteriophage adaptation in response to phenotypic resistance in Salmonella Typhimurium","volume":"122","author":"Wenner","year":"2025","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2026.09.009_bib77","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-025-58540-9","article-title":"A toxin-antitoxin system provides phage defense via DNA damage and repair","volume":"16","author":"Pu","year":"2025","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2026.09.009_bib78","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.1016\/j.molcel.2021.03.027","article-title":"Shutoff of host transcription triggers a toxin-antitoxin system to cleave phage RNA and abort infection","volume":"81","author":"Guegler","year":"2021","journal-title":"Mol. Cell"},{"key":"10.1016\/j.chom.2026.09.009_bib79","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2022.111752","article-title":"Bacterial MazF\/MazE toxin-antitoxin suppresses lytic propagation of arbitrium-containing phages","volume":"41","author":"Cui","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.chom.2026.09.009_bib80","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1016\/j.virol.2006.04.001","article-title":"Induction of the SOS response by bacteriophage lytic development in Salmonella enterica","volume":"351","author":"Campoy","year":"2006","journal-title":"Virology"},{"key":"10.1016\/j.chom.2026.09.009_bib81","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/s41586-023-06855-2","article-title":"Structural basis of Gabija anti-phage defence and viral immune evasion","volume":"625","author":"Antine","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.chom.2026.09.009_bib82","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-026-76315-8","article-title":"Phage terminase recognition by the bacterial immune sensors Avs2 and Upx","author":"Evans","year":"2026","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2026.09.009_bib83","doi-asserted-by":"crossref","first-page":"5397","DOI":"10.1093\/nar\/gkaa290","article-title":"Phage T7 DNA mimic protein Ocr is a potent inhibitor of BREX defence","volume":"48","author":"Isaev","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2026.09.009_bib84","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-025-56887-7","article-title":"Phages carry orphan antitoxin-like enzymes to neutralize the DarTG1 toxin-antitoxin defense system","volume":"16","author":"Johannesman","year":"2025","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2026.09.009_bib85","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.0020011","article-title":"Genome-Wide Screen for Salmonella Genes Required for Long-Term Systemic Infection of the Mouse","volume":"2","author":"Lawley","year":"2006","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.chom.2026.09.009_bib86","doi-asserted-by":"crossref","first-page":"e00306-15","DOI":"10.1128\/mBio.00306-15","article-title":"Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons","volume":"6","author":"Wetmore","year":"2015","journal-title":"mBio"},{"key":"10.1016\/j.chom.2026.09.009_bib87","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1186\/s12866-020-01819-2","article-title":"Efficient dual-negative selection for bacterial genome editing","volume":"20","author":"Cianfanelli","year":"2020","journal-title":"BMC Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib88","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1007077","article-title":"A bacterial toxin-antitoxin module is the origin of inter-bacterial and inter-kingdom effectors of Bartonella","volume":"13","author":"Harms","year":"2017","journal-title":"PLoS Genet."},{"key":"10.1016\/j.chom.2026.09.009_bib89","doi-asserted-by":"crossref","first-page":"2702","DOI":"10.1111\/j.1462-2920.2011.02538.x","article-title":"Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440","volume":"13","author":"Mart\u00ednez-Garc\u00eda","year":"2011","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.chom.2026.09.009_bib90","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1016\/j.cell.2008.11.015","article-title":"The Structure of the Phage T4 DNA Packaging Motor Suggests a Mechanism Dependent on Electrostatic Forces","volume":"135","author":"Sun","year":"2008","journal-title":"Cell"},{"key":"10.1016\/j.chom.2026.09.009_bib91","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1128\/IAI.74.1.461-468.2006","article-title":"Effect of Inactivation of the Global Oxidative Stress Regulator oxyR on the Colonization Ability of Escherichia coli O1:K1:H7 in a Mouse Model of Ascending Urinary Tract Infection","volume":"74","author":"Johnson","year":"2006","journal-title":"Infect. Immun."}],"container-title":["Cell Host &amp; Microbe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312826003987?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312826003987?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T20:37:20Z","timestamp":1791578240000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1931312826003987"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10]]},"references-count":91,"alternative-id":["S1931312826003987"],"URL":"https:\/\/doi.org\/10.1016\/j.chom.2026.09.009","relation":{},"ISSN":["1931-3128"],"issn-type":[{"value":"1931-3128","type":"print"}],"subject":[],"published":{"date-parts":[[2026,10]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Native pathogen-phage networks reveal multilayered defense and gut-active anti-phage immunity","name":"articletitle","label":"Article Title"},{"value":"Cell Host & Microbe","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.chom.2026.09.009","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}