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Within a healthy human its population structure is highly dynamic, where typically a dominant <jats:italic>E. coli<\/jats:italic> strain is accompanied by several low abundance satellite strains. However, the factors underlying <jats:italic>E. coli<\/jats:italic> strain dynamics and evolution within hosts are still poorly understood. Here, we colonised germ-free immune-competent (wild-type) or immune-compromised (<jats:italic>Rag2KO<\/jats:italic>) mice, with two phylogenetically distinct strains of <jats:italic>E. coli<\/jats:italic>, to determine if strain co-existence and within-strain evolution are shaped by the adaptive immune system. Irrespectively of the immune status of the mice one strain reaches a 100-fold larger abundance than the other. However, the abundance of the dominant strain is significantly higher in <jats:italic>Rag2KO<\/jats:italic> mice. Strains co-exist for thousands of generations and accumulate beneficial mutations in genes coding for different resource preferences. A higher rate of mutation accumulation in immune-compromised <jats:italic>vs.<\/jats:italic> immune-competent mice is observed and adaptative mutations specific to immune-competent mice are identified. Importantly, the presence of the adaptive immune system selects for mutations that increase stress resistance and the dynamics of such evolutionary events associates with the onset of an antibody response.<\/jats:p>","DOI":"10.1371\/journal.ppat.1012442","type":"journal-article","created":{"date-parts":[[2025,4,24]],"date-time":"2025-04-24T17:21:38Z","timestamp":1745515298000},"page":"e1012442","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Evolution of Escherichia coli strains under competent or compromised adaptive immunity"],"prefix":"10.1371","volume":"21","author":[{"given":"Camille","family":"Ameline","sequence":"first","affiliation":[]},{"given":"Elsa","family":"Seixas","sequence":"additional","affiliation":[]},{"given":"Hugo C.","family":"Barreto","sequence":"additional","affiliation":[]},{"given":"Nelson","family":"Fraz\u00e3o","sequence":"additional","affiliation":[]},{"given":"Miguel V.","family":"Rodrigues","sequence":"additional","affiliation":[]},{"given":"M. Rita","family":"Ventura","sequence":"additional","affiliation":[]},{"given":"Marta","family":"Louren\u00e7o","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1622-5143","authenticated-orcid":true,"given":"Isabel","family":"Gordo","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2025,4,24]]},"reference":[{"issue":"3","key":"ppat.1012442.ref001","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nrmicro2298","article-title":"The population genetics of commensal Escherichia coli","volume":"8","author":"O Tenaillon","year":"2010","journal-title":"Nat Rev Microbiol"},{"issue":"10369","key":"ppat.1012442.ref002","doi-asserted-by":"crossref","first-page":"2221","DOI":"10.1016\/S0140-6736(22)02185-7","article-title":"Global mortality associated with 33 bacterial pathogens in 2019: a systematic analysis for the Global Burden of Disease Study 2019","volume":"400","author":"GBD 2019 Antimicrobial Resistance Collaborators","year":"2022","journal-title":"Lancet"},{"key":"ppat.1012442.ref003","doi-asserted-by":"crossref","first-page":"2912","DOI":"10.1016\/j.celrep.2016.03.015","article-title":"Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants","volume":"14","author":"DV Ward","year":"2016","journal-title":"Cell Reports"},{"issue":"2","key":"ppat.1012442.ref004","doi-asserted-by":"crossref","first-page":"e00060-18","DOI":"10.1128\/CMR.00060-18","article-title":"Escherichia coli Pathobionts Associated with Inflammatory Bowel Disease","volume":"32","author":"HC Mirsepasi-Lauridsen","year":"2019","journal-title":"Clin Microbiol Rev"},{"issue":"3","key":"ppat.1012442.ref005","doi-asserted-by":"crossref","first-page":"fuac008","DOI":"10.1093\/femsre\/fuac008","article-title":"The microbial ecology of Escherichia coli in the vertebrate gut","volume":"46","author":"E Foster-Nyarko","year":"2022","journal-title":"FEMS Microbiol Rev"},{"issue":"3","key":"ppat.1012442.ref006","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1093\/genetics\/98.3.467","article-title":"Genetic diversity and temporal variation in the E. coli population of a human host","volume":"98","author":"DA Caugant","year":"1981","journal-title":"Genetics"},{"issue":"2","key":"ppat.1012442.ref007","doi-asserted-by":"crossref","first-page":"110239","DOI":"10.1016\/j.celrep.2021.110239","article-title":"Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome","volume":"38","author":"D Hu","year":"2022","journal-title":"Cell Rep"},{"issue":"1","key":"ppat.1012442.ref008","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1038\/s41579-020-0416-x","article-title":"The population genetics of pathogenic Escherichia coli","volume":"19","author":"E Denamur","year":"2021","journal-title":"Nat Rev 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Zaneveld","year":"2017","journal-title":"Nat Microbiol"},{"issue":"1","key":"ppat.1012442.ref034","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/bies.201600176","article-title":"What drives parallel evolution?: How population size and mutational variation contribute to repeated evolution","volume":"39","author":"SF Bailey","year":"2017","journal-title":"Bioessays"},{"issue":"11","key":"ppat.1012442.ref035","doi-asserted-by":"crossref","first-page":"3213","DOI":"10.1111\/j.1558-5646.2010.01058.x","article-title":"Fisher\u2019s model and the genomics of adaptation: restricted pleiotropy, heterogenous mutation, and parallel evolution","volume":"64","author":"L-M Chevin","year":"2010","journal-title":"Evolution"},{"issue":"1","key":"ppat.1012442.ref036","first-page":"216","article-title":"The probability of parallel evolution","volume":"59","author":"HA Orr","year":"2005","journal-title":"Evolution"},{"issue":"19","key":"ppat.1012442.ref037","doi-asserted-by":"crossref","first-page":"2811","DOI":"10.1093\/bioinformatics\/btu393","article-title":"circlize Implements and enhances circular visualization in R","volume":"30","author":"Z Gu","year":"2014","journal-title":"Bioinformatics"},{"issue":"2","key":"ppat.1012442.ref038","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1111\/mmi.14608","article-title":"Transcriptional regulation of the N\u03b5 -fructoselysine metabolism in Escherichia coli by global and substrate-specific cues","volume":"115","author":"B Graf von Armansperg","year":"2021","journal-title":"Mol Microbiol"},{"issue":"Pt 3","key":"ppat.1012442.ref039","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1042\/bj20031527","article-title":"Fructoselysine 3-epimerase, an enzyme involved in the metabolism of the unusual Amadori compound psicoselysine in Escherichia coli","volume":"378","author":"E Wiame","year":"2004","journal-title":"Biochem J"},{"issue":"4","key":"ppat.1012442.ref040","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1111\/mmi.12573","article-title":"Interplay of transcriptional and small RNA-dependent control mechanisms regulates chitosugar uptake in Escherichia coli and Salmonella","volume":"92","author":"J Plumbridge","year":"2014","journal-title":"Mol Microbiol"},{"issue":"2","key":"ppat.1012442.ref041","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1042\/bj1320341","article-title":"The utilization of fructose by Escherichia coli. Properties of a mutant defective in fructose 1-phosphate kinase activity","volume":"132","author":"T Ferenci","year":"1973","journal-title":"Biochem J"},{"issue":"9","key":"ppat.1012442.ref042","doi-asserted-by":"crossref","first-page":"2672","DOI":"10.1128\/JB.182.9.2672-2674.2000","article-title":"A common regulator for the operons encoding the enzymes involved in D-galactarate, D-glucarate, and D-glycerate utilization in Escherichia coli","volume":"182","author":"R Monterrubio","year":"2000","journal-title":"J Bacteriol"},{"issue":"1","key":"ppat.1012442.ref043","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1046\/j.1365-2958.1998.00764.x","article-title":"The Escherichia coli ATP-binding cassette (ABC) proteins","volume":"28","author":"KJ Linton","year":"1998","journal-title":"Mol Microbiol"},{"issue":"1","key":"ppat.1012442.ref044","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1006\/jmbi.2000.4284","article-title":"Projection structure of the monomeric porin 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Dorich","year":"2019","journal-title":"Genes Dev"},{"issue":"2","key":"ppat.1012442.ref048","doi-asserted-by":"crossref","first-page":"e107","DOI":"10.1002\/imt2.107","article-title":"Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp","volume":"2","author":"S Chen","year":"2023","journal-title":"Imeta"},{"issue":"21","key":"ppat.1012442.ref049","doi-asserted-by":"crossref","first-page":"3340","DOI":"10.1093\/bioinformatics\/btx433","article-title":"ISEScan: automated identification of insertion sequence elements in prokaryotic genomes","volume":"33","author":"Z Xie","year":"2017","journal-title":"Bioinformatics"},{"key":"ppat.1012442.ref050","doi-asserted-by":"crossref","first-page":"468","DOI":"10.3389\/fgene.2014.00468","article-title":"Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq","volume":"5","author":"DE Deatherage","year":"2015","journal-title":"Front 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Armarego","year":"2009"},{"key":"ppat.1012442.ref055","volume-title":"Encyclopedia of biological chemistry","author":"J Jez","year":"2021"},{"issue":"Pt 3","key":"ppat.1012442.ref056","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1042\/bj20020325","article-title":"Fructosamine 3-kinase is involved in an intracellular deglycation pathway in human erythrocytes","volume":"365","author":"G Delpierre","year":"2002","journal-title":"Biochem J"}],"container-title":["PLOS 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