{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T02:03:11Z","timestamp":1791424991133,"version":"4.3.3"},"reference-count":70,"publisher":"Springer Science and Business Media LLC","issue":"7","license":[{"start":{"date-parts":[[2021,5,27]],"date-time":"2021-05-27T00:00:00Z","timestamp":1622073600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2021,5,27]],"date-time":"2021-05-27T00:00:00Z","timestamp":1622073600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Microbiol"],"DOI":"10.1038\/s41564-021-00911-1","type":"journal-article","created":{"date-parts":[[2021,5,27]],"date-time":"2021-05-27T13:21:09Z","timestamp":1622121669000},"page":"830-841","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants"],"prefix":"10.1038","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5914-8059","authenticated-orcid":false,"given":"M\u00e9d\u00e9ric","family":"Diard","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik","family":"Bakkeren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7440-4604","authenticated-orcid":false,"given":"Verena","family":"Lentsch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Rocker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nahimi Amare","family":"Bekele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1451-5166","authenticated-orcid":false,"given":"Daniel","family":"Hoces","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Selma","family":"Aslani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Arnoldini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Flurina","family":"B\u00f6hi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathrin","family":"Schumann-Moor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4545-3826","authenticated-orcid":false,"given":"Jozef","family":"Adamcik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Piccoli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3041-7240","authenticated-orcid":false,"given":"Antonio","family":"Lanzavecchia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beth M.","family":"Stadtmueller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0055-640X","authenticated-orcid":false,"given":"Nicholas","family":"Donohue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0446-8829","authenticated-orcid":false,"given":"Marjan W.","family":"van der Woude","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alyson","family":"Hockenberry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5249-9910","authenticated-orcid":false,"given":"Patrick H.","family":"Viollier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8102-7579","authenticated-orcid":false,"given":"Laurent","family":"Falquet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"W\u00fcthrich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ferdinando","family":"Bonfiglio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0888-1717","authenticated-orcid":false,"given":"Claude","family":"Loverdo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adrian","family":"Egli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9452-8751","authenticated-orcid":false,"given":"Giorgia","family":"Zandomeneghi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5739-2610","authenticated-orcid":false,"given":"Raffaele","family":"Mezzenga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Otto","family":"Holst","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9107-4464","authenticated-orcid":false,"given":"Beat H.","family":"Meier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9892-6420","authenticated-orcid":false,"given":"Wolf-Dietrich","family":"Hardt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2473-1145","authenticated-orcid":false,"given":"Emma","family":"Slack","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,5,27]]},"reference":[{"key":"911_CR1","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1172\/JCI12561","volume":"107","author":"J Fierer","year":"2001","unstructured":"Fierer, J. & Guiney, D. G. Diverse virulence traits underlying different clinical outcomes of Salmonella infection. J. Clin. Invest. 107, 775\u2013780 (2001).","journal-title":"J. Clin. Invest."},{"key":"911_CR2","doi-asserted-by":"publisher","first-page":"4227","DOI":"10.1128\/IAI.05398-11","volume":"79","author":"Q Kong","year":"2011","unstructured":"Kong, Q. et al. Effect of deletion of genes involved in lipopolysaccharide core and O-antigen synthesis on virulence and immunogenicity of Salmonella enterica serovar Typhimurium. Infect. Immun. 79, 4227\u20134239 (2011).","journal-title":"Infect. Immun."},{"key":"911_CR3","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1128\/iai.59.3.1079-1085.1991","volume":"59","author":"LV Collins","year":"1991","unstructured":"Collins, L. V., Attridge, S. & Hackett, J. Mutations at rfc or pmi attenuate Salmonella Typhimurium virulence for mice. Infect. Immun. 59, 1079\u20131085 (1991).","journal-title":"Infect. Immun."},{"key":"911_CR4","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1111\/j.1365-2958.2010.07203.x","volume":"77","author":"SE Broadbent","year":"2010","unstructured":"Broadbent, S. E., Davies, M. R. & van der Woude, M. W. Phase variation controls expression of Salmonella lipopolysaccharide modification genes by a DNA methylation-dependent mechanism. Mol. Microbiol. 77, 337\u2013353 (2010).","journal-title":"Mol. Microbiol."},{"key":"911_CR5","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1111\/j.1365-2958.2008.06461.x","volume":"70","author":"LM Bogomolnaya","year":"2008","unstructured":"Bogomolnaya, L. M., Santiviago, C. A., Yang, H.-J., Baumler, A. J. & Andrews-Polymenis, H. L. \u2018Form variation\u2019 of the O12 antigen is critical for persistence of Salmonella Typhimurium in the murine intestine. Mol. Microbiol. 70, 1105\u20131119 (2008).","journal-title":"Mol. Microbiol."},{"key":"911_CR6","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1128\/jb.168.1.449-451.1986","volume":"168","author":"P Van der Ley","year":"1986","unstructured":"Van der Ley, P., de Graaff, P. & Tommassen, J. Shielding of Escherichia coli outer membrane proteins as receptors for bacteriophages and colicins by O-antigenic chains of lipopolysaccharide. J. Bacteriol. 168, 449\u2013451 (1986).","journal-title":"J. Bacteriol."},{"key":"911_CR7","doi-asserted-by":"publisher","first-page":"1063","DOI":"10.1128\/jb.170.3.1063-1068.1988","volume":"170","author":"AT Bentley","year":"1988","unstructured":"Bentley, A. T. & Klebba, P. E. Effect of lipopolysaccharide structure on reactivity of antiporin monoclonal antibodies with the bacterial cell surface. J. Bacteriol. 170, 1063\u20131068 (1988).","journal-title":"J. Bacteriol."},{"key":"911_CR8","doi-asserted-by":"publisher","first-page":"5904","DOI":"10.1128\/jb.178.20.5904-5909.1996","volume":"178","author":"JM Slauch","year":"1996","unstructured":"Slauch, J. M., Lee, A. A., Mahan, M. J. & Mekalanos, J. J. Molecular characterization of the oafA locus responsible for acetylation of Salmonella Typhimurium O-antigen: OafA is a member of a family of integral membrane trans-acylases. J. Bacteriol. 178, 5904\u20135909 (1996).","journal-title":"J. Bacteriol."},{"key":"911_CR9","doi-asserted-by":"publisher","first-page":"e1003568","DOI":"10.1371\/journal.pgen.1003568","volume":"9","author":"MR Davies","year":"2013","unstructured":"Davies, M. R., Broadbent, S. E., Harris, S. R., Thomson, N. R. & van der Woude, M. W. Horizontally acquired glycosyltransferase operons drive salmonellae lipopolysaccharide diversity. PLoS Genet. 9, e1003568 (2013).","journal-title":"PLoS Genet."},{"key":"911_CR10","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1111\/j.1574-695X.1999.tb01375.x","volume":"26","author":"ML Kim","year":"1999","unstructured":"Kim, M. L. & Slauch, J. M. Effect of acetylation (O-factor 5) on the polyclonal antibody response to Salmonella Typhimurium O-antigen. FEMS Immunol. Med. Microbiol. 26, 83\u201392 (1999).","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"911_CR11","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1016\/j.vetmic.2017.03.033","volume":"204","author":"I Szabo","year":"2017","unstructured":"Szabo, I., Grafe, M., Kemper, N., Junker, E. & Malorny, B. Genetic basis for loss of immuno-reactive O-chain in Salmonella enterica serovar Enteritidis veterinary isolates. Vet. Microbiol. 204, 165\u2013173 (2017).","journal-title":"Vet. Microbiol."},{"key":"911_CR12","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1038\/s41586-018-0344-3","volume":"559","author":"ER Rojas","year":"2018","unstructured":"Rojas, E. R. et al. The outer membrane is an essential load-bearing element in Gram-negative bacteria. Nature 559, 617\u2013621 (2018).","journal-title":"Nature"},{"key":"911_CR13","doi-asserted-by":"publisher","first-page":"e02831-19","DOI":"10.1128\/mBio.02831-19","volume":"11","author":"V Ricci","year":"2020","unstructured":"Ricci, V., Zhang, D., Teale, C. & Piddock, L. J. V. The O-antigen epitope governs susceptibility to colistin in Salmonella enterica. mBio 11, e02831-19 (2020).","journal-title":"mBio"},{"key":"911_CR14","doi-asserted-by":"publisher","first-page":"e1001097","DOI":"10.1371\/journal.ppat.1001097","volume":"6","author":"K Endt","year":"2010","unstructured":"Endt, K. et al. The microbiota mediates pathogen clearance from the gut lumen after non-typhoidal Salmonella diarrhea. PLoS Pathog. 6, e1001097 (2010).","journal-title":"PLoS Pathog."},{"key":"911_CR15","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1038\/nature22058","volume":"544","author":"K Moor","year":"2017","unstructured":"Moor, K. et al. High-avidity IgA protects the intestine by enchaining growing bacteria. Nature 544, 498\u2013502 (2017).","journal-title":"Nature"},{"key":"911_CR16","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1016\/j.chom.2017.08.020","volume":"22","author":"NT Porter","year":"2017","unstructured":"Porter, N. T., Canales, P., Peterson, D. A. & Martens, E. C. A subset of polysaccharide capsules in the human symbiont Bacteroides thetaiotaomicron promote increased competitive fitness in the mouse gut. Cell Host Microbe 22, 494\u2013506 (2017).","journal-title":"Cell Host Microbe"},{"key":"911_CR17","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1016\/j.chom.2016.06.008","volume":"20","author":"T Dolowschiak","year":"2016","unstructured":"Dolowschiak, T. et al. IFN-\u03b3 hinders recovery from mucosal inflammation during antibiotic therapy for Salmonella gut infection. Cell Host Microbe 20, 238\u2013249 (2016).","journal-title":"Cell Host Microbe"},{"key":"911_CR18","doi-asserted-by":"publisher","first-page":"e77204","DOI":"10.1371\/journal.pone.0077204","volume":"8","author":"B Felmy","year":"2013","unstructured":"Felmy, B. et al. NADPH oxidase deficient mice develop colitis and bacteremia upon infection with normally avirulent, TTSS-1- and TTSS-2-deficient Salmonella Typhimurium. PLoS ONE 8, e77204 (2013).","journal-title":"PLoS ONE"},{"key":"911_CR19","doi-asserted-by":"publisher","first-page":"768","DOI":"10.1053\/j.gastro.2007.12.043","volume":"134","author":"GA Grassl","year":"2008","unstructured":"Grassl, G. A., Valdez, Y., Bergstrom, K. S. B., Vallance, B. A. & Finlay, B. B. Chronic enteric Salmonella infection in mice leads to severe and persistent intestinal fibrosis. Gastroenterology 134, 768\u2013780 (2008).","journal-title":"Gastroenterology"},{"key":"911_CR20","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1126\/science.aaf8451","volume":"355","author":"M Diard","year":"2017","unstructured":"Diard, M. et al. Inflammation boosts bacteriophage transfer between Salmonella spp. Science 355, 1211\u20131215 (2017).","journal-title":"Science"},{"key":"911_CR21","doi-asserted-by":"publisher","first-page":"34","DOI":"10.3389\/fimmu.2016.00034","volume":"7","author":"K Moor","year":"2016","unstructured":"Moor, K. et al. Peracetic acid treatment generates potent inactivated oral vaccines from a broad range of culturable bacterial species. Front. Immunol. 7, 34 (2016).","journal-title":"Front. Immunol."},{"key":"911_CR22","doi-asserted-by":"publisher","first-page":"2164","DOI":"10.1038\/s41564-019-0568-5","volume":"4","author":"SY Wotzka","year":"2019","unstructured":"Wotzka, S. Y. et al. Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice. Nat. Microbiol. 4, 2164\u20132174 (2019).","journal-title":"Nat. Microbiol."},{"key":"911_CR23","doi-asserted-by":"publisher","first-page":"2839","DOI":"10.1128\/IAI.71.5.2839-2858.2003","volume":"71","author":"M Barthel","year":"2003","unstructured":"Barthel, M. et al. Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host. Infect. Immun. 71, 2839\u20132858 (2003).","journal-title":"Infect. Immun."},{"key":"911_CR24","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1111\/j.1600-065X.2011.01070.x","volume":"245","author":"P Kaiser","year":"2012","unstructured":"Kaiser, P., Diard, M., Stecher, B. & Hardt, W.-D. The streptomycin mouse model for Salmonella diarrhea: functional analysis of the microbiota, the pathogen\u2019s virulence factors, and the host\u2019s mucosal immune response. Immunol. Rev. 245, 56\u201383 (2012).","journal-title":"Immunol. Rev."},{"key":"911_CR25","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1111\/j.1365-2672.2010.04877.x","volume":"110","author":"E Hauser","year":"2011","unstructured":"Hauser, E., Junker, E., Helmuth, R. & Malorny, B. Different mutations in the oafA gene lead to loss of O5-antigen expression in Salmonella enterica serovar Typhimurium. J. Appl. Microbiol. 110, 248\u2013253 (2011).","journal-title":"J. Appl. Microbiol."},{"key":"911_CR26","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1093\/gbe\/evaa010","volume":"12","author":"JL Cherry","year":"2020","unstructured":"Cherry, J. L. Selection-driven gene inactivation in Salmonella. Genome Biol. Evol. 12, 18\u201334 (2020).","journal-title":"Genome Biol. Evol."},{"key":"911_CR27","doi-asserted-by":"publisher","first-page":"2735","DOI":"10.1128\/JB.188.7.2735-2739.2006","volume":"188","author":"GL Murray","year":"2006","unstructured":"Murray, G. L., Attridge, S. R. & Morona, R. Altering the length of the lipopolysaccharide O antigen has an impact on the interaction of Salmonella enterica serovar Typhimurium with macrophages and complement. J. Bacteriol. 188, 2735\u20132739 (2006).","journal-title":"J. Bacteriol."},{"key":"911_CR28","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1111\/j.1365-2958.2012.08202.x","volume":"86","author":"M Kim","year":"2012","unstructured":"Kim, M. & Ryu, S. Spontaneous and transient defence against bacteriophage by phase-variable glucosylation of O-antigen in Salmonella enterica serovar Typhimurium. Mol. Microbiol. 86, 411\u2013425 (2012).","journal-title":"Mol. Microbiol."},{"key":"911_CR29","doi-asserted-by":"publisher","first-page":"760","DOI":"10.1038\/s41579-018-0070-8","volume":"16","author":"FL Nobrega","year":"2018","unstructured":"Nobrega, F. L. et al. Targeting mechanisms of tailed bacteriophages. Nat. Rev. Microbiol. 16, 760\u2013773 (2018).","journal-title":"Nat. Rev. Microbiol."},{"key":"911_CR30","doi-asserted-by":"publisher","first-page":"S103","DOI":"10.1017\/S0031182000073054","volume":"100","author":"BR Levin","year":"1990","unstructured":"Levin, B. R. Selection and evolution of virulence in bacteria: an ecumenical excursion and modest suggestion. Parasitology 100, S103\u2013S115 (1990).","journal-title":"Parasitology"},{"key":"911_CR31","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1093\/femsre\/fux023","volume":"41","author":"M Diard","year":"2017","unstructured":"Diard, M. & Hardt, W.-D. Evolution of bacterial virulence. FEMS Microbiol. Rev. 41, 679\u2013697 (2017).","journal-title":"FEMS Microbiol. Rev."},{"key":"911_CR32","doi-asserted-by":"publisher","first-page":"10644","DOI":"10.1073\/pnas.0404028101","volume":"101","author":"H Wildschutte","year":"2004","unstructured":"Wildschutte, H., Wolfe, D. M., Tamewitz, A. & Lawrence, J. G. Protozoan predation, diversifying selection, and the evolution of antigenic diversity in Salmonella. Proc. Natl Acad. Sci. USA 101, 10644\u201310649 (2004).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"911_CR33","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1128\/MMBR.68.3.560-602.2004","volume":"68","author":"H Brussow","year":"2004","unstructured":"Brussow, H., Canchaya, C. & Hardt, W.-D. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68, 560\u2013602 (2004).","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"911_CR34","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.4049\/jimmunol.1901206","volume":"204","author":"S Hsieh","year":"2020","unstructured":"Hsieh, S. et al. Polysaccharide capsules equip the human symbiont Bacteroides thetaiotaomicron to modulate immune responses to a dominant antigen in the intestine. J. Immunol. 204, 1035\u20131046 (2020).","journal-title":"J. Immunol."},{"key":"911_CR35","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1038\/s41586-018-0730-x","volume":"563","author":"D Gerlach","year":"2018","unstructured":"Gerlach, D. et al. Methicillin-resistant Staphylococcus aureus alters cell wall glycosylation to evade immunity. Nature 563, 705\u2013709 (2018).","journal-title":"Nature"},{"key":"911_CR36","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1146\/annurev-micro-090816-093813","volume":"71","author":"D Hughes","year":"2017","unstructured":"Hughes, D. & Andersson, D. I. Evolutionary trajectories to antibiotic resistance. Annu. Rev. Microbiol. 71, 579\u2013596 (2017).","journal-title":"Annu. Rev. Microbiol."},{"key":"911_CR37","doi-asserted-by":"publisher","first-page":"684","DOI":"10.1093\/femsre\/fuaa017","volume":"44","author":"DP Pires","year":"2020","unstructured":"Pires, D. P., Costa, A. R., Pinto, G., Meneses, L. & Azeredo, J. Current challenges and future opportunities of phage therapy. FEMS Microbiol. Rev. 44, 684\u2013700 (2020).","journal-title":"FEMS Microbiol. Rev."},{"key":"911_CR38","doi-asserted-by":"publisher","first-page":"1146","DOI":"10.1038\/nbt.3043","volume":"32","author":"D Bikard","year":"2014","unstructured":"Bikard, D. et al. Exploiting CRISPR\u2013Cas nucleases to produce sequence-specific antimicrobials. Nat. Biotechnol. 32, 1146\u20131150 (2014).","journal-title":"Nat. Biotechnol."},{"key":"911_CR39","doi-asserted-by":"crossref","first-page":"2521","DOI":"10.4049\/jimmunol.162.5.2521","volume":"162","author":"GR Harriman","year":"1999","unstructured":"Harriman, G. R. et al. Targeted deletion of the IgA constant region in mice leads to IgA deficiency with alterations in expression of other Ig isotypes. J. Immunol. 162, 2521\u20132529 (1999).","journal-title":"J. Immunol."},{"key":"911_CR40","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1016\/0092-8674(93)90644-6","volume":"73","author":"H Gu","year":"1993","unstructured":"Gu, H., Zou, Y. R. & Rajewsky, K. Independent control of immunoglobulin switch recombination at individual switch regions evidenced through Cre-loxP-mediated gene targeting. Cell 73, 1155\u20131164 (1993).","journal-title":"Cell"},{"key":"911_CR41","doi-asserted-by":"publisher","first-page":"869","DOI":"10.1016\/0092-8674(92)90030-G","volume":"68","author":"P Mombaerts","year":"1992","unstructured":"Mombaerts, P. et al. RAG-1-deficient mice have no mature B and T lymphocytes. Cell 68, 869\u2013877 (1992).","journal-title":"Cell"},{"key":"911_CR42","doi-asserted-by":"publisher","first-page":"6640","DOI":"10.1073\/pnas.120163297","volume":"97","author":"KA Datsenko","year":"2000","unstructured":"Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640\u20136645 (2000).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"911_CR43","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/0076-6879(91)04004-8","volume":"204","author":"NL Sternberg","year":"1991","unstructured":"Sternberg, N. L. & Maurer, R. Bacteriophage-mediated generalized transduction in Escherichia coli and Salmonella Typhimurium. Methods Enzymol. 204, 18\u201343 (1991).","journal-title":"Methods Enzymol."},{"key":"911_CR44","doi-asserted-by":"publisher","first-page":"4138","DOI":"10.1128\/IAI.72.7.4138-4150.2004","volume":"72","author":"B Stecher","year":"2004","unstructured":"Stecher, B. et al. Flagella and chemotaxis are required for efficient induction of Salmonella enterica serovar Typhimurium colitis in streptomycin-pretreated mice. Infect. Immun. 72, 4138\u20134150 (2004).","journal-title":"Infect. Immun."},{"key":"911_CR45","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"911_CR46","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"911_CR47","doi-asserted-by":"crossref","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","volume":"9","author":"BJ Walker","year":"2014","unstructured":"Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).","journal-title":"PLoS ONE"},{"key":"911_CR48","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","volume":"6","author":"P Cingolani","year":"2012","unstructured":"Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 80\u201392 (2012).","journal-title":"Fly (Austin)"},{"key":"911_CR49","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1038\/291238a0","volume":"291","author":"SK Hoiseth","year":"1981","unstructured":"Hoiseth, S. K. & Stocker, B. A. D. Aromatic-dependent Salmonella Typhimurium are non-virulent and effective as live vaccines. Nature 291, 238\u2013239 (1981).","journal-title":"Nature"},{"key":"911_CR50","doi-asserted-by":"publisher","first-page":"1531","DOI":"10.1038\/nprot.2016.091","volume":"11","author":"K Moor","year":"2016","unstructured":"Moor, K. et al. Analysis of bacterial-surface-specific antibodies in body fluids using bacterial flow cytometry. Nat. Protoc. 11, 1531\u20131553 (2016).","journal-title":"Nat. Protoc."},{"key":"911_CR51","doi-asserted-by":"publisher","first-page":"e1001928","DOI":"10.1371\/journal.pbio.1001928","volume":"12","author":"M Arnoldini","year":"2014","unstructured":"Arnoldini, M. et al. Bistable expression of virulence genes in Salmonella leads to the formation of an antibiotic-tolerant subpopulation. PLoS Biol. 12, e1001928 (2014).","journal-title":"PLoS Biol."},{"key":"911_CR52","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1016\/j.cels.2018.03.009","volume":"6","author":"S Van Vliet","year":"2018","unstructured":"Van Vliet, S. et al. Spatially correlated gene expression in bacterial groups: the role of lineage history, spatial gradients, and cell-cell interactions. Cell Syst 6, 496\u2013507 (2018).","journal-title":"Cell Syst"},{"key":"911_CR53","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1016\/j.carres.2013.10.002","volume":"382","author":"K Ilg","year":"2013","unstructured":"Ilg, K., Zandomeneghi, G., Rugarabamu, G., Meier, B. H. & Aebi, M. HR-MAS NMR reveals a pH-dependent LPS alteration by de-O-acetylation at abequose in the O-antigen of Salmonella enterica serovar Typhimurium. Carbohydr. Res. 382, 58\u201364 (2013).","journal-title":"Carbohydr. Res."},{"key":"911_CR54","first-page":"83","volume":"5","author":"O Westphal","year":"1965","unstructured":"Westphal, O. & Jann, K. Bacterial lipopolysaccharides extraction with phenol\u2013water and further applications of the procedure. Methods Carbohydr. Chem. 5, 83\u201391 (1965).","journal-title":"Methods Carbohydr. Chem."},{"key":"911_CR55","first-page":"264","volume":"27","author":"T Steffens","year":"2017","unstructured":"Steffens, T. et al. The lipopolysaccharide of the crop pathogen Xanthomonas translucens pv. translucens: chemical characterization and determination of signaling events in plant cells. Glycobiology 27, 264\u2013274 (2017).","journal-title":"Glycobiology"},{"key":"911_CR56","doi-asserted-by":"publisher","first-page":"e1006499","DOI":"10.1371\/journal.pgen.1006499","volume":"12","author":"S Ardissone","year":"2016","unstructured":"Ardissone, S. et al. Cell cycle constraints and environmental control of local DNA hypomethylation in \u03b1-proteobacteria. PLoS Genet. 12, e1006499 (2016).","journal-title":"PLoS Genet."},{"key":"911_CR57","doi-asserted-by":"publisher","first-page":"2987","DOI":"10.1093\/bioinformatics\/btr509","volume":"27","author":"H Li","year":"2011","unstructured":"Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987\u20132993 (2011).","journal-title":"Bioinformatics"},{"key":"911_CR58","doi-asserted-by":"publisher","first-page":"1691","DOI":"10.1093\/bioinformatics\/btr174","volume":"27","author":"DW Barnett","year":"2011","unstructured":"Barnett, D. W., Garrison, E. K., Quinlan, A. R., Str\u00f6mberg, M. P. & Marth, G. T. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics 27, 1691\u20131692 (2011).","journal-title":"Bioinformatics"},{"key":"911_CR59","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841\u2013842 (2010).","journal-title":"Bioinformatics"},{"key":"911_CR60","doi-asserted-by":"publisher","first-page":"D574","DOI":"10.1093\/nar\/gkv1209","volume":"44","author":"PJ Kersey","year":"2016","unstructured":"Kersey, P. J. et al. Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res. 44, D574\u2013D580 (2016).","journal-title":"Nucleic Acids Res."},{"key":"911_CR61","unstructured":"R Core Development Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2019)."},{"key":"911_CR62","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"911_CR63","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1016\/j.jmb.2012.05.018","volume":"422","author":"H Yamashita","year":"2012","unstructured":"Yamashita, H. et al. Single-molecule imaging on living bacterial cell surface by high-speed AFM. J. Mol. Biol. 422, 300\u2013309 (2012).","journal-title":"J. Mol. Biol."},{"key":"911_CR64","first-page":"e01068","volume":"1","author":"M Hoffmann","year":"2013","unstructured":"Hoffmann, M. et al. Complete genome sequence of a multidrug-resistant Salmonella enterica serovar Typhimurium var. 5\u2212 strain isolated from chicken breast. Genome Announc. 1, e01068\u201313 (2013).","journal-title":"Genome Announc."},{"key":"911_CR65","first-page":"e00285","volume":"4","author":"C Silva","year":"2016","unstructured":"Silva, C., Calva, E., Puente, J. L., Zaidi, M. B. & Vinuesa, P. Complete genome sequence of Salmonella enterica serovar Typhimurium strain SO2 (sequence type 302) isolated from an asymptomatic child in Mexico.Genome Announc. 4, e00285\u201316 (2016).","journal-title":"Genome Announc."},{"key":"911_CR66","doi-asserted-by":"publisher","first-page":"e00154","DOI":"10.1128\/JB.00154-17","volume":"200","author":"Y Hong","year":"2018","unstructured":"Hong, Y., Liu, M. A. & Reeves, P. R. Progress in our understanding of Wzx flippase for translocation of bacterial membrane lipid-linked oligosaccharide. J. Bacteriol. 200, e00154\u201317 (2018).","journal-title":"J. Bacteriol."},{"key":"911_CR67","doi-asserted-by":"publisher","first-page":"1675","DOI":"10.4049\/jimmunol.174.3.1675","volume":"174","author":"S Hapfelmeier","year":"2005","unstructured":"Hapfelmeier, S. et al. The Salmonella pathogenicity island (SPI)-2 and SPI-1 type III secretion systems allow Salmonella serovar Typhimurium to trigger colitis via myd88-dependent and myd88-independent mechanisms. J. Immunol. 174, 1675\u20131685 (2005).","journal-title":"J. Immunol."},{"key":"911_CR68","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1016\/j.chom.2013.11.002","volume":"14","author":"L Maier","year":"2013","unstructured":"Maier, L. et al. Microbiota-derived hydrogen fuels Salmonella Typhimurium invasion of the gut ecosystem. Cell Host Microbe 14, 641\u2013651 (2013).","journal-title":"Cell Host Microbe"},{"key":"911_CR69","doi-asserted-by":"publisher","first-page":"632","DOI":"10.1128\/IAI.74.1.632-644.2006","volume":"74","author":"M Suar","year":"2006","unstructured":"Suar, M. et al. Virulence of broad- and narrow-host-range Salmonella enterica serovars in the streptomycin-pretreated mouse model. Infect. Immun. 74, 632\u2013644 (2006).","journal-title":"Infect. Immun."},{"key":"911_CR70","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1016\/j.immuni.2015.08.011","volume":"43","author":"F Fransen","year":"2015","unstructured":"Fransen, F. et al. BALB\/c and C57BL\/6 mice differ in polyreactive IgA abundance, which impacts the generation of antigen-specific IgA and microbiota diversity. Immunity 43, 527\u2013540 (2015).","journal-title":"Immunity"}],"container-title":["Nature Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00911-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00911-1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00911-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,4]],"date-time":"2023-11-04T02:51:14Z","timestamp":1699066274000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00911-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,5,27]]},"references-count":70,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2021,7]]}},"alternative-id":["911"],"URL":"https:\/\/doi.org\/10.1038\/s41564-021-00911-1","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/824821","asserted-by":"object"}]},"ISSN":["2058-5276"],"issn-type":[{"value":"2058-5276","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,5,27]]},"assertion":[{"value":"26 November 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 April 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 May 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Evolutionary trap vaccines are covered by European patent application number EP19177251, submitted by M.D. W.-D.H. and E.S. All other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}