{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T20:02:22Z","timestamp":1789761742299,"version":"4.0.1"},"reference-count":120,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2023,7,1]],"date-time":"2023-07-01T00:00:00Z","timestamp":1688169600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2023,7,1]],"date-time":"2023-07-01T00:00:00Z","timestamp":1688169600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,7,1]],"date-time":"2023-07-01T00:00:00Z","timestamp":1688169600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2023,7,1]],"date-time":"2023-07-01T00:00:00Z","timestamp":1688169600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2023,7,1]],"date-time":"2023-07-01T00:00:00Z","timestamp":1688169600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2023,7,1]],"date-time":"2023-07-01T00:00:00Z","timestamp":1688169600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2023,7,1]],"date-time":"2023-07-01T00:00:00Z","timestamp":1688169600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Biotechnology Advances"],"published-print":{"date-parts":[[2023,7]]},"DOI":"10.1016\/j.biotechadv.2023.108152","type":"journal-article","created":{"date-parts":[[2023,4,8]],"date-time":"2023-04-08T10:56:21Z","timestamp":1680951381000},"page":"108152","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":35,"special_numbering":"C","title":["Recent advances in phage defense systems and potential overcoming strategies"],"prefix":"10.1016","volume":"65","author":[{"given":"Xiaoming","family":"Yuan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhichao","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenjun","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jumei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingping","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Xue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Ding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.biotechadv.2023.108152_bb0005","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.784949","article-title":"Genomic analysis of molecular bacterial mechanisms of resistance to phage infection","volume":"12","author":"Ambroa","year":"2022","journal-title":"Front. Microbiol."},{"issue":"15","key":"10.1016\/j.biotechadv.2023.108152_bb0015","doi-asserted-by":"crossref","first-page":"2894","DOI":"10.1016\/j.jmb.2019.04.041","article-title":"A type III CRISPR ancillary ribonuclease degrades its cyclic oligoadenylate activator","volume":"431","author":"Athukoralage","year":"2019","journal-title":"J. Mol. Biol."},{"issue":"7791","key":"10.1016\/j.biotechadv.2023.108152_bb0020","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1038\/s41586-019-1909-5","article-title":"An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity","volume":"577","author":"Athukoralage","year":"2020","journal-title":"Nature"},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0025","doi-asserted-by":"crossref","first-page":"1939","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."},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0030","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1080\/22221751.2020.1747950","article-title":"Non-active antibiotic and bacteriophage synergism to successfully treat recurrent urinary tract infection caused by extensively drug-resistant Klebsiella pneumoniae","volume":"9","author":"Bao","year":"2020","journal-title":"Emerg. Microbes Infect."},{"issue":"2","key":"10.1016\/j.biotechadv.2023.108152_bb0035","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/s41579-019-0278-2","article-title":"The pan-immune system of bacteria: antiviral defence as a community resource","volume":"18","author":"Bernheim","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"issue":"7840","key":"10.1016\/j.biotechadv.2023.108152_bb0040","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/s41586-020-2762-2","article-title":"Prokaryotic viperins produce diverse antiviral molecules","volume":"589","author":"Bernheim","year":"2021","journal-title":"Nature"},{"issue":"4","key":"10.1016\/j.biotechadv.2023.108152_bb0045","doi-asserted-by":"crossref","first-page":"fnw002","DOI":"10.1093\/femsle\/fnw002","article-title":"Host receptors for bacteriophage adsorption","volume":"363","author":"Bertozzi Silva","year":"2016","journal-title":"FEMS Microbiol. Lett."},{"issue":"2","key":"10.1016\/j.biotechadv.2023.108152_bb0050","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1002\/jcp.25973","article-title":"BacteRiophage EXclusion (BREX): A novel anti-phage mechanism in the arsenal of bacterial defense system","volume":"233","author":"Bhushan","year":"2018","journal-title":"J. Cell. Physiol."},{"issue":"6","key":"10.1016\/j.biotechadv.2023.108152_bb0055","doi-asserted-by":"crossref","first-page":"3348","DOI":"10.1093\/nar\/gkac147","article-title":"A mobile restriction-modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease","volume":"50","author":"Birkholz","year":"2022","journal-title":"Nucleic Acids Res."},{"issue":"7925","key":"10.1016\/j.biotechadv.2023.108152_bb0060","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1038\/s41586-022-05091-4","article-title":"Bacterial retrons encode phage-defending tripartite toxin-antitoxin systems","volume":"609","author":"Bobonis","year":"2022","journal-title":"Nature"},{"issue":"7432","key":"10.1016\/j.biotechadv.2023.108152_bb0065","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1038\/nature11723","article-title":"Bacteriophage genes that inactivate the CRISPR\/Cas bacterial immune system","volume":"493","author":"Bondy-Denomy","year":"2013","journal-title":"Nature"},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0070","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1038\/s41467-022-30673-1","article-title":"Structural basis for broad anti-phage immunity by DISARM","volume":"13","author":"Bravo","year":"2022","journal-title":"Nat. Commun."},{"issue":"7780","key":"10.1016\/j.biotechadv.2023.108152_bb0075","doi-asserted-by":"crossref","first-page":"691","DOI":"10.1038\/s41586-019-1605-5","article-title":"Cyclic GMP-AMP signalling protects bacteria against viral infection","volume":"574","author":"Cohen","year":"2019","journal-title":"Nature"},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0080","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1186\/s12864-019-6137-8","article-title":"Horizontal gene transfer contributes to virulence and antibiotic resistance of Vibrio harveyi 345 based on complete genome sequence analysis","volume":"20","author":"Deng","year":"2019","journal-title":"BMC Genomics"},{"issue":"3","key":"10.1016\/j.biotechadv.2023.108152_bb0085","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."},{"issue":"D1","key":"10.1016\/j.biotechadv.2023.108152_bb0090","doi-asserted-by":"crossref","first-page":"D393","DOI":"10.1093\/nar\/gkx835","article-title":"Anti-CRISPRdb: a comprehensive online resource for anti-CRISPR proteins","volume":"46","author":"Dong","year":"2018","journal-title":"Nucleic Acids Res."},{"issue":"20","key":"10.1016\/j.biotechadv.2023.108152_bb0095","doi-asserted-by":"crossref","first-page":"eaba1590","DOI":"10.1126\/sciadv.aba1590","article-title":"Bioinorganic hybrid bacteriophage for modulation of intestinal microbiota to remodel tumor-immune microenvironment against colorectal cancer","volume":"6","author":"Dong","year":"2020","journal-title":"Sci. Adv."},{"issue":"6379","key":"10.1016\/j.biotechadv.2023.108152_bb0100","doi-asserted-by":"crossref","first-page":"eaar4120","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"},{"issue":"2","key":"10.1016\/j.biotechadv.2023.108152_bb0105","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1093\/femsre\/fuv048","article-title":"Computational approaches to predict bacteriophage-host relationships","volume":"40","author":"Edwards","year":"2016","journal-title":"FEMS Microbiol. Rev."},{"issue":"9","key":"10.1016\/j.biotechadv.2023.108152_bb0110","doi-asserted-by":"crossref","first-page":"4698","DOI":"10.1093\/nar\/gkaa219","article-title":"Machine learning predicts new anti-CRISPR proteins","volume":"48","author":"Eitzinger","year":"2020","journal-title":"Nucleic Acids Res."},{"issue":"9","key":"10.1016\/j.biotechadv.2023.108152_bb0115","doi-asserted-by":"crossref","first-page":"1434","DOI":"10.1016\/j.chembiol.2022.06.003","article-title":"Cell-free production of personalized therapeutic phages targeting multidrug-resistant bacteria","volume":"29","author":"Emslander","year":"2022","journal-title":"Cell Chem. Biol"},{"key":"10.1016\/j.biotechadv.2023.108152_bb0120","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/j.mib.2020.06.002","article-title":"Beyond the CRISPR-Cas safeguard: PICI-encoded innate immune systems protect bacteria from bacteriophage predation","volume":"56","author":"Fillol-Salom","year":"2020","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.biotechadv.2023.108152_bb0125","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.copbio.2020.10.003","article-title":"Looking into the future of phage-based control of zoonotic pathogens in food and animal production","volume":"68","author":"Gambino","year":"2021","journal-title":"Curr. Opin. Biotechnol."},{"issue":"11","key":"10.1016\/j.biotechadv.2023.108152_bb0130","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1038\/s41564-022-01207-8","article-title":"Multiple phage resistance systems inhibit infection via SIR2-dependent NAD+ depletion","volume":"7","author":"Garb","year":"2022","journal-title":"Nat. Microbiol."},{"issue":"7711","key":"10.1016\/j.biotechadv.2023.108152_bb0135","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1038\/s41586-018-0238-4","article-title":"A naturally occurring antiviral ribonucleotide encoded by the human genome","volume":"558","author":"Gizzi","year":"2018","journal-title":"Nature"},{"issue":"2","key":"10.1016\/j.biotechadv.2023.108152_bb0140","doi-asserted-by":"crossref","first-page":"169","DOI":"10.15252\/embj.201489455","article-title":"BREX is a novel phage resistance system widespread in microbial genomes","volume":"34","author":"Goldfarb","year":"2015","journal-title":"EMBO J."},{"issue":"11","key":"10.1016\/j.biotechadv.2023.108152_bb0145","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"},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0150","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.03753-21","article-title":"A bacterial dynamin-like protein confers a novel phage resistance strategy on the population level in Bacillus subtilis","volume":"13","author":"Guo","year":"2022","journal-title":"mBio"},{"key":"10.1016\/j.biotechadv.2023.108152_bb0155","series-title":"Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach. BioRxiv","author":"Gussow","year":"2020"},{"issue":"6","key":"10.1016\/j.biotechadv.2023.108152_bb0160","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1111\/mmi.14231","article-title":"A mutant bacteriophage evolved to infect resistant bacteria gained a broader host range","volume":"111","author":"Habusha","year":"2019","journal-title":"Mo. Microbiol."},{"issue":"7790","key":"10.1016\/j.biotechadv.2023.108152_bb0165","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/s41586-019-1894-8","article-title":"The arms race between bacteria and their phage foes","volume":"577","author":"Hampton","year":"2020","journal-title":"Nature"},{"issue":"5","key":"10.1016\/j.biotechadv.2023.108152_bb0170","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1016\/j.molcel.2018.01.003","article-title":"Toxins, targets, and triggers: an overview of toxin-antitoxin biology","volume":"70","author":"Harms","year":"2018","journal-title":"Mol. Cell"},{"issue":"8","key":"10.1016\/j.biotechadv.2023.108152_bb0175","doi-asserted-by":"crossref","first-page":"3959","DOI":"10.1021\/jacs.9b12936","article-title":"Phage-guided targeting, discriminative imaging, and synergistic killing of bacteria by AIE bioconjugates","volume":"142","author":"He","year":"2020","journal-title":"J. Am. Chem. Soc."},{"issue":"7910","key":"10.1016\/j.biotechadv.2023.108152_bb0180","doi-asserted-by":"crossref","first-page":"522","DOI":"10.1038\/s41586-022-04716-y","article-title":"Phage anti-CBASS and anti-Pycsar nucleases subvert bacterial immunity","volume":"605","author":"Hobbs","year":"2022","journal-title":"Nature"},{"issue":"D1","key":"10.1016\/j.biotechadv.2023.108152_bb0185","doi-asserted-by":"crossref","first-page":"D622","DOI":"10.1093\/nar\/gkaa857","article-title":"AcrDB: a database of anti-CRISPR operons in prokaryotes and viruses","volume":"49","author":"Huang","year":"2021","journal-title":"Nucleic Acids Res."},{"issue":"6566","key":"10.1016\/j.biotechadv.2023.108152_bb0190","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1126\/science.abb1083","article-title":"Rapid evolutionary turnover of mobile genetic elements drives bacterial resistance to phages","volume":"374","author":"Hussain","year":"2021","journal-title":"Science"},{"issue":"10","key":"10.1016\/j.biotechadv.2023.108152_bb0195","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."},{"issue":"3","key":"10.1016\/j.biotechadv.2023.108152_bb0200","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1134\/S0006297921030081","article-title":"Microbial qrsenal of qntiviral eefenses - part I Biochemistry (Mosc)","volume":"86","author":"Isaev","year":"2021","journal-title":"Biokhimiia"},{"issue":"9","key":"10.1016\/j.biotechadv.2023.108152_bb0205","doi-asserted-by":"crossref","first-page":"1809","DOI":"10.3390\/v13091809","article-title":"Phage therapy for multi-drug resistant respiratory tract infections","volume":"13","author":"Iszatt","year":"2021","journal-title":"Viruses"},{"issue":"3","key":"10.1016\/j.biotechadv.2023.108152_bb0210","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1111\/jam.14851","article-title":"Bacteriophages as antibiotic resistance genes carriers in agro-food systems","volume":"130","author":"Jebri","year":"2021","journal-title":"J. Appl. Microbiol."},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0215","doi-asserted-by":"crossref","first-page":"6382","DOI":"10.1038\/s41467-021-26636-7","article-title":"The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes","volume":"12","author":"Jian","year":"2021","journal-title":"Nat. Commun."},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0220","doi-asserted-by":"crossref","first-page":"2816","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."},{"issue":"17","key":"10.1016\/j.biotechadv.2023.108152_bb0225","doi-asserted-by":"crossref","first-page":"6240","DOI":"10.3390\/ijms21176240","article-title":"CRISPR-Cas9 DNA base-editing and prime-editing","volume":"21","author":"Kantor","year":"2020","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.biotechadv.2023.108152_bb0230","series-title":"StatPearls [Internet]","article-title":"Bacteriophages","author":"Kasman","year":"2021"},{"issue":"6351","key":"10.1016\/j.biotechadv.2023.108152_bb0235","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1126\/science.aao0100","article-title":"A cyclic oligonucleotide signaling pathway in type III CRISPR-Cas systems","volume":"357","author":"Kazlauskiene","year":"2017","journal-title":"Science"},{"issue":"3","key":"10.1016\/j.biotechadv.2023.108152_bb0240","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1073\/pnas.1714658115","article-title":"Cross-genus rebooting of custom-made, synthetic bacteriophage genomes in L-form bacteria","volume":"115","author":"Kilcher","year":"2018","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"2","key":"10.1016\/j.biotechadv.2023.108152_bb0245","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.chom.2019.01.014","article-title":"Phage therapy: A renewed approach to combat antibiotic-resistant bacteria","volume":"25","author":"Kortright","year":"2019","journal-title":"Cell Host Microbe"},{"issue":"7735","key":"10.1016\/j.biotechadv.2023.108152_bb0250","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1038\/s41586-018-0767-x","article-title":"A chemical defence against phage infection","volume":"564","author":"Kronheim","year":"2018","journal-title":"Nature"},{"issue":"7835","key":"10.1016\/j.biotechadv.2023.108152_bb0255","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1038\/s41586-020-2605-1","article-title":"DNA targeting and interference by a bacterial Argonaute nuclease","volume":"587","author":"Kuzmenko","year":"2020","journal-title":"Nature"},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0260","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1038\/s41467-017-00158-7","article-title":"Long-term genomic coevolution of host-parasite interaction in the natural environment","volume":"8","author":"Laanto","year":"2017","journal-title":"Nat. Commun."},{"issue":"6","key":"10.1016\/j.biotechadv.2023.108152_bb0265","doi-asserted-by":"crossref","first-page":"291","DOI":"10.3390\/antibiotics9060291","article-title":"Adapting a phage to combat phage resistance","volume":"9","author":"Laanto","year":"2020","journal-title":"Antibiotics (Basel)"},{"key":"10.1016\/j.biotechadv.2023.108152_bb0270","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.envint.2018.03.019","article-title":"Phage particles harboring antibiotic resistance genes in fresh-cut vegetables and agricultural soil","volume":"115","author":"Larra\u00f1aga","year":"2018","journal-title":"Environ. Int."},{"issue":"4","key":"10.1016\/j.biotechadv.2023.108152_bb0275","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/j.molcel.2019.12.010","article-title":"Structure and mechanism of a cyclic trinucleotide-activatedbacterial endonuclease mediating bacteriophage immunity","volume":"77","author":"Lau","year":"2020","journal-title":"Mol. Cell"},{"issue":"7","key":"10.1016\/j.biotechadv.2023.108152_bb0280","doi-asserted-by":"crossref","first-page":"415","DOI":"10.3390\/antibiotics9070415","article-title":"Application of bacteriophages to control Vibrio alginolyticus contamination in oyster (Saccostrea glomerata) larvae","volume":"9","author":"Le","year":"2020","journal-title":"Antibiotics (Basel)"},{"issue":"7935","key":"10.1016\/j.biotechadv.2023.108152_bb0285","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1038\/s41586-022-05375-9","article-title":"Viruses inhibit TIR gcADPR signalling to overcome bacterial defence","volume":"611","author":"Leavitt","year":"2022","journal-title":"Nature"},{"issue":"6554","key":"10.1016\/j.biotechadv.2023.108152_bb0290","doi-asserted-by":"crossref","first-page":"eabg2166","DOI":"10.1126\/science.abg2166","article-title":"Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts","volume":"373","author":"LeGault","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.biotechadv.2023.108152_bb0295","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/978-1-4614-0980-9_5","article-title":"Contractile tail machines of bacteriophages","volume":"726","author":"Leiman","year":"2012","journal-title":"Adv. Exp. Med. Biol."},{"key":"10.1016\/j.biotechadv.2023.108152_bb0300","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.copbio.2020.11.003","article-title":"Enhancing phage therapy through synthetic biology and genome engineering","volume":"68","author":"Lenneman","year":"2021","journal-title":"Curr. Opin. Biotechnol."},{"key":"10.1016\/j.biotechadv.2023.108152_bb0305","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijfoodmicro.2022.109615","article-title":"A novel Bacillus cereus bacteriophage DLn1 and its endolysin as biocontrol agents against Bacillus cereus in milk","volume":"369","author":"Li","year":"2022","journal-title":"Int. J. Food Microbiol."},{"key":"10.1016\/j.biotechadv.2023.108152_bb0310","doi-asserted-by":"crossref","first-page":"218","DOI":"10.3389\/fmicb.2020.00218","article-title":"Identification of two depolymerases from phage IME205 and their antivirulent functions on K47 capsule of Klebsiella pneumoniae","volume":"11","author":"Liu","year":"2020","journal-title":"Front. Microbiol."},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0315","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1146\/annurev-virology-011620-040628","article-title":"Abortive infection: bacterial suicide as an antiviral immune strategy","volume":"7","author":"Lopatina","year":"2020","journal-title":"Ann. Re. virol."},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0320","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.cell.2020.05.019","article-title":"CBASS immunity uses CARF-related effectors to sense 3\u2032-5\u2032- and 2\u2032-5\u2032-linked cyclic oligonucleotide signals and protect bacteria from phage infection","volume":"182","author":"Lowey","year":"2020","journal-title":"Cell"},{"issue":"23","key":"10.1016\/j.biotechadv.2023.108152_bb0325","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2026354118","article-title":"A phage mechanism for selective nicking of dUMP-containing DNA","volume":"118","author":"Mahata","year":"2021","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"12","key":"10.1016\/j.biotechadv.2023.108152_bb0330","doi-asserted-by":"crossref","first-page":"7723","DOI":"10.1111\/1462-2920.15476","article-title":"The evolutionary trade-offs in phage-resistant Klebsiella pneumoniae entail cross-phage sensitization and loss of multidrug resistance","volume":"23","author":"Majkowska-Skrobek","year":"2021","journal-title":"Environ. Microbiol."},{"issue":"10","key":"10.1016\/j.biotechadv.2023.108152_bb0335","doi-asserted-by":"crossref","first-page":"1310","DOI":"10.3390\/pathogens10101310","article-title":"Bacterial antibiotic resistance: the most critical pathogens","volume":"10","author":"Mancuso","year":"2021","journal-title":"Pathogens"},{"issue":"2","key":"10.1016\/j.biotechadv.2023.108152_bb0340","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/s41396-021-01096-5","article-title":"Genome-driven elucidation of phage-host interplay and impact of phage resistance evolution on bacterial fitness","volume":"16","author":"Markwitz","year":"2022","journal-title":"ISME J."},{"issue":"4","key":"10.1016\/j.biotechadv.2023.108152_bb0345","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1089\/crispr.2020.29100.kma","article-title":"Retrons: complementing CRISPR in phage defense","volume":"3","author":"Maxwell","year":"2020","journal-title":"CRISPR J."},{"key":"10.1016\/j.biotechadv.2023.108152_bb0350","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/j.mib.2020.02.002","article-title":"Horizontal transfer of antibiotic resistance genes in the human gut microbiome","volume":"53","author":"McInnes","year":"2020","journal-title":"Curr. Opin. Microbiol."},{"issue":"4","key":"10.1016\/j.biotechadv.2023.108152_bb0355","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1016\/j.chom.2019.09.006","article-title":"Viral satellites exploit phage proteins to escape degradation of the bacterial host chromosome","volume":"26","author":"McKitterick","year":"2019","journal-title":"Cell Host Microbe"},{"issue":"7760","key":"10.1016\/j.biotechadv.2023.108152_bb0360","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/s41586-019-1257-5","article-title":"Cas13-induced cellular dormancy prevents the rise of CRISPR-resistant bacteriophage","volume":"570","author":"Meeske","year":"2019","journal-title":"Nature"},{"issue":"6499","key":"10.1016\/j.biotechadv.2023.108152_bb0365","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1126\/science.abb6151","article-title":"A phage-encoded anti-CRISPR enables complete evasion of type VI-A CRISPR-Cas immunity","volume":"369","author":"Meeske","year":"2020","journal-title":"Science"},{"issue":"6","key":"10.1016\/j.biotechadv.2023.108152_bb0370","doi-asserted-by":"crossref","first-page":"1551","DOI":"10.1016\/j.cell.2020.09.065","article-title":"Bacterial retrons function in anti-phage defense","volume":"183","author":"Millman","year":"2020","journal-title":"Cell"},{"issue":"12","key":"10.1016\/j.biotechadv.2023.108152_bb0375","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1038\/s41564-020-0777-y","article-title":"Diversity and classification of cyclic-oligonucleotide-based anti-phage signalling systems","volume":"5","author":"Millman","year":"2020","journal-title":"Nat. Microbiol."},{"issue":"11","key":"10.1016\/j.biotechadv.2023.108152_bb0380","doi-asserted-by":"crossref","first-page":"1556","DOI":"10.1016\/j.chom.2022.09.017","article-title":"An expanded arsenal of immune systems that protect bacteria from phages","volume":"30","author":"Millman","year":"2022","journal-title":"Cell Host Microbe"},{"issue":"4","key":"10.1016\/j.biotechadv.2023.108152_bb0385","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1016\/j.tim.2018.10.008","article-title":"Phage therapy: going temperate?","volume":"27","author":"Monteiro","year":"2019","journal-title":"Trends Microbiol."},{"issue":"10","key":"10.1016\/j.biotechadv.2023.108152_bb0390","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3000877","article-title":"High-throughput mapping of the phage resistance landscape in E. coli","volume":"18","author":"Mutalik","year":"2020","journal-title":"PLoS Biol."},{"issue":"11","key":"10.1016\/j.biotechadv.2023.108152_bb0395","doi-asserted-by":"crossref","first-page":"1860","DOI":"10.1016\/j.cell.2022.04.024","article-title":"Host and pathogen response to bacteriophage engineered against Mycobacterium abscessus lung infection","volume":"185","author":"Nick","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.biotechadv.2023.108152_bb0400","article-title":"Phylogenetic analysis of anti-CRISPR and member addition in the families","author":"Nidhi","year":"2022","journal-title":"Mol. Biotechnol."},{"issue":"7669","key":"10.1016\/j.biotechadv.2023.108152_bb0405","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/nature23467","article-title":"Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers","volume":"548","author":"Niewoehner","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.biotechadv.2023.108152_bb0410","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."},{"issue":"7","key":"10.1016\/j.biotechadv.2023.108152_bb0415","doi-asserted-by":"crossref","first-page":"351","DOI":"10.3390\/v10070351","article-title":"Resistance development to bacteriophages occurring during bacteriophage therapy","volume":"10","author":"Oechslin","year":"2018","journal-title":"Viruses"},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0420","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/s41564-017-0051-0","article-title":"DISARM is a widespread bacterial defence system with broad anti-phage activities","volume":"3","author":"Ofir","year":"2018","journal-title":"Nat. Microbiol."},{"issue":"11","key":"10.1016\/j.biotechadv.2023.108152_bb0425","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.biotechadv.2023.108152_bb0430","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.copbio.2020.09.009","article-title":"Phage engineering and the evolutionary arms race","volume":"68","author":"Peng","year":"2021","journal-title":"Curr. Opin. Biotechnol."},{"issue":"4","key":"10.1016\/j.biotechadv.2023.108152_bb0435","doi-asserted-by":"crossref","first-page":"1951","DOI":"10.1073\/pnas.1913234117","article-title":"Controlled phage therapy by photothermal ablation of specific bacterial species using gold nanorods targeted by chimeric phages","volume":"117","author":"Peng","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"issue":"22","key":"10.1016\/j.biotechadv.2023.108152_bb0440","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.02138-20","article-title":"Mutant and recombinant ohages selected from in vitro coevolution conditions overcome phage-resistant Listeria monocytogenes","volume":"86","author":"Peters","year":"2020","journal-title":"Appl. Environ. Microbiol."},{"issue":"19","key":"10.1016\/j.biotechadv.2023.108152_bb0445","doi-asserted-by":"crossref","first-page":"11257","DOI":"10.1093\/nar\/gkab906","article-title":"The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses","volume":"49","author":"Picton","year":"2021","journal-title":"Nucleic Acids Res."},{"issue":"7","key":"10.1016\/j.biotechadv.2023.108152_bb0450","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1038\/s41564-022-01157-1","article-title":"Phage-host coevolution in natural populations","volume":"7","author":"Piel","year":"2022","journal-title":"Nat. Microbiol."},{"issue":"12","key":"10.1016\/j.biotechadv.2023.108152_bb0455","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1007\/s12033-021-00372-1","article-title":"Identification of a novel cleavage site and confirmation of the effectiveness of NgAgo gene editing on RNA targets","volume":"63","author":"Qu","year":"2021","journal-title":"Mol. Biotechnol."},{"key":"10.1016\/j.biotechadv.2023.108152_bb0460","series-title":"Prophage-encoded hotspots of bacterial immune systems. bioRxiv","author":"Rousset","year":"2021"},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0465","doi-asserted-by":"crossref","first-page":"bbab385","DOI":"10.1093\/bib\/bbab385","article-title":"DeepHost: phage host prediction with convolutional neural network","volume":"23","author":"Ruohan","year":"2022","journal-title":"Brief. Bioinform."},{"issue":"6","key":"10.1016\/j.biotechadv.2023.108152_bb0470","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01935-18","article-title":"The expanded universe of prokaryotic Argonaute proteins","volume":"9","author":"Ryazansky","year":"2018","journal-title":"mBio"},{"key":"10.1016\/j.biotechadv.2023.108152_bb0475","article-title":"Development of phage cocktails to treat E. coli catheter-associated urinary tract infection and associated biofilms","volume":"13","author":"Sanchez","year":"2022","journal-title":"Front. Microbiol."},{"issue":"2","key":"10.1016\/j.biotechadv.2023.108152_bb0480","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00019-20","article-title":"In vivo targeting of Clostridioides difficile using phage-delivered CRISPR-Cas3 antimicrobials","volume":"11","author":"Selle","year":"2020","journal-title":"mBio"},{"issue":"3","key":"10.1016\/j.biotechadv.2023.108152_bb0485","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1007\/s12275-021-0674-y","article-title":"Prokaryotic DNA methylation and its functional roles","volume":"59","author":"Seong","year":"2021","journal-title":"J. Microbiol."},{"key":"10.1016\/j.biotechadv.2023.108152_bb0490","series-title":"A broadly conserved deoxycytidine deaminase protects bacteria from phage infection. bioRxiv","author":"Severin","year":"2021"},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0495","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1186\/s12915-021-01180-4","article-title":"Predicting the hosts of prokaryotic viruses using GCN-based semi-supervised learning","volume":"19","author":"Shang","year":"2021","journal-title":"BMC Biol."},{"key":"10.1016\/j.biotechadv.2023.108152_bb0500","doi-asserted-by":"crossref","first-page":"2783","DOI":"10.3389\/fmicb.2019.02783","article-title":"K5 capsule and lipopolysaccharide are important in resistance to T4 phage attack in probiotic E. coli strain Nissle 1917","volume":"10","author":"Soundararajan","year":"2019","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.biotechadv.2023.108152_bb0505","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.79549","article-title":"The evolution of a counter-defense mechanism in a virus constrains its host range","volume":"11","author":"Srikant","year":"2022","journal-title":"ELife"},{"issue":"9","key":"10.1016\/j.biotechadv.2023.108152_bb0510","doi-asserted-by":"crossref","first-page":"5445","DOI":"10.1007\/s00203-021-02522-0","article-title":"In vitro efficiency evaluation of phage cocktail for biocontrol of Salmonella spp. in food products","volume":"203","author":"Sritha","year":"2021","journal-title":"Arch. Microbiol."},{"issue":"23","key":"10.1016\/j.biotechadv.2023.108152_bb0515","doi-asserted-by":"crossref","first-page":"5728","DOI":"10.1016\/j.cell.2021.09.031","article-title":"Cyclic CMP and cyclic UMP mediate bacterial immunity against phages","volume":"184","author":"Tal","year":"2021","journal-title":"Cell"},{"issue":"8","key":"10.1016\/j.biotechadv.2023.108152_bb0520","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1038\/s41564-022-01158-0","article-title":"Bacteria deplete deoxynucleotides to defend against bacteriophage infection","volume":"7","author":"Tal","year":"2022","journal-title":"Nat. Microbiol."},{"issue":"3","key":"10.1016\/j.biotechadv.2023.108152_bb0525","doi-asserted-by":"crossref","DOI":"10.15252\/embj.2021109247","article-title":"Bacteria elicit a phage tolerance response subsequent to infection of their neighbors","volume":"41","author":"Tzipilevich","year":"2022","journal-title":"EMBO J."},{"issue":"10","key":"10.1016\/j.biotechadv.2023.108152_bb0530","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."},{"issue":"2","key":"10.1016\/j.biotechadv.2023.108152_bb0540","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1093\/femsre\/fuy036","article-title":"DNA phosphorothioate modification-a new multi-functional epigenetic system in bacteria","volume":"43","author":"Wang","year":"2019","journal-title":"FEMS Microbiol. Rev."},{"issue":"2","key":"10.1016\/j.biotechadv.2023.108152_bb0545","doi-asserted-by":"crossref","first-page":"e00613","DOI":"10.1128\/mBio.00613-21","article-title":"SspABCD-SspFGH constitutes a new type of DNA phosphorothioate-based bacterial defense system","volume":"12","author":"Wang","year":"2021","journal-title":"mBio"},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0550","doi-asserted-by":"crossref","first-page":"2205","DOI":"10.1080\/22221751.2021.2002671","article-title":"Colistin-phage combinations decrease antibiotic resistance in Acinetobacter baumannii via changes in envelope architecture","volume":"10","author":"Wang","year":"2021","journal-title":"Emerg. Microbes. Infect."},{"issue":"17","key":"10.1016\/j.biotechadv.2023.108152_bb0555","doi-asserted-by":"crossref","DOI":"10.1002\/advs.202105668","article-title":"Photocatalytic quantum dot-armed bacteriophage for combating drug-resistant bacterial infection","volume":"9","author":"Wang","year":"2022","journal-title":"Adv. Sci."},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0560","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1080\/22221751.2021.1902754","article-title":"Pre-optimized phage therapy on secondary Acinetobacter baumannii infection in four critical COVID-19 patients","volume":"10","author":"Wu","year":"2021","journal-title":"Emerg. Microbes Infect."},{"issue":"7","key":"10.1016\/j.biotechadv.2023.108152_bb0565","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1038\/s41564-020-0700-6","article-title":"SspABCD-SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities","volume":"5","author":"Xiong","year":"2020","journal-title":"Nat. Microbiol."},{"issue":"8","key":"10.1016\/j.biotechadv.2023.108152_bb0570","doi-asserted-by":"crossref","first-page":"3349","DOI":"10.1111\/1750-3841.15843","article-title":"Phage and phage lysins: new era of bio-preservatives and food safety agents","volume":"86","author":"Xu","year":"2021","journal-title":"J. Food Sci."},{"issue":"3","key":"10.1016\/j.biotechadv.2023.108152_bb0575","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/s43016-022-00470-6","article-title":"Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China","volume":"3","author":"Yang","year":"2022","journal-title":"Nat. Food"},{"issue":"2","key":"10.1016\/j.biotechadv.2023.108152_bb0580","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/j.cell.2019.09.015","article-title":"Engineering phage host-range and suppressing bacterial resistance through phage tail fiber mutagenesis","volume":"179","author":"Yehl","year":"2019","journal-title":"Cell"},{"issue":"11","key":"10.1016\/j.biotechadv.2023.108152_bb0585","doi-asserted-by":"crossref","first-page":"1857","DOI":"10.1038\/s41564-022-01239-0","article-title":"Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD+ depletion","volume":"7","author":"Zaremba","year":"2022","journal-title":"Nat. Microbiol."},{"issue":"9","key":"10.1016\/j.biotechadv.2023.108152_bb0590","doi-asserted-by":"crossref","first-page":"1904","DOI":"10.3390\/v14091904","article-title":"The life cycle transitions of temperate phages: regulating factors and potential ecological implications","volume":"14","author":"Zhang","year":"2022","journal-title":"Viruses"},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0595","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2022.111026","article-title":"Bacteriophage protein PEIP is a potent Bacillus subtilis enolase inhibitor","volume":"40","author":"Zhang","year":"2022","journal-title":"Cell Rep."},{"issue":"7938","key":"10.1016\/j.biotechadv.2023.108152_bb0600","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"},{"issue":"1","key":"10.1016\/j.biotechadv.2023.108152_bb0605","doi-asserted-by":"crossref","first-page":"1553","DOI":"10.1038\/s41467-022-29283-8","article-title":"Assessment of global health risk of antibiotic resistance genes","volume":"13","author":"Zhang","year":"2022","journal-title":"Nat. Commun."},{"issue":"6541","key":"10.1016\/j.biotechadv.2023.108152_bb0610","doi-asserted-by":"crossref","first-page":"512","DOI":"10.1126\/science.abe4882","article-title":"A widespread pathway for substitution of adenine by diaminopurine in phage genomes","volume":"372","author":"Zhou","year":"2021","journal-title":"Science"}],"container-title":["Biotechnology Advances"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0734975023000599?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0734975023000599?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T12:15:40Z","timestamp":1760012140000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0734975023000599"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7]]},"references-count":120,"alternative-id":["S0734975023000599"],"URL":"https:\/\/doi.org\/10.1016\/j.biotechadv.2023.108152","relation":{},"ISSN":["0734-9750"],"issn-type":[{"value":"0734-9750","type":"print"}],"subject":[],"published":{"date-parts":[[2023,7]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Recent advances in phage defense systems and potential overcoming strategies","name":"articletitle","label":"Article Title"},{"value":"Biotechnology Advances","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.biotechadv.2023.108152","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 Elsevier Inc. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"108152"}}