{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T05:48:07Z","timestamp":1792043287520,"version":"4.4.0"},"reference-count":61,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2025,6,27]],"date-time":"2025-06-27T00:00:00Z","timestamp":1750982400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["310030_192567"],"award-info":[{"award-number":["310030_192567"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"publisher","award":["10.001.588"],"award-info":[{"award-number":["10.001.588"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NCCR Microbiomes","award":["51NF40_225148"],"award-info":[{"award-number":["51NF40_225148"]}]},{"DOI":"10.13039\/100004410","name":"European Molecular Biology Organization","doi-asserted-by":"publisher","award":["ALTF-234-2020"],"award-info":[{"award-number":["ALTF-234-2020"]}],"id":[{"id":"10.13039\/100004410","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NCCR MICROBIOMES","award":["51NF40_180575"],"award-info":[{"award-number":["51NF40_180575"]}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"crossref","award":["SCHU 3606\/1-1"],"award-info":[{"award-number":["SCHU 3606\/1-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"crossref","award":["LA 4572\/1-1"],"award-info":[{"award-number":["LA 4572\/1-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    <jats:italic>Salmonella enterica<\/jats:italic>\n                    serovar Typhimurium (\n                    <jats:italic>S<\/jats:italic>\n                    . Tm) is a major cause of gastrointestinal diseases worldwide. To date, options for prevention or curative therapy remain limited. The gut microbiota plays a protective role against enteric diseases, particularly in preventing establishment and proliferation of\n                    <jats:italic>S<\/jats:italic>\n                    . Tm. While most research has focused on microbiota-mediated pathogen exclusion during the later, inflammation-dominated stages of infection, little is known about how microbiota members mitigate\n                    <jats:italic>S<\/jats:italic>\n                    . Tm early gut colonization. To address this gap, we conducted 24\u2009h\n                    <jats:italic>in vivo<\/jats:italic>\n                    competitive experiments using\n                    <jats:italic>S<\/jats:italic>\n                    . Tm and different commensal\n                    <jats:italic>E. coli<\/jats:italic>\n                    strains. We observed a significant reduction in pathogen load, which was strain-specific and particularly evident with\n                    <jats:italic>E. coli<\/jats:italic>\n                    8178. To investigate the underlying molecular mechanisms, we performed an\n                    <jats:italic>in vivo<\/jats:italic>\n                    screen using a rationally designed\n                    <jats:italic>S<\/jats:italic>\n                    . Tm library\u2014which includes a wide range of carbohydrate utilization mutants\u2014both in the absence and presence of\n                    <jats:italic>E. coli<\/jats:italic>\n                    strains. Our findings revealed that\n                    <jats:italic>E. coli<\/jats:italic>\n                    8178-mediated\n                    <jats:italic>S<\/jats:italic>\n                    . Tm competition was driven by the exploitation of galactose during the early stage of infection. Identifying galactose as a key metabolite in pathogen exclusion by gut microbiota members enhances our mechanistic understanding of microbiota-mediated protection and opens new avenues for developing microbiota- and dietary-based strategies to better control intestinal infections.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1013232","type":"journal-article","created":{"date-parts":[[2025,6,27]],"date-time":"2025-06-27T13:24:30Z","timestamp":1751030670000},"page":"e1013232","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Strain-specific galactose utilization by commensal E. coli mitigates Salmonella establishment in the gut"],"prefix":"10.1371","volume":"21","author":[{"given":"Christopher","family":"Schubert","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jana","family":"N\u00e4f","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa","family":"Petukhov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leanid","family":"Laganenka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yassine","family":"Cherrak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9892-6420","authenticated-orcid":true,"given":"Wolf-Dietrich","family":"Hardt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,6,27]]},"reference":[{"key":"ppat.1013232.ref001","volume-title":"WHO estimates of the global burden of foodborne diseases: foodborne diseases burden epidemiology reference group 2007-2015","author":"WHO U","year":"2015"},{"key":"ppat.1013232.ref002","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.fm.2017.08.018","article-title":"Salmonella epidemiology: A whirlwind of change","volume":"71","author":"JM Besser","year":"2018","journal-title":"Food Microbiol"},{"issue":"1","key":"ppat.1013232.ref003","doi-asserted-by":"crossref","first-page":"2447832","DOI":"10.1080\/19490976.2024.2447832","article-title":"Comparing Campylobacter jejuni to three other enteric pathogens in OligoMM12 mice reveals pathogen-specific host and microbiota responses","volume":"17","author":"MK-M Herzog","year":"2025","journal-title":"Gut Microbes"},{"issue":"12","key":"ppat.1013232.ref004","article-title":"The European Union One Health 2021 Zoonoses Report","volume":"20","author":"EFSA","year":"2022","journal-title":"EFSA J"},{"issue":"4","key":"ppat.1013232.ref005","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/j.chom.2017.03.009","article-title":"Salmonella Typhimurium diarrhea reveals basic principles of enteropathogen infection and disease-promoted DNA exchange","volume":"21","author":"SY Wotzka","year":"2017","journal-title":"Cell Host Microbe"},{"issue":"10","key":"ppat.1013232.ref006","doi-asserted-by":"crossref","first-page":"1758","DOI":"10.1016\/j.chom.2024.08.015","article-title":"Salmonella Typhimurium screen identifies shifts in mixed-acid fermentation during gut colonization","volume":"32","author":"BD Nguyen","year":"2024","journal-title":"Cell Host Microbe"},{"issue":"6","key":"ppat.1013232.ref007","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1016\/j.chom.2020.04.013","article-title":"Import of aspartate and malate by DcuABC Drives H2\/fumarate respiration to promote initial Salmonella Gut-Lumen Colonization in Mice","volume":"27","author":"BD Nguyen","year":"2020","journal-title":"Cell Host Microbe"},{"issue":"1","key":"ppat.1013232.ref008","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1038\/s41467-025-56890-y","article-title":"Monosaccharides drive Salmonella gut colonization in a context-dependent or -independent manner","volume":"16","author":"C Schubert","year":"2025","journal-title":"Nat Commun"},{"issue":"10","key":"ppat.1013232.ref009","doi-asserted-by":"crossref","first-page":"1774","DOI":"10.1016\/j.chom.2024.07.025","article-title":"Salmonella re-engineers the intestinal environment to break colonization resistance in the presence of a compositionally intact microbiota","volume":"32","author":"AWL Rogers","year":"2024","journal-title":"Cell Host Microbe"},{"issue":"2","key":"ppat.1013232.ref010","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1016\/j.chom.2007.06.010","article-title":"Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae","volume":"2","author":"C Lupp","year":"2007","journal-title":"Cell Host Microbe"},{"issue":"10","key":"ppat.1013232.ref011","doi-asserted-by":"crossref","first-page":"2177","DOI":"10.1371\/journal.pbio.0050244","article-title":"Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota","volume":"5","author":"B Stecher","year":"2007","journal-title":"PLoS Biol"},{"issue":"7314","key":"ppat.1013232.ref012","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/nature09415","article-title":"Gut inflammation provides a respiratory electron acceptor for Salmonella","volume":"467","author":"SE Winter","year":"2010","journal-title":"Nature"},{"issue":"42","key":"ppat.1013232.ref013","doi-asserted-by":"crossref","first-page":"17480","DOI":"10.1073\/pnas.1107857108","article-title":"Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota","volume":"108","author":"P Thiennimitr","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"ppat.1013232.ref014","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1073\/pnas.1113246109","article-title":"Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae","volume":"109","author":"B Stecher","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6","key":"ppat.1013232.ref015","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1016\/j.chom.2013.11.002","article-title":"Microbiota-derived hydrogen fuels Salmonella typhimurium invasion of the gut ecosystem","volume":"14","author":"L Maier","year":"2013","journal-title":"Cell Host Microbe"},{"issue":"1","key":"ppat.1013232.ref016","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1006129","article-title":"Respiration of microbiota-derived 1,2-propanediol drives Salmonella expansion during Colitis","volume":"13","author":"F Faber","year":"2017","journal-title":"PLoS Pathog"},{"issue":"4","key":"ppat.1013232.ref017","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1016\/j.chom.2018.03.013","article-title":"Dysbiosis-associated change in host metabolism generates lactate to support Salmonella growth","volume":"23","author":"CC Gillis","year":"2018","journal-title":"Cell Host Microbe"},{"issue":"3","key":"ppat.1013232.ref018","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1038\/s41385-021-00381-y","article-title":"Epithelium-autonomous NAIP\/NLRC4 prevents TNF-driven inflammatory destruction of the gut epithelial barrier in Salmonella-infected mice","volume":"14","author":"SA Fattinger","year":"2021","journal-title":"Mucosal Immunol"},{"key":"ppat.1013232.ref019","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1093\/infdis\/111.2.117","article-title":"Enhanced susceptibility to Salmonella infection in streptomycin-treated mice","volume":"111","author":"M Bohnhoff","year":"1962","journal-title":"J Infect Dis"},{"issue":"11","key":"ppat.1013232.ref020","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/nri3535","article-title":"Microbiota-mediated colonization resistance against intestinal pathogens","volume":"13","author":"CG Buffie","year":"2013","journal-title":"Nat Rev Immunol"},{"issue":"6","key":"ppat.1013232.ref021","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/s41579-022-00833-7","article-title":"Microbiota-mediated colonization resistance: mechanisms and regulation","volume":"21","author":"G Caballero-Flores","year":"2023","journal-title":"Nat Rev Microbiol"},{"key":"ppat.1013232.ref022","doi-asserted-by":"crossref","first-page":"16215","DOI":"10.1038\/nmicrobiol.2016.215","article-title":"Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium","volume":"2","author":"S Brugiroux","year":"2016","journal-title":"Nat Microbiol"},{"issue":"1","key":"ppat.1013232.ref023","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41385-018-0053-0","article-title":"Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them","volume":"12","author":"MT Sorbara","year":"2019","journal-title":"Mucosal Immunol"},{"issue":"1","key":"ppat.1013232.ref024","article-title":"Salmonella versus the Microbiome","volume":"85","author":"AWL Rogers","year":"2020","journal-title":"Microbiol Mol Biol Rev"},{"issue":"6676","key":"ppat.1013232.ref025","doi-asserted-by":"crossref","DOI":"10.1126\/science.adj3502","article-title":"Microbiome diversity protects against pathogens by nutrient blocking","volume":"382","author":"F Spragge","year":"2023","journal-title":"Science"},{"issue":"2","key":"ppat.1013232.ref026","doi-asserted-by":"crossref","DOI":"10.1016\/j.chom.2018.07.002","article-title":"A gut commensal-produced metabolite mediates colonization resistance to Salmonella infection","volume":"24","author":"A Jacobson","year":"2018","journal-title":"Cell Host Microbe"},{"issue":"7632","key":"ppat.1013232.ref027","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1038\/nature20557","article-title":"Microcins mediate competition among Enterobacteriaceae in the inflamed gut","volume":"540","author":"M Sassone-Corsi","year":"2016","journal-title":"Nature"},{"issue":"6","key":"ppat.1013232.ref028","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3002616","article-title":"Commensal E. coli limits Salmonella gut invasion during inflammation by producing toxin-bound siderophores in a tonB-dependent manner","volume":"22","author":"Y Cherrak","year":"2024","journal-title":"PLoS Biol"},{"issue":"1","key":"ppat.1013232.ref029","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.chom.2013.06.007","article-title":"Probiotic bacteria reduce salmonella typhimurium intestinal colonization by competing for iron","volume":"14","author":"E Deriu","year":"2013","journal-title":"Cell Host Microbe"},{"issue":"1","key":"ppat.1013232.ref030","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.chom.2018.12.003","article-title":"Commensal Enterobacteriaceae protect against Salmonella Colonization through oxygen competition","volume":"25","author":"Y Litvak","year":"2019","journal-title":"Cell Host Microbe"},{"issue":"6","key":"ppat.1013232.ref031","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1038\/s41564-019-0407-8","article-title":"Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection","volume":"4","author":"EM Velazquez","year":"2019","journal-title":"Nat Microbiol"},{"issue":"6","key":"ppat.1013232.ref032","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1016\/j.chom.2022.04.012","article-title":"Host cells subdivide nutrient niches into discrete biogeographical microhabitats for gut microbes","volume":"30","author":"MJ Liou","year":"2022","journal-title":"Cell Host Microbe"},{"issue":"11","key":"ppat.1013232.ref033","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.1016\/j.chom.2021.09.004","article-title":"E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source","volume":"29","author":"C Eberl","year":"2021","journal-title":"Cell Host Microbe"},{"issue":"3","key":"ppat.1013232.ref034","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1016\/j.chom.2025.02.004","article-title":"Neutrophil recruitment during intestinal inflammation primes Salmonella elimination by commensal E. coli in a context-dependent manner","volume":"33","author":"Y Cherrak","year":"2025","journal-title":"Cell Host Microbe"},{"issue":"10","key":"ppat.1013232.ref035","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0206214","article-title":"Microbiota stability in healthy individuals after single-dose lactulose challenge-A randomized controlled study","volume":"13","author":"SY Wotzka","year":"2018","journal-title":"PLoS One"},{"issue":"2","key":"ppat.1013232.ref036","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/s41564-022-01286-7","article-title":"Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut","volume":"8","author":"L Laganenka","year":"2023","journal-title":"Nat Microbiol"},{"issue":"5","key":"ppat.1013232.ref037","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1013156","article-title":"Interplay between chemotaxis, quorum sensing, and metabolism regulates Escherichia coli-Salmonella Typhimurium interactions in vivo","volume":"21","author":"L Laganenka","year":"2025","journal-title":"PLoS Pathog"},{"issue":"4","key":"ppat.1013232.ref038","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1038\/s41564-024-01634-9","article-title":"Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags","volume":"9","author":"BBJ Daniel","year":"2024","journal-title":"Nat Microbiol"},{"issue":"12","key":"ppat.1013232.ref039","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004557","article-title":"Granulocytes impose a tight bottleneck upon the gut luminal pathogen population during Salmonella typhimurium colitis","volume":"10","author":"L Maier","year":"2014","journal-title":"PLoS Pathog"},{"key":"ppat.1013232.ref040","article-title":"Unravelling the Core and Accessory Genome Diversity of Enterobacteriaceaein Carbon Metabolism","author":"N N\u00e4pflin","year":"2025","journal-title":"bioRxiv"},{"issue":"9","key":"ppat.1013232.ref041","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1038\/s41576-020-0244-x","article-title":"A decade of advances in transposon-insertion sequencing","volume":"21","author":"AK Cain","year":"2020","journal-title":"Nat Rev Genet"},{"issue":"10","key":"ppat.1013232.ref042","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1038\/nmeth.1377","article-title":"Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms","volume":"6","author":"T van Opijnen","year":"2009","journal-title":"Nat Methods"},{"issue":"2","key":"ppat.1013232.ref043","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1128\/iai.39.2.686-703.1983","article-title":"Survival and implantation of Escherichia coli in the intestinal tract","volume":"39","author":"R Freter","year":"1983","journal-title":"Infect Immun"},{"issue":"2","key":"ppat.1013232.ref044","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1128\/iai.39.2.676-685.1983","article-title":"Mechanisms that control bacterial populations in continuous-flow culture models of mouse large intestinal flora","volume":"39","author":"R Freter","year":"1983","journal-title":"Infect Immun"},{"issue":"4","key":"ppat.1013232.ref045","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/s41564-019-0658-4","article-title":"Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition","volume":"5","author":"RA Oliveira","year":"2020","journal-title":"Nat Microbiol"},{"issue":"7","key":"ppat.1013232.ref046","doi-asserted-by":"crossref","first-page":"1140","DOI":"10.1016\/j.chom.2023.05.029","article-title":"Differences in carbon metabolic capacity fuel co-existence and plasmid transfer between Salmonella strains in the mouse gut","volume":"31","author":"E G\u00fcl","year":"2023","journal-title":"Cell Host Microbe"},{"issue":"7","key":"ppat.1013232.ref047","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1038\/s41564-024-01710-0","article-title":"Klebsiella oxytoca inhibits Salmonella infection through multiple microbiota-context-dependent mechanisms","volume":"9","author":"L Osbelt","year":"2024","journal-title":"Nat Microbiol"},{"key":"ppat.1013232.ref048","article-title":"Nutritional characterization and measurement of dietary carbohydrates","author":"KN Englyst","year":"2007","journal-title":"Eur J Clin Nutr"},{"issue":"8","key":"ppat.1013232.ref049","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.3390\/nu14081639","article-title":"The development of the davis food glycopedia-a glycan encyclopedia of food","volume":"14","author":"JJ Castillo","year":"2022","journal-title":"Nutrients"},{"issue":"1","key":"ppat.1013232.ref050","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.tjnut.2022.12.008","article-title":"Dietary intake of monosaccharides from foods is associated with characteristics of the gut microbiota and gastrointestinal inflammation in healthy US adults","volume":"153","author":"JA Larke","year":"2023","journal-title":"J Nutr"},{"issue":"5","key":"ppat.1013232.ref051","doi-asserted-by":"crossref","first-page":"1166","DOI":"10.1111\/j.1462-5822.2008.01118.x","article-title":"Motility allows S. Typhimurium to benefit from the mucosal defence","volume":"10","author":"B Stecher","year":"2008","journal-title":"Cell Microbiol"},{"issue":"1","key":"ppat.1013232.ref052","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1038\/s41564-019-0610-7","article-title":"Regulation underlying hierarchical and simultaneous utilization of carbon substrates by flux sensors in Escherichia coli","volume":"5","author":"H Okano","year":"2020","journal-title":"Nat Microbiol"},{"issue":"18","key":"ppat.1013232.ref053","doi-asserted-by":"crossref","first-page":"3441","DOI":"10.1016\/j.cell.2022.07.020","article-title":"Gut bacterial nutrient preferences quantified in vivo","volume":"185","author":"X Zeng","year":"2022","journal-title":"Cell"},{"issue":"10","key":"ppat.1013232.ref054","doi-asserted-by":"crossref","first-page":"2696","DOI":"10.1038\/s41564-024-01775-x","article-title":"Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut","volume":"9","author":"Y Cherrak","year":"2024","journal-title":"Nat Microbiol"},{"issue":"7688","key":"ppat.1013232.ref055","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/nature25178","article-title":"Dietary trehalose enhances virulence of epidemic Clostridium difficile","volume":"553","author":"J Collins","year":"2018","journal-title":"Nature"},{"issue":"12","key":"ppat.1013232.ref056","doi-asserted-by":"crossref","first-page":"6640","DOI":"10.1073\/pnas.120163297","article-title":"One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products","volume":"97","author":"KA Datsenko","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1013232.ref057","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1007\/978-1-61779-197-0_5","article-title":"Genome engineering using targeted oligonucleotide libraries and functional selection","volume-title":"Strain Engineering: Methods and Protocols","author":"EJ Diner","year":"2011"},{"issue":"5","key":"ppat.1013232.ref058","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.1128\/IAI.71.5.2839-2858.2003","article-title":"Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host","volume":"71","author":"M Barthel","year":"2003","journal-title":"Infect Immun"},{"issue":"2","key":"ppat.1013232.ref059","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1128\/jb.117.2.619-630.1974","article-title":"Molecular nature of two nonconjugative plasmids carrying drug resistance genes","volume":"117","author":"P Guerry","year":"1974","journal-title":"J Bacteriol"},{"issue":"2","key":"ppat.1013232.ref060","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae078","article-title":"mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations","volume":"40","author":"A Sintsova","year":"2024","journal-title":"Bioinformatics"},{"issue":"7","key":"ppat.1013232.ref061","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1101\/gr.186501","article-title":"Phenotype microarrays for high-throughput phenotypic testing and assay of gene function","volume":"11","author":"BR Bochner","year":"2001","journal-title":"Genome Res"}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1013232","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,27]],"date-time":"2025-06-27T13:24:42Z","timestamp":1751030682000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1013232"}},"subtitle":[],"editor":[{"given":"David","family":"Skurnik","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,6,27]]},"references-count":61,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2025,6,27]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1013232","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.03.03.641131","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,27]]}}}