{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T23:32:04Z","timestamp":1793748724713,"version":"4.6.1"},"reference-count":48,"publisher":"Elsevier BV","issue":"7","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":[[2023,6,1]],"date-time":"2023-06-01T00:00:00Z","timestamp":1685577600000},"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":["310030B_173338"],"award-info":[{"award-number":["310030B_173338"]}],"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":["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":["NRP 72 407240_167121"],"award-info":[{"award-number":["NRP 72 407240_167121"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003357","name":"Gebert R\u00fcf Stiftung","doi-asserted-by":"publisher","award":["GRS-060\/18"],"award-info":[{"award-number":["GRS-060\/18"]}],"id":[{"id":"10.13039\/501100003357","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021831","name":"Institute of Microbiology, Chinese Academy of Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100021831","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100023650","name":"NCCR Catalysis","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100023650","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Host & Microbe"],"published-print":{"date-parts":[[2023,7]]},"DOI":"10.1016\/j.chom.2023.05.029","type":"journal-article","created":{"date-parts":[[2023,6,21]],"date-time":"2023-06-21T10:29:34Z","timestamp":1687343374000},"page":"1140-1153.e3","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":39,"title":["Differences in carbon metabolic capacity fuel co-existence and plasmid transfer between Salmonella strains in the mouse gut"],"prefix":"10.1016","volume":"31","author":[{"given":"Ersin","family":"G\u00fcl","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Abi Younes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jemina","family":"Huuskonen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheickna","family":"Diawara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bidong D.","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luca","family":"Maurer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik","family":"Bakkeren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wolf-Dietrich","family":"Hardt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.chom.2023.05.029_bib1","first-page":"e1403","article-title":"A review on antibiotic resistance: alarm bells are ringing","volume":"9","author":"Zaman","year":"2017","journal-title":"Cureus"},{"key":"10.1016\/j.chom.2023.05.029_bib2","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1038\/nrmicro1614","article-title":"The antibiotic resistome: the nexus of chemical and genetic diversity","volume":"5","author":"Wright","year":"2007","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.chom.2023.05.029_bib3","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."},{"key":"10.1016\/j.chom.2023.05.029_bib4","first-page":"277","article-title":"The antibiotic resistance crisis: part 1: causes and threats","volume":"40","author":"Ventola","year":"2015","journal-title":"P T"},{"key":"10.1016\/j.chom.2023.05.029_bib5","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1111\/1462-2920.13659","article-title":"Microbial nutrient niches in the gut","volume":"19","author":"Pereira","year":"2017","journal-title":"Environ. Microbiol."},{"key":"10.1016\/j.chom.2023.05.029_bib6","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1146\/annurev-micro-020420-013457","article-title":"How food affects colonization resistance against enteropathogenic bacteria","volume":"74","author":"Kreuzer","year":"2020","journal-title":"Annu. Rev. Microbiol."},{"key":"10.1016\/j.chom.2023.05.029_bib7","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":"Freter","year":"1983","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2023.05.029_bib8","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":"Freter","year":"1983","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2023.05.029_bib9","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":"Brugiroux","year":"2016","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2023.05.029_bib10","doi-asserted-by":"crossref","first-page":"1680","DOI":"10.1016\/j.chom.2021.09.004","article-title":"E.\u00a0coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source","volume":"29","author":"Eberl","year":"2021","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2023.05.029_bib11","doi-asserted-by":"crossref","DOI":"10.1093\/femsre\/fuac008","article-title":"The microbial ecology of Escherichia coli in the vertebrate gut","volume":"46","author":"Foster-Nyarko","year":"2022","journal-title":"FEMS Microbiol. Rev."},{"key":"10.1016\/j.chom.2023.05.029_bib12","doi-asserted-by":"crossref","first-page":"2306","DOI":"10.1038\/s41396-019-0435-7","article-title":"Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults","volume":"13","author":"Martinson","year":"2019","journal-title":"ISME J."},{"key":"10.1016\/j.chom.2023.05.029_bib13","doi-asserted-by":"crossref","first-page":"e69744","DOI":"10.7554\/eLife.69744","article-title":"Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut","volume":"10","author":"Bakkeren","year":"2021","journal-title":"eLife"},{"key":"10.1016\/j.chom.2023.05.029_bib14","doi-asserted-by":"crossref","first-page":"e0123039","DOI":"10.1371\/journal.pone.0123039","article-title":"Factors that affect transfer of the IncI1 \u03b2-lactam resistance plasmid pESBL-283 between E. coli Strains","volume":"10","author":"H\u00e4ndel","year":"2015","journal-title":"PLoS One"},{"key":"10.1016\/j.chom.2023.05.029_bib15","doi-asserted-by":"crossref","first-page":"e1004527","DOI":"10.1371\/journal.ppat.1004527","article-title":"Intraspecies competition for niches in the distal gut dictate transmission during persistent salmonella infection","volume":"10","author":"Lam","year":"2014","journal-title":"PLoS Pathog."},{"key":"10.1016\/j.chom.2023.05.029_bib16","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":"Sorbara","year":"2019","journal-title":"Mucosal Immunol."},{"key":"10.1016\/j.chom.2023.05.029_bib17","doi-asserted-by":"crossref","first-page":"e0206214","DOI":"10.1371\/journal.pone.0206214","article-title":"Microbiota stability in healthy individuals after single-dose lactulose challenge\u2014a randomized controlled study","volume":"13","author":"Wotzka","year":"2018","journal-title":"PLoS One"},{"key":"10.1016\/j.chom.2023.05.029_bib18","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41586-019-1521-8","article-title":"Salmonella persisters promote the spread of antibiotic resistance plasmids in the gut","volume":"573","author":"Bakkeren","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.chom.2023.05.029_bib19","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1038\/s41564-021-00879-y","article-title":"Pervasive transmission of a carbapenem resistance plasmid in the gut microbiota of hospitalized patients","volume":"6","author":"Le\u00f3n-Sampedro","year":"2021","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2023.05.029_bib20","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1111\/zph.12453","article-title":"Relationship between Salmonella infection, shedding and serology in fattening pigs in low\u2013moderate prevalence areas","volume":"65","author":"San Rom\u00e1n","year":"2018","journal-title":"Zoonoses Public Health"},{"key":"10.1016\/j.chom.2023.05.029_bib21","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nrmicro2298","article-title":"The population genetics of commensal Escherichia coli","volume":"8","author":"Tenaillon","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.chom.2023.05.029_bib22","doi-asserted-by":"crossref","first-page":"167","DOI":"10.2147\/IDR.S48820","article-title":"Horizontal gene transfer in the human gastrointestinal tract: potential spread of antibiotic resistance genes","volume":"7","author":"Huddleston","year":"2014","journal-title":"Infect. Drug Resist."},{"key":"10.1016\/j.chom.2023.05.029_bib23","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":"Stecher","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2023.05.029_bib24","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1038\/291238a0","article-title":"Aromatic-dependent Salmonella typhimurium are non-virulent and effective as live vaccines","volume":"291","author":"Hoiseth","year":"1981","journal-title":"Nature"},{"key":"10.1016\/j.chom.2023.05.029_bib25","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1128\/JB.01233-09","article-title":"Short-term signatures of evolutionary change in the Salmonella enterica serovar Typhimurium 14028 genome","volume":"192","author":"Jarvik","year":"2010","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.chom.2023.05.029_bib26","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":"Barthel","year":"2003","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2023.05.029_bib27","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1128\/IAI.01189-07","article-title":"Host transmission of Salmonella enterica serovar Typhimurium is controlled by virulence factors and indigenous intestinal microbiota","volume":"76","author":"Lawley","year":"2008","journal-title":"Infect. Immun."},{"key":"10.1016\/j.chom.2023.05.029_bib28","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1126\/science.1232467","article-title":"Host-derived nitrate boosts growth of E. coli in the inflamed gut","volume":"339","author":"Winter","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.chom.2023.05.029_bib29","doi-asserted-by":"crossref","first-page":"1094","DOI":"10.3201\/eid2206.150554","article-title":"Prospective validation of cessation of contact precautions for extended-spectrum \u03b2-lactamase\u2013producing Escherichia coli","volume":"22","author":"Tschudin-Sutter","year":"2016","journal-title":"Emerging Infect. Dis. J."},{"key":"10.1016\/j.chom.2023.05.029_bib30","doi-asserted-by":"crossref","DOI":"10.1128\/JB.00595-16","article-title":"Genetic characterization of the galactitol utilization pathway of Salmonella enterica serovar Typhimurium","volume":"199","author":"Nolle","year":"2017","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.chom.2023.05.029_bib31","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s42523-021-00082-8","article-title":"A diet-specific microbiota drives Salmonella Typhimurium to adapt its in\u00a0vivo response to plant-derived substrates","volume":"3","author":"Prax","year":"2021","journal-title":"Anim. Microbiome"},{"key":"10.1016\/j.chom.2023.05.029_bib32","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":"Oliveira","year":"2020","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2023.05.029_bib33","doi-asserted-by":"crossref","first-page":"7055","DOI":"10.1016\/j.psj.2020.09.073","article-title":"Highly nutritious diet resists Salmonella Typhimurium infections by improving intestinal microbiota and morphology in broiler chickens","volume":"99","author":"He","year":"2020","journal-title":"Poult. Sci."},{"key":"10.1016\/j.chom.2023.05.029_bib34","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1126\/science.aba3683","article-title":"High-fat diet\u2013induced colonocyte dysfunction escalates microbiota-derived trimethylamine N-oxide","volume":"373","author":"Yoo","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.chom.2023.05.029_bib35","doi-asserted-by":"crossref","first-page":"2164","DOI":"10.1038\/s41564-019-0568-5","article-title":"Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice","volume":"4","author":"Wotzka","year":"2019","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2023.05.029_bib36","doi-asserted-by":"crossref","DOI":"10.1016\/j.chom.2023.01.017","article-title":"Salmonella-liberated dietary L-arabinose promotes expansion in superspreaders","volume":"31","author":"Ruddle","year":"2023","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2023.05.029_bib37","doi-asserted-by":"crossref","first-page":"698146","DOI":"10.3389\/fcimb.2021.698146","article-title":"L-arabinose transport and metabolism in salmonella influences biofilm formation","volume":"11","author":"Vasicek","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.chom.2023.05.029_bib38","doi-asserted-by":"crossref","first-page":"12879","DOI":"10.1073\/pnas.0603038103","article-title":"How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains","volume":"103","author":"Brzuszkiewicz","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.chom.2023.05.029_bib39","doi-asserted-by":"crossref","first-page":"4470","DOI":"10.1111\/mec.15232","article-title":"Long-term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon","volume":"28","author":"Ghalayini","year":"2019","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.chom.2023.05.029_bib40","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1038\/s41579-020-0378-z","article-title":"Evolutionary causes and consequences of bacterial antibiotic persistence","volume":"18","author":"Bakkeren","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.chom.2023.05.029_bib41","doi-asserted-by":"crossref","first-page":"e1001221","DOI":"10.1371\/journal.pbio.1001221","article-title":"Recognition and degradation of plant cell wall polysaccharides by two human gut symbionts","volume":"9","author":"Martens","year":"2011","journal-title":"PLoS Biol."},{"key":"10.1016\/j.chom.2023.05.029_bib42","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/0305-1978(88)90095-6","article-title":"Sorbitol and dulcitol in some celastraceous and rosaceous plants, hosts of Yponomeuta spp","volume":"16","author":"Fung","year":"1988","journal-title":"Biochem. Syst. Ecol."},{"key":"10.1016\/j.chom.2023.05.029_bib43","doi-asserted-by":"crossref","first-page":"e1004182","DOI":"10.1371\/journal.pgen.1004182","article-title":"The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps","volume":"10","author":"Barroso-Batista","year":"2014","journal-title":"PLoS Genet."},{"key":"10.1016\/j.chom.2023.05.029_bib44","doi-asserted-by":"crossref","first-page":"2879","DOI":"10.1093\/molbev\/msx221","article-title":"Recurrent reverse evolution maintains polymorphism after strong bottlenecks in commensal gut bacteria","volume":"34","author":"Sousa","year":"2017","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.chom.2023.05.029_bib45","doi-asserted-by":"crossref","first-page":"e14712","DOI":"10.1371\/journal.pone.0014712","article-title":"E.\u00a0coli Nissle 1917 affects salmonella adhesion to porcine intestinal epithelial cells","volume":"6","author":"Schierack","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.chom.2023.05.029_bib46","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1126\/science.277.5331.1453","article-title":"The Complete Genome Sequence of Escherichia coli K-12","volume":"277","author":"Blattner","year":"1997","journal-title":"Science"},{"key":"10.1016\/j.chom.2023.05.029_bib47","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/0076-6879(91)04004-8","article-title":"Bacteriophage-mediated generalized transduction in Escherichia coli and Salmonella typhimurium","volume":"204","author":"Sternberg","year":"1991","journal-title":"Methods Enzymol."},{"key":"10.1016\/j.chom.2023.05.029_bib48","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":"Datsenko","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Cell Host & Microbe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312823002226?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312823002226?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T12:31:32Z","timestamp":1761827492000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1931312823002226"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,7]]},"references-count":48,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2023,7]]}},"alternative-id":["S1931312823002226"],"URL":"https:\/\/doi.org\/10.1016\/j.chom.2023.05.029","relation":{},"ISSN":["1931-3128"],"issn-type":[{"value":"1931-3128","type":"print"}],"subject":[],"published":{"date-parts":[[2023,7]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Differences in carbon metabolic capacity fuel co-existence and plasmid transfer between Salmonella strains in the mouse gut","name":"articletitle","label":"Article Title"},{"value":"Cell Host & Microbe","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.chom.2023.05.029","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}