{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T02:50:26Z","timestamp":1792637426675,"version":"4.5.0"},"reference-count":331,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2022,2,4]],"date-time":"2022-02-04T00:00:00Z","timestamp":1643932800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Escherichia coli has a rich history as biology's \u2018rock star\u2019, driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance\u2014including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.<\/jats:p>","DOI":"10.1093\/femsre\/fuac008","type":"journal-article","created":{"date-parts":[[2022,2,2]],"date-time":"2022-02-02T07:19:28Z","timestamp":1643786368000},"source":"Crossref","is-referenced-by-count":140,"title":["The microbial ecology of\n                    <i>Escherichia coli<\/i>\n                    in the vertebrate gut"],"prefix":"10.1093","volume":"46","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6620-9403","authenticated-orcid":false,"given":"Ebenezer","family":"Foster-Nyarko","sequence":"first","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park , Norwich, NR4 7UQ, United Kingdom"},{"name":"Norwich Medical School, University of East Anglia, Norwich Research Park , Norwich, NR4 7TJ, United Kingdom"},{"name":"Department of Infection Biology, London School of Hygiene and Tropical Medicine , Keppel Street , London WC1E 7HT, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark J","family":"Pallen","sequence":"additional","affiliation":[{"name":"Quadram Institute Bioscience, Norwich Research Park , Norwich, NR4 7UQ, United Kingdom"},{"name":"School of Veterinary Medicine, University of Surrey , Guildford, Surrey, GU2 7AL, United Kingdom"},{"name":"School of Biological Sciences, University of East Anglia, Norwich Research Park , Norwich, NR4 7TU, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,2,4]]},"reference":[{"key":"2022070111263263700_bib1","first-page":"849","article-title":"Dirty money on holy ground: isolation of potentially pathogenic bacteria and fungi on money collected from church offerings","volume":"48","author":"Abia","year":"2019","journal-title":"Iran J Public Health"},{"key":"2022070111263263700_bib2","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1128\/iai.51.1.268-276.1986","article-title":"Clonal analysis of Escherichiacoli O2:K1 isolated from diseased humans and animals","volume":"51","author":"Achtman","year":"1986","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib3","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.ijfoodmicro.2018.04.018","article-title":"Enteroaggregative Escherichiacoli is the predominant diarrheagenic E. coli pathotype among irrigation water and food sources in South Africa","volume":"278","author":"Aijuka","year":"2018","journal-title":"Int J Food Microbiol"},{"key":"2022070111263263700_bib4","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/1756-0500-7-16","article-title":"Public health implications of contamination of Franc CFA (XAF) circulating in Buea (Cameroon) with drug resistant pathogens","volume":"7","author":"Akoachere","year":"2014","journal-title":"BMC Res Notes"},{"key":"2022070111263263700_bib5","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1128\/iai.59.4.1507-1513.1991","article-title":"Hafnia alvei, a probable cause of diarrhea in humans","volume":"59","author":"Albert","year":"1991","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib6","doi-asserted-by":"crossref","first-page":"1699","DOI":"10.3201\/eid1910.130309","article-title":"Multidrug-resistant Escherichiacoli bacteremia","volume":"19","author":"Alhashash","year":"2013","journal-title":"Emerg Infect Dis"},{"key":"2022070111263263700_bib7","first-page":"67","volume-title":"Population Genetics of Bacteria: A tribute to Thomas S. Whittam","author":"Alm","year":"2011"},{"key":"2022070111263263700_bib8","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/S0928-8244(03)00368-7","article-title":"The probiotic Escherichiacoli strain Nissle 1917 interferes with invasion of human intestinal epithelial cells by different enteroinvasive bacterial pathogens","volume":"40","author":"Altenhoefer","year":"2004","journal-title":"FEMS Immunol Med Microbiol"},{"key":"2022070111263263700_bib9","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1016\/S0959-437X(99)00024-6","article-title":"Insights into the evolutionary process of genome degradation","volume":"9","author":"Andersson","year":"1999","journal-title":"Curr Opin Genet Dev"},{"key":"2022070111263263700_bib10","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1126\/science.1104816","article-title":"Host-bacterial mutualism in the human intestine","volume":"307","author":"B\u00e4ckhed","year":"2005","journal-title":"Science"},{"key":"2022070111263263700_bib316_1645528955624","doi-asserted-by":"crossref","first-page":"953","DOI":"10.4014\/jmb.1412.12079","article-title":"Production of biopharmaceuticals in E. coli: Current scenario and future perspectives","volume":"25","author":"Baeshen","year":"2015","journal-title":"J Microbiol Biotechnol"},{"key":"2022070111263263700_bib11","doi-asserted-by":"crossref","first-page":"4997","DOI":"10.1128\/AAC.02824-14","article-title":"A new clone sweeps clean: the enigmatic emergence of Escherichiacoli sequence type 131","volume":"58","author":"Banerjee","year":"2014","journal-title":"Antimicrob Agents Chemother"},{"key":"2022070111263263700_bib12","doi-asserted-by":"crossref","first-page":"e000192","DOI":"10.1099\/mgen.0.000192","article-title":"ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping","volume":"4","author":"Beghain","year":"2018","journal-title":"Microb Genomics"},{"key":"2022070111263263700_bib13","first-page":"e00347","article-title":"Sequential acquisition of virulence and fluoroquinolone resistance has shaped the evolution of Escherichiacoli ST131","volume":"7","author":"Ben\u00a0Zakour","year":"2016","journal-title":"Mbio"},{"key":"2022070111263263700_bib14","doi-asserted-by":"crossref","first-page":"49","DOI":"10.3390\/antibiotics9020049","article-title":"Overview of evidence of antimicrobial use and antimicrobial resistance in the food chain","volume":"9","author":"Bennani","year":"2020","journal-title":"Antibiotics"},{"key":"2022070111263263700_bib15","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1038\/s41396-020-00819-4","article-title":"Plasmid- and strain-specific factors drive variation in ESBL-plasmid spread in vitro and in vivo","volume":"15","author":"Benz","year":"2021","journal-title":"ISME J"},{"key":"2022070111263263700_bib16","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1016\/0966-842X(96)10057-3","article-title":"The indigenous gastrointestinal microflora","volume":"4","author":"Berg","year":"1996","journal-title":"Trends Microbiol"},{"key":"2022070111263263700_bib17","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1111\/j.1462-2920.2010.02334.x","article-title":"Enterohaemorrhagic Escherichiacoli gains a competitive advantage by using ethanolamine as a nitrogen source in the bovine intestinal content","volume":"13","author":"Bertin","year":"2011","journal-title":"Environ Microbiol"},{"key":"2022070111263263700_bib18","first-page":"1223","article-title":"Serotypes of Escherichiacoli in normal stools","volume":"2","author":"Bettelheim","year":"1972","journal-title":"Lancet"},{"key":"2022070111263263700_bib19","first-page":"255","article-title":"Commemoration of the publication 100 years ago of the papers by Dr. Th. Escherich in which are described for the first time the organisms that bear his name","volume":"261","author":"Bettelheim","year":"1986","journal-title":"Zentralbl Bakteriol Mikrobiol Hyg A"},{"key":"2022070111263263700_bib20","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1002\/emmm.201303133","article-title":"Heteropathogenic virulence and phylogeny reveal phased pathogenic metamorphosis in Escherichiacoli O2:H6","volume":"6","author":"Bielaszewska","year":"2014","journal-title":"EMBO Mol Med"},{"key":"2022070111263263700_bib22","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1126\/science.277.5331.1453","article-title":"The complete genome sequence of Escherichiacoli K-12","volume":"277","author":"Blattner","year":"1997","journal-title":"Science"},{"key":"2022070111263263700_bib21","first-page":"719","article-title":"Biological frontiers","volume-title":"Science","author":"Blattner","year":"1983"},{"key":"2022070111263263700_bib323_1645530317658","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1038\/nature11514","article-title":"Genomic analysis of a key innovation in an experimental Escherichia coli population","volume":"489","author":"Blount","year":"2012","journal-title":"Nature"},{"key":"2022070111263263700_bib23","doi-asserted-by":"crossref","first-page":"e05826","DOI":"10.7554\/eLife.05826","article-title":"The unexhausted potential of E. coli","volume":"4","author":"Blount","year":"2015","journal-title":"Elife"},{"key":"2022070111263263700_bib330_1645541132568","doi-asserted-by":"crossref","first-page":"e0136387","DOI":"10.1371\/journal.pone.0136387","article-title":"Genomic and phenomic study of mammary pathogenic Escherichia coli","volume":"10","author":"Blum","year":"2015","journal-title":"PLoS One"},{"key":"2022070111263263700_bib24","doi-asserted-by":"crossref","first-page":"2162","DOI":"10.1111\/1462-2920.12088","article-title":"High temporal variability in commensal Escherichiacoli strain communities of a herbivorous marsupial","volume":"15","author":"Blyton","year":"2013","journal-title":"Environ Microbiol"},{"key":"2022070111263263700_bib25","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1080\/01652176.1995.9694555","article-title":"Antimicrobial resistance of Escherichiacoli isolates from the faecal flora of veterinarians with different professional specialties","volume":"17","author":"Bongers","year":"1995","journal-title":"Vet Q"},{"key":"2022070111263263700_bib26","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1089\/fpd.2019.2680","article-title":"Escherichia coli from commercial broiler and backyard chickens share sequence types, antimicrobial resistance profiles, and resistance genes with human extraintestinal pathogenic Escherichiacoli","volume":"16","author":"Borges","year":"2019","journal-title":"Foodborne Pathog Dis"},{"key":"2022070111263263700_bib27","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1046\/j.1365-2036.2003.01638.x","article-title":"Inhibitory effect of probiotic Escherichiacoli strain Nissle 1917 on adhesion to and invasion of intestinal epithelial cells by adherent-invasive E. coli strains isolated from patients with Crohn's disease","volume":"18","author":"Boudeau","year":"2003","journal-title":"Aliment Pharmacol Ther"},{"key":"2022070111263263700_bib28","first-page":"101","article-title":"Influence of oral antibiotics on resistance and enterotoxigenicity of Escherichiacoli","volume":"44","author":"Bourque","year":"1980","journal-title":"Can J Comp Med"},{"key":"2022070111263263700_bib29","doi-asserted-by":"crossref","first-page":"198","DOI":"10.3181\/00379727-114-28624","article-title":"Effect of colicine production on Escherichiacoli in the normal human intestine","volume":"114","author":"Branche","year":"1963","journal-title":"Exp Biol Med"},{"key":"2022070111263263700_bib30","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1128\/jcm.15.4.703-713.1982","article-title":"Atypical biogroups of Escherichiacoli found in clinical specimens and description of Escherichiahermannii sp. nov","volume":"15","author":"Brenner","year":"1982","journal-title":"J Clin Microbiol"},{"key":"2022070111263263700_bib31","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1128\/jcm.15.6.1133-1140.1982","article-title":"Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds","volume":"15","author":"Brenner","year":"1982","journal-title":"J Clin Microbiol"},{"key":"2022070111263263700_bib32","first-page":"56","article-title":"Probiotics and medical nutrition therapy","volume":"7","author":"Brown","year":"2004","journal-title":"Nutr Clin Care"},{"key":"2022070111263263700_bib33","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1093\/cid\/ciw678","article-title":"Antimicrobial resistance: a call to action!","volume":"64","author":"Brown","year":"2017","journal-title":"Clin Infect Dis"},{"key":"2022070111263263700_bib34","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.2217\/fmb.12.108","article-title":"Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences","volume":"7","author":"Bryant","year":"2012","journal-title":"Fut Microbiol"},{"key":"2022070111263263700_bib35","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1128\/IAI.05496-11","article-title":"Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridiumdifficile-induced colitis","volume":"80","author":"Buffie","year":"2012","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib36","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/nri3535","article-title":"Microbiota-mediated colonization resistance against intestinal pathogens","volume":"13","author":"Buffie","year":"2013","journal-title":"Nat Rev Immunol"},{"key":"2022070111263263700_bib37","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1017\/S0022172400046155","article-title":"Aerobic bacteria occurring in the hind-gut of the cockroach, Blattaorientalis","volume":"71","author":"Burgess","year":"1973","journal-title":"J Hyg"},{"key":"2022070111263263700_bib38","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1093\/emph\/eov018","article-title":"Horizontal gene transfer","volume":"2015","author":"Burmeister","year":"2015","journal-title":"Evol Med Public Health"},{"key":"2022070111263263700_bib39","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1136\/gutjnl-2014-307345","article-title":"Progressive genomic convergence of two Helicobacterpylori strains during mixed infection of a patient with chronic gastritis","volume":"64","author":"Cao","year":"2015","journal-title":"Gut"},{"key":"2022070111263263700_bib313_1645528131461","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1242\/jeb.203.1.29","article-title":"Cross-linking and electron microscopy studies of the structure and functioning of the Escherichia coli ATP synthase","volume":"203","author":"Capaldi","year":"2000","journal-title":"J Exp Biol"},{"key":"2022070111263263700_bib40","doi-asserted-by":"crossref","first-page":"2466","DOI":"10.3382\/ps.2007-00249","article-title":"History of the use of antibiotic as growth promoters in European poultry feeds","volume":"86","author":"Castanon","year":"2007","journal-title":"Poult Sci"},{"key":"2022070111263263700_bib41","doi-asserted-by":"crossref","first-page":"941","DOI":"10.5962\/bhl.title.84653","volume-title":"Manual of Tropical Medicine","author":"Castellani","year":"1919","edition":"3rd edn"},{"key":"2022070111263263700_bib42","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":"Caugant","year":"1981","journal-title":"Genetics"},{"key":"2022070111263263700_bib43","doi-asserted-by":"crossref","first-page":"7427","DOI":"10.1073\/pnas.0307888101","article-title":"Carbon nutrition of Escherichiacoli in the mouse intestine","volume":"101","author":"Chang","year":"2004","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022070111263263700_bib44","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/nrg2526","article-title":"Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation","volume":"10","author":"Charlesworth","year":"2009","journal-title":"Nat Rev Genet"},{"key":"2022070111263263700_bib45","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.meegid.2012.01.005","article-title":"The evolution of the Escherichiacoli phylogeny","volume":"12","author":"Chaudhuri","year":"2012","journal-title":"Infect Genet Evol"},{"key":"2022070111263263700_bib46","doi-asserted-by":"crossref","first-page":"e8801","DOI":"10.1371\/journal.pone.0008801","article-title":"Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichiacoli strain 042","volume":"5","author":"Chaudhuri","year":"2010","journal-title":"PLoS ONE"},{"key":"2022070111263263700_bib47","doi-asserted-by":"crossref","first-page":"1925","DOI":"10.1093\/bioinformatics\/btz848","article-title":"GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database","volume":"36","author":"Chaumeil","year":"2019","journal-title":"Bioinformatics"},{"key":"2022070111263263700_bib48","doi-asserted-by":"crossref","first-page":"184ra160","DOI":"10.1126\/scitranslmed.3005497","article-title":"Genomic diversity and fitness of E. coli strains recovered from the intestinal and urinary tracts of women with recurrent urinary tract infection","volume":"5","author":"Chen","year":"2013","journal-title":"Sci Transl Med"},{"key":"2022070111263263700_bib49","doi-asserted-by":"crossref","first-page":"470","DOI":"10.3389\/fmicb.2016.00470","article-title":"Antimicrobial drugs in fghting against antimicrobial resistance","volume":"7","author":"Cheng","year":"2016","journal-title":"Front Microbiol"},{"key":"2022070111263263700_bib50","doi-asserted-by":"crossref","first-page":"e6669","DOI":"10.1371\/journal.pone.0006669","article-title":"Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine","volume":"4","author":"Claesson","year":"2009","journal-title":"PLoS ONE"},{"key":"2022070111263263700_bib51","doi-asserted-by":"crossref","first-page":"16003","DOI":"10.1038\/npjbiofilms.2016.3","article-title":"The gut microbiota: a major player in the toxicity of environmental pollutants?","volume":"2","author":"Claus","year":"2016","journal-title":"NPJ Biofilms Microbiomes"},{"key":"2022070111263263700_bib52","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1111\/1758-2229.12019","article-title":"The clermont Escherichiacoli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups","volume":"5","author":"Clermont","year":"2013","journal-title":"Environ Microbiol Rep"},{"key":"2022070111263263700_bib53","doi-asserted-by":"crossref","first-page":"2468","DOI":"10.1111\/j.1462-2920.2011.02519.x","article-title":"Characterization of the cryptic Escherichia lineages: rapid identification and prevalence","volume":"13","author":"Clermont","year":"2011","journal-title":"Environ Microbiol"},{"key":"2022070111263263700_bib54","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1007\/s10620-009-0934-x","article-title":"A molecular analysis of fecal and mucosal bacterial communities in irritable bowel syndrome","volume":"55","author":"Codling","year":"2010","journal-title":"Dig Dis Sci"},{"key":"2022070111263263700_bib55","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1093\/jac\/dkz484","article-title":"Escherichia coli O80 hybrid pathotype strains producing Shiga toxin and ESBL: molecular characterization and potential therapeutic options","volume":"75","author":"Cointe","year":"2020","journal-title":"J Antimicrob Chemother"},{"key":"2022070111263263700_bib56","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/microbiolspec.MBP-0006-2014","article-title":"Commensal and pathogenic Escherichiacoli metabolism in the gut","volume":"3","author":"Conway","year":"2015","journal-title":"Microbiol Spectr"},{"key":"2022070111263263700_bib321_1645530063260","doi-asserted-by":"crossref","first-page":"e225","DOI":"10.1371\/journal.pbio.0050225","article-title":"Recombination speeds adaptation by reducing competition between beneficial mutations in populations of Escherichia coli","volume":"5","author":"Cooper","year":"2007","journal-title":"PLoS Biol"},{"key":"2022070111263263700_bib57","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/cid\/cir849","article-title":"HIV-1 dual infection is associated with faster CD4+ T-cell decline in a cohort of men with primary HIV infection","volume":"54","author":"Cornelissen","year":"2012","journal-title":"Clin Infect Dis"},{"key":"2022070111263263700_bib302_1645525900189","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1038\/1921227a0","article-title":"General nature of the genetic code for proteins","volume":"192","author":"Crick","year":"1961","journal-title":"Nature"},{"key":"2022070111263263700_bib58","doi-asserted-by":"crossref","first-page":"2501","DOI":"10.1093\/jac\/dkr349","article-title":"Molecular epidemiology of extraintestinal pathogenic Escherichiacoli isolates from a regional cohort of elderly patients highlights the prevalence of ST131 strains with increased antimicrobial resistance in both community and hospital care settings","volume":"66","author":"Croxall","year":"2011","journal-title":"J Antimicrob Chemother"},{"key":"2022070111263263700_bib59","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1038\/nrmicro2265","article-title":"Molecular mechanisms of Escherichiacoli pathogenicity","volume":"8","author":"Croxen","year":"2010","journal-title":"Nat Rev Microbiol"},{"key":"2022070111263263700_bib60","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1017\/S095026880900226X","article-title":"Escherichia coli shedding patterns in humans and dogs: insights into within-household transmission of phylotypes associated with urinary tract infections","volume":"137","author":"Damborg","year":"2009","journal-title":"Epidemiol Infect"},{"key":"2022070111263263700_bib61","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1136\/bmj.2.5654.407","article-title":"Drug resistance and R factors in the bowel bacteria of London patients before and after admission to hospital","volume":"2","author":"Datta","year":"1969","journal-title":"BMJ"},{"key":"2022070111263263700_bib62","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1038\/nature12820","article-title":"Diet rapidly and reproducibly alters the human gut microbiome","volume":"505","author":"David","year":"2014","journal-title":"Nature"},{"key":"2022070111263263700_bib63","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1111\/j.1751-0813.1978.tb00316.x","article-title":"Transferable drug resistance in man and animals: genetic relationship between R-plasmids in enteric bacteria from man and domestic pets","volume":"54","author":"Davies","year":"1978","journal-title":"Aust Vet J"},{"key":"2022070111263263700_bib64","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1111\/1469-0691.12028","article-title":"The changing epidemiology of bacteraemias in Europe: trends from the European Antimicrobial Resistance Surveillance System","volume":"19","author":"de\u00a0Kraker","year":"2013","journal-title":"Clin Microbiol Infect"},{"key":"2022070111263263700_bib65","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/S0966-842X(00)01703-0","article-title":"Horizontal gene transfer and the origin of species: lessons from bacteria","volume":"8","author":"de\u00a0la\u00a0Cruz","year":"2000","journal-title":"Trends Microbiol"},{"key":"2022070111263263700_bib66","first-page":"111","article-title":"Characteristics of Shiga toxin producing- and enteropathogenic Escherichiacoli of the emerging serotype O80:H2 isolated from humans and diarrhoeic calves in Belgium","volume":"25","author":"De\u00a0Rauw","year":"2019","journal-title":"Clin Microbiol Infect"},{"key":"2022070111263263700_bib67","doi-asserted-by":"crossref","first-page":"17394","DOI":"10.1038\/s41598-019-54004-5","article-title":"An Escherichiacoli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates","volume":"9","author":"Decano","year":"2019","journal-title":"Sci Rep"},{"key":"2022070111263263700_bib68","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1038\/s41579-020-0416-x","article-title":"The population genetics of pathogenic Escherichiacoli","volume":"19","author":"Denamur","year":"2020","journal-title":"Nat Rev Microbiol"},{"key":"2022070111263263700_bib69","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.micpath.2018.01.041","article-title":"Virulence factors, antibiotic resistance genes and genetic relatedness of commensal Escherichiacoli isolates from dogs and their owners","volume":"116","author":"Derakhshandeh","year":"2018","journal-title":"Microb Pathog"},{"key":"2022070111263263700_bib70","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.chom.2013.06.007","article-title":"Probiotic bacteria reduce Salmonellatyphimurium intestinal colonization by competing for iron","volume":"14","author":"Deriu","year":"2013","journal-title":"Cell Host Microbe"},{"key":"2022070111263263700_bib71","doi-asserted-by":"crossref","first-page":"e280","DOI":"10.1371\/journal.pbio.0060280","article-title":"The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing","volume":"6","author":"Dethlefsen","year":"2008","journal-title":"PLoS Biol"},{"key":"2022070111263263700_bib72","doi-asserted-by":"crossref","first-page":"192","DOI":"10.3390\/antibiotics9040192","article-title":"Genomic characterization of Escherichia coli isolates belonging to a new hybrid aEPEC\/ExPEC pathotype O153:H10-A-ST10 eae-beta1 occurred in meat, poultry, wildlife and human diarrheagenic samples","volume":"9","author":"D\u00edaz-Jim\u00e9nez","year":"2020","journal-title":"Antibiotics"},{"key":"2022070111263263700_bib73","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1186\/1471-2164-13-256","article-title":"Impact of homologous and non-homologous recombination in the genomic evolution of Escherichiacoli","volume":"13","author":"Didelot","year":"2012","journal-title":"BMC Genomics"},{"key":"2022070111263263700_bib74","doi-asserted-by":"crossref","first-page":"13880","DOI":"10.1073\/pnas.1304681110","article-title":"Genomic evolution and transmission of Helicobacterpylori in two South African families","volume":"110","author":"Didelot","year":"2013","journal-title":"Proc Natl Acad Sci"},{"key":"2022070111263263700_bib75","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1038\/nrmicro.2015.13","article-title":"Within-host evolution of bacterial pathogens","volume":"14","author":"Didelot","year":"2016","journal-title":"Nat Rev Microbiol"},{"key":"2022070111263263700_bib76","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1111\/1462-2920.14028","article-title":"Within-host evolution versus immigration as a determinant of Escherichiacoli diversity in the human gastrointestinal tract","volume":"20","author":"Dixit","year":"2018","journal-title":"Environ Microbiol"},{"key":"2022070111263263700_bib331_1645541278698","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.vetmic.2012.03.033","article-title":"Phylogroup and lpfA influence epithelial invasion by mastitis associated Escherichia coli","volume":"159","author":"Dogan","year":"2012","journal-title":"Vet Microbiol"},{"key":"2022070111263263700_bib77","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1038\/ismej.2013.198","article-title":"Syntrophy in microbial fuel cells","volume":"8","author":"Dolfing","year":"2014","journal-title":"ISME J"},{"key":"2022070111263263700_bib78","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.mib.2019.06.004","article-title":"The evolution and transmission of multi-drug resistant Escherichiacoli and Klebsiellapneumoniae: the complexity of clones and plasmids","volume":"51","author":"Dunn","year":"2019","journal-title":"Curr Opin Microbiol"},{"key":"2022070111263263700_bib79","doi-asserted-by":"crossref","first-page":"1671","DOI":"10.1099\/00221287-147-6-1671","article-title":"Commensal Escherichiacoli isolates are phylogenetically distributed among geographically distinct human populations","volume":"147","author":"Duriez","year":"2001","journal-title":"Microbiology"},{"key":"2022070111263263700_bib80","doi-asserted-by":"crossref","first-page":"6466","DOI":"10.1128\/AEM.70.11.6466-6472.2004","article-title":"Measurements of fitness and competition in commensal Escherichiacoli and E. coli O157:H7 strains","volume":"70","author":"Durso","year":"2004","journal-title":"Appl Environ Microbiol"},{"key":"2022070111263263700_bib81","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.ijmm.2014.10.006","article-title":"Heterogenic virulence in a diarrheagenic Escherichiacoli: evidence for an EPEC expressing heat-labile toxin of ETEC","volume":"305","author":"Dutta","year":"2015","journal-title":"Int J Med Microbiol"},{"key":"2022070111263263700_bib305_1645526618647","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1085\/jgp.22.3.365","article-title":"The growth of bacteriophage","volume":"22","author":"Ellis","year":"1939","journal-title":"J Gen Physiol"},{"key":"2022070111263263700_bib82","doi-asserted-by":"crossref","first-page":"8725","DOI":"10.1021\/acs.est.7b01710","article-title":"Animal feces contribute to domestic fecal contamination: evidence from E. coli measured in water, hands, food, flies, and soil in Bangladesh","volume":"51","author":"Ercumen","year":"2017","journal-title":"Environ Sci Technol"},{"key":"2022070111263263700_bib83","first-page":"334","article-title":"Bacterium coli commune","volume-title":"Handbuch der pathogenen mikroorganismen","author":"Escherich","year":"1903"},{"key":"2022070111263263700_bib84","volume-title":"Die darmbakterien des d\u00e4uglings und ihre beziehungen zur physiologie der verdauung","author":"Escherich","year":"1886"},{"key":"2022070111263263700_bib86","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1093\/clinids\/10.6.1220","article-title":"The intestinal bacteria of the neonate and breast-fed infant. 1884","volume":"10","author":"Escherich","year":"1988","journal-title":"Clin Infect Dis"},{"key":"2022070111263263700_bib85","first-page":"243","article-title":"Ueber die bacterien des milchkotes","volume":"32","author":"Escherich","year":"1888","journal-title":"\u00c6erztliches Intelligenz-Blatt, M\u00fcnchner Medicinische Wochenschrift"},{"key":"2022070111263263700_bib87","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1093\/molbev\/msh118","article-title":"A specific genetic background is required for acquisition and expression of virulence factors in Escherichiacoli","volume":"21","author":"Escobar-P\u00e1ramo","year":"2004","journal-title":"Mol Biol Evol"},{"key":"2022070111263263700_bib88","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1007\/s00239-003-2460-3","article-title":"The evolutionary history of Shigella and enteroinvasive Escherichiacoli revised","volume":"57","author":"Escobar-P\u00e1ramo","year":"2003","journal-title":"J Mol Evol"},{"key":"2022070111263263700_bib89","doi-asserted-by":"crossref","first-page":"5698","DOI":"10.1128\/AEM.70.9.5698-5700.2004","article-title":"Large-scale population structure of human commensal Escherichiacoli isolates","volume":"70","author":"Escobar-P\u00e1ramo","year":"2004","journal-title":"Appl Environ Microbiol"},{"key":"2022070111263263700_bib90","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1093\/jac\/dkq004","article-title":"Emergence of human pandemic O25:H4-ST131 CTX-M-15 extended-spectrum-\u03b2-lactamase-producing Escherichiacoli among companion animals","volume":"65","author":"Ewers","year":"2010","journal-title":"J Antimicrob Chemother"},{"key":"2022070111263263700_bib91","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1128\/IAI.01386-07","article-title":"Comparison of carbon nutrition for pathogenic and commensal Escherichiacoli strains in the mouse intestine","volume":"76","author":"Fabich","year":"2008","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib92","doi-asserted-by":"crossref","first-page":"2430","DOI":"10.1128\/IAI.01199-10","article-title":"Genotype and phenotypes of an intestine-adapted Escherichiacoli K-12 mutant selected by animal passage for superior colonization","volume":"79","author":"Fabich","year":"2011","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib93","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1128\/jcm.21.1.77-81.1985","article-title":"Escherichia fergusonii and Enterobactertaylorae, two new species of Enterobacteriaceae isolated from clinical specimens","volume":"21","author":"Farmer","year":"1985","journal-title":"J Clin Microbiol"},{"key":"2022070111263263700_bib94","doi-asserted-by":"crossref","first-page":"S10","DOI":"10.1111\/j.1753-4887.2012.00499.x","article-title":"The impact of nutrition on the human microbiome","volume":"70 Suppl 1","author":"Flint","year":"2012","journal-title":"Nutr Rev"},{"key":"2022070111263263700_bib95","doi-asserted-by":"crossref","first-page":"e10572","DOI":"10.7717\/peerj.10572","article-title":"Genomic diversity of Escherichiacoli from healthy children in rural Gambia","volume":"9","author":"Foster-Nyarko","year":"2021","journal-title":"PeerJ"},{"key":"2022070111263263700_bib96","first-page":"mgen000484","article-title":"Genomic diversity of Escherichia coli from non-human primates in the Gambia","volume-title":"Microb Genom","author":"Foster-Nyarko","year":"2020"},{"key":"2022070111263263700_bib97","first-page":"mgen000428","article-title":"Genomic diversity of Escherichiacoli from non-human primates in the Gambia","volume":"6","author":"Foster-Nyarko","year":"2020","journal-title":"Microb Genom"},{"key":"2022070111263263700_bib98","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1038\/nrurol.2010.190","article-title":"The epidemiology of urinary tract infection","volume":"7","author":"Foxman","year":"2010","journal-title":"Nat Rev Urol"},{"key":"2022070111263263700_bib99","doi-asserted-by":"crossref","first-page":"1771","DOI":"10.1056\/NEJMoa1106483","article-title":"Epidemic profile of Shiga-toxin-producing Escherichiacoli O104:H4 outbreak in Germany","volume":"365","author":"Frank","year":"2011","journal-title":"N Engl J Med"},{"key":"2022070111263263700_bib100","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":"2022070111263263700_bib101","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1128\/iai.39.2.686-703.1983","article-title":"Survival and implantation of Escherichiacoli in the intestinal tract","volume":"39","author":"Freter","year":"1983","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib102","doi-asserted-by":"crossref","DOI":"10.1128\/ecosalplus.ESP-0025-2013","article-title":"Escherich and Escherichia","volume":"6","author":"Friedmann","year":"2014","journal-title":"EcoSal Plus"},{"key":"2022070111263263700_bib103","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1353\/pbm.2004.0007","article-title":"From \u201cbutyribacterium\u201d to \u201cE. coli\u201d: an essay on unity in biochemistry","volume":"47","author":"Friedmann","year":"2004","journal-title":"Perspect Biol Med"},{"key":"2022070111263263700_bib104","doi-asserted-by":"crossref","first-page":"3911","DOI":"10.1128\/JB.186.12.3911-3921.2004","article-title":"Extensive genomic diversity in pathogenic Escherichiacoli and Shigella strains revealed by comparative genomic hybridization microarray","volume":"186","author":"Fukiya","year":"2004","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib105","doi-asserted-by":"crossref","first-page":"e01309","DOI":"10.1128\/JCM.01309-19","article-title":"Origin and evolution of hybrid Shiga toxin-producing and uropathogenic Escherichiacoli strains of sequence type 141","volume":"58","author":"Gati","year":"2019","journal-title":"J Clin Microbiol"},{"key":"2022070111263263700_bib106","doi-asserted-by":"crossref","first-page":"3315","DOI":"10.1128\/IAI.00052-07","article-title":"Role of motility and the flhDC Operon in Escherichiacoli MG1655 colonization of the mouse intestine","volume":"75","author":"Gauger","year":"2007","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib107","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1016\/j.tim.2016.06.011","article-title":"The ecology and evolution of microbial competition","volume":"24","author":"Ghoul","year":"2016","journal-title":"Trends Microbiol"},{"key":"2022070111263263700_bib108","doi-asserted-by":"crossref","first-page":"e10941","DOI":"10.7717\/peerj.10941","article-title":"Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture","volume":"9","author":"Gilroy","year":"2021","journal-title":"PeerJ"},{"key":"2022070111263263700_bib109","doi-asserted-by":"crossref","first-page":"2975","DOI":"10.3389\/fmicb.2018.02975","article-title":"Novel hybrid of typical enteropathogenic Escherichiacoli and Shiga-toxin-producing E. coli (tEPEC\/STEC) emerging from pet birds","volume":"9","author":"Gioia-Di\u00a0Chiacchio","year":"2018","journal-title":"Front Microbiol"},{"key":"2022070111263263700_bib110","doi-asserted-by":"crossref","first-page":"e61319","DOI":"10.1371\/journal.pone.0061319","article-title":"Within-host evolution of Staphylococcusaureus during asymptomatic aarriage","volume":"8","author":"Golubchik","year":"2013","journal-title":"PLoS ONE"},{"key":"2022070111263263700_bib317_1645529333030","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/nature24287","article-title":"The dynamics of molecular evolution over 60,000 generations","volume":"551","author":"Good","year":"2017","journal-title":"Nature"},{"key":"2022070111263263700_bib111","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1016\/S0002-9270(99)00806-0","article-title":"Probiotics and gastrointestinal health","volume":"95","author":"Gorbach","year":"2000","journal-title":"Am J Gastroenterol"},{"key":"2022070111263263700_bib112","doi-asserted-by":"crossref","first-page":"3575","DOI":"10.1099\/mic.0.26486-0","article-title":"The distribution and genetic structure of Escherichiacoli in Australian vertebrates: host and geographic effects","volume":"149","author":"Gordon","year":"2003","journal-title":"Microbiology (Reading)"},{"key":"2022070111263263700_bib113","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1111\/1758-2229.12300","article-title":"Escherichia coli diversity in the lower intestinal tract of humans","volume":"7","author":"Gordon","year":"2015","journal-title":"Environ Microbiol Rep"},{"key":"2022070111263263700_bib114","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1093\/cid\/cir632","article-title":"Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridiumdifficile infection","volume":"53","author":"Gough","year":"2011","journal-title":"Clin Infect Dis"},{"key":"2022070111263263700_bib115","doi-asserted-by":"crossref","first-page":"R521","DOI":"10.1016\/j.cub.2019.04.024","article-title":"The evolution and ecology of bacterial warfare","volume":"29","author":"Granato","year":"2019","journal-title":"Curr Biol"},{"key":"2022070111263263700_bib116","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1128\/am.20.4.531-535.1970","article-title":"Escherichia coli with resistance factors in vegetarians, babies, and nonvegetarians","volume":"20","author":"Guin\u00e9e","year":"1970","journal-title":"Appl Microbiol"},{"key":"2022070111263263700_bib117","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1126\/science.333581","article-title":"Naturally occurring plasmid carrying genes for enterotoxin production and drug resistance","volume":"198","author":"Gyles","year":"1977","journal-title":"Science"},{"key":"2022070111263263700_bib118","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1093\/embo-reports\/kve097","article-title":"Ecological fitness, genomic islands and bacterial pathogenicity. A Darwinian view of the evolution of microbes","volume":"2","author":"Hacker","year":"2001","journal-title":"EMBO Rep"},{"key":"2022070111263263700_bib119","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1186\/s13073-014-0070-x","article-title":"Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England","volume":"6","author":"Halachev","year":"2014","journal-title":"Genom Med"},{"key":"2022070111263263700_bib120","doi-asserted-by":"crossref","first-page":"e46402","DOI":"10.7554\/eLife.46402","article-title":"Improved characterisation of MRSA transmission using within-host bacterial sequence diversity","volume":"8","author":"Hall","year":"2019","journal-title":"Elife"},{"key":"2022070111263263700_bib121","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1099\/jmm.0.008672-0","article-title":"Probiotic Escherichiacoli strain Nissle 1917 outcompetes intestinal pathogens during biofilm formation","volume":"59","author":"Hancock","year":"2010","journal-title":"J Med Microbiol"},{"key":"2022070111263263700_bib122","doi-asserted-by":"crossref","first-page":"1292","DOI":"10.1126\/science.131.3409.1292","article-title":"The competitive exclusion principle","volume":"131","author":"Hardin","year":"1960","journal-title":"Science"},{"key":"2022070111263263700_bib310_1645527446322","doi-asserted-by":"crossref","first-page":"8631","DOI":"10.1073\/pnas.91.18.8631","article-title":"Dimorphic transition in Escherichia coli and Salmonella typhimurium: surface-induced differentiation into hyperflagellate swarmer cells","volume":"91","author":"Harshey","year":"1994","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022070111263263700_bib123","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1111\/1348-0421.12374","article-title":"Phylogenetics of family Enterobacteriaceae and proposal to reclassify Escherichiahermannii and Salmonellasubterranea as Atlantibacterhermannii and Atlantibactersubterranea gen. nov., comb. nov","volume":"60","author":"Hata","year":"2016","journal-title":"Microbiol Immunol"},{"key":"2022070111263263700_bib124","doi-asserted-by":"crossref","first-page":"2006.0007","DOI":"10.1038\/msb4100049","article-title":"Highly accurate genome sequences of Escherichiacoli K-12 strains MG1655 and W3110","volume":"2","author":"Hayashi","year":"2006","journal-title":"Mol Syst Biol"},{"key":"2022070111263263700_bib125","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/dnares\/8.1.11","article-title":"Complete genome sequence of enterohemorrhagic Escherichiacoli O157:H7 and genomic comparison with a laboratory strain K-12","volume":"8","author":"Hayashi","year":"2001","journal-title":"DNA Res"},{"key":"2022070111263263700_bib126","doi-asserted-by":"crossref","first-page":"2661","DOI":"10.3389\/fmicb.2017.02661","article-title":"Mycobacterium tuberculosis acquires limited genetic diversity in prolonged infections, reactivations and transmissions involving multiple hosts","volume":"8","author":"Herranz","year":"2017","journal-title":"Front Microbiol"},{"key":"2022070111263263700_bib326_1645531206245","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.jbiotec.2013.07.033","article-title":"Engineering Escherichia coli for improved ethanol production from gluconate","volume":"168","author":"Hildebrand","year":"2013","journal-title":"J Biotechnol"},{"key":"2022070111263263700_bib127","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/nrgastro.2014.66","article-title":"Expert consensus document. The International Scientific Association for probiotics and prebiotics consensus statement on the scope and appropriate use of the term probiotic","volume":"11","author":"Hill","year":"2014","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"2022070111263263700_bib128","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1038\/nri2710","article-title":"Immune adaptations that maintain homeostasis with the intestinal microbiota","volume":"10","author":"Hooper","year":"2010","journal-title":"Nat Rev Immunol"},{"key":"2022070111263263700_bib307_1645526992210","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.femsle.2004.11.049","article-title":"Transposon mutagenesis identifies genes which control antimicrobial drug tolerance in stationary-phase Escherichia coli","volume":"243","author":"Hu","year":"2005","journal-title":"FEMS Microbiol Lett"},{"key":"2022070111263263700_bib315_1645528488650","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1007\/s10295-011-1082-9","article-title":"Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements","volume":"39","author":"Huang","year":"2012","journal-title":"J Ind Microbiol Biotechnol"},{"key":"2022070111263263700_bib129","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1099\/ijs.0.02475-0","article-title":"Escherichia albertii sp. nov., a diarrhoeagenic species isolated from stool specimens of Bangladeshi children","volume":"53","author":"Huys","year":"2003","journal-title":"Int J Syst Evol Microbiol"},{"key":"2022070111263263700_bib130","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1128\/JB.187.2.619-628.2005","article-title":"Evolutionary genetics of a new pathogenic Escherichia species: Escherichiaalbertii and related Shigellaboydii strains","volume":"187","author":"Hyma","year":"2005","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib131","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/j.gene.2006.01.005","article-title":"Spontaneous recombination between homologous prophage regions causes large-scale inversions within the Escherichiacoli O157:H7 chromosome","volume":"372","author":"Iguchi","year":"2006","journal-title":"Gene"},{"key":"2022070111263263700_bib132","doi-asserted-by":"crossref","first-page":"2695","DOI":"10.1128\/AEM.02401-10","article-title":"Biofilm formation by and thermal niche and virulence characteristics of Escherichia spp","volume":"77","author":"Ingle","year":"2011","journal-title":"Appl Environ Microbiol"},{"key":"2022070111263263700_bib311_1645527778541","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1128\/JB.01294-06","article-title":"Genome-wide screening of genes required for swarming motility in Escherichia coli K-12","volume":"189","author":"Inoue","year":"2007","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib312_1645527954665","first-page":"1727","article-title":"[Operon: a group of genes with the expression coordinated by an operator]","volume":"250","author":"Jacob","year":"1960","journal-title":"C R Hebd Seances Acad Sci"},{"key":"2022070111263263700_bib133","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1159\/000333307","article-title":"Escherichia coli Nissle 1917 (Mutaflor): new insights into an old probiotic bacterium","volume":"29","author":"Jacobi","year":"2011","journal-title":"Dig Dis"},{"key":"2022070111263263700_bib134","doi-asserted-by":"crossref","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K\u00a0prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat Commun"},{"key":"2022070111263263700_bib135","doi-asserted-by":"crossref","first-page":"4078","DOI":"10.1128\/JCM.00980-08","article-title":"Multiple-host sharing, long-term persistence, and virulence of Escherichiacoli clones from human and animal household members","volume":"46","author":"Johnson","year":"2008","journal-title":"J Clin Microbiol"},{"key":"2022070111263263700_bib136","doi-asserted-by":"crossref","first-page":"e101","DOI":"10.1086\/508541","article-title":"Sharing of virulent Escherichiacoli clones among household members of a woman with acute cystitis","volume":"43","author":"Johnson","year":"2006","journal-title":"Clin Infect Dis"},{"key":"2022070111263263700_bib137","doi-asserted-by":"crossref","first-page":"3721","DOI":"10.1128\/JCM.01581-09","article-title":"Sharing of Escherichiacoli sequence type ST131 and other multidrug-resistant and urovirulent E. coli strains among dogs and cats within a household","volume":"47","author":"Johnson","year":"2009","journal-title":"J Clin Microbiol"},{"key":"2022070111263263700_bib138","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1086\/524844","article-title":"Escherichia coli colonization patterns among human household members and pets, with attention to acute urinary tract infection","volume":"197","author":"Johnson","year":"2008","journal-title":"J Infect Dis"},{"key":"2022070111263263700_bib139","first-page":"73","article-title":"Conservation of the family name Enterobacteriaceae, of the name of the type genus, and designation of the type species. Opinion No. 15","volume":"8","author":"Judicial Commission of the International Committee on Bacterial Nomenclature","year":"1958","journal-title":"Int Bull Bacteriol Nomencl Taxon"},{"key":"2022070111263263700_bib140","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1038\/ejcn.2010.19","article-title":"Regulation of abdominal adiposity by probiotics (Lactobacillus gasseri SBT2055) in adults with obese tendencies in a randomized controlled trial","volume":"64","author":"Kadooka","year":"2010","journal-title":"Eur J Clin Nutr"},{"key":"2022070111263263700_bib141","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1038\/ni.2608","article-title":"Control of pathogens and pathobionts by the gut microbiota","volume":"14","author":"Kamada","year":"2013","journal-title":"Nat Immunol"},{"key":"2022070111263263700_bib142","doi-asserted-by":"crossref","first-page":"e54617","DOI":"10.1371\/journal.pone.0054617","article-title":"Anti-obesity effect of Lactobacillusgasseri BNR17 in high-sucrose diet-induced obese mice","volume":"8","author":"Kang","year":"2013","journal-title":"PLoS ONE"},{"key":"2022070111263263700_bib143","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/nrmicro818","article-title":"Pathogenic Escherichiacoli","volume":"2","author":"Kaper","year":"2004","journal-title":"Nat Rev Microbiol"},{"key":"2022070111263263700_bib144","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1002\/emmm.201201662","article-title":"The enemy within us: lessons from the 2011 European Escherichiacoli O104:H4 outbreak","volume":"4","author":"Karch","year":"2012","journal-title":"EMBO Mol Med"},{"key":"2022070111263263700_bib325_1645531067809","article-title":"Metabolic engineering of Escherichia coli: construction of an efficient biocatalyst for D-mannitol formation","author":"Kaup"},{"key":"2022070111263263700_bib145","doi-asserted-by":"crossref","first-page":"6717","DOI":"10.1038\/ncomms7717","article-title":"Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe","volume":"6","author":"Kay","year":"2015","journal-title":"Nat Commun"},{"key":"2022070111263263700_bib146","doi-asserted-by":"crossref","first-page":"5033","DOI":"10.1073\/pnas.1018444108","article-title":"Helicobacter pylori genome evolution during human infection","volume":"108","author":"Kennemann","year":"2011","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022070111263263700_bib147","first-page":"ftv076","article-title":"Diarrhea, bacteremia and multiorgan dysfunction due to an extraintestinal pathogenic Escherichia coli strain with enteropathogenic E. coli genes","volume-title":"Pathog Dis","author":"Kessler","year":"2015"},{"key":"2022070111263263700_bib324_1645530491948","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1002\/biot.201300263","article-title":"Metabolic engineering of Escherichia coli for the production of phenol from glucose","volume":"9","author":"Kim","year":"2014","journal-title":"Biotechnol J"},{"key":"2022070111263263700_bib148","doi-asserted-by":"crossref","first-page":"e0187618","DOI":"10.1371\/journal.pone.0187618","article-title":"Impact of extensive antibiotic treatment on faecal carriage of antibiotic-resistant enterobacteria in children in a low resistance prevalence setting","volume":"12","author":"Knudsen","year":"2017","journal-title":"PLoS ONE"},{"key":"2022070111263263700_bib149","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1038\/s41598-017-18659-2","article-title":"Transfer of a blaCTX-M-1-carrying plasmid between different Escherichi coli strains within the human gut explored by whole genome sequencing analyses","volume":"8","author":"Knudsen","year":"2018","journal-title":"Sci Rep"},{"key":"2022070111263263700_bib150","first-page":"197","article-title":"The global burden of diarrhoeal disease, as estimated from studies published between 1992 and 2000","volume":"81","author":"Kosek","year":"2003","journal-title":"Bull World Health Organ"},{"key":"2022070111263263700_bib151","doi-asserted-by":"crossref","first-page":"2267","DOI":"10.1056\/NEJMoa1109910","article-title":"Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak","volume":"366","author":"K\u00f6ser","year":"2012","journal-title":"N Engl J Med"},{"key":"2022070111263263700_bib152","doi-asserted-by":"crossref","first-page":"1450","DOI":"10.1101\/gr.091785.109","article-title":"The consequences of genetic drift for bacterial genome complexity","volume":"19","author":"Kuo","year":"2009","journal-title":"Genome Res"},{"key":"2022070111263263700_bib153","doi-asserted-by":"crossref","first-page":"5080","DOI":"10.1128\/IAI.72.9.5080-5088.2004","article-title":"Molecular evolutionary relationships of enteroinvasive Escherichiacoli and Shigella spp","volume":"72","author":"Lan","year":"2004","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib154","doi-asserted-by":"crossref","first-page":"1911","DOI":"10.1099\/00221287-137-8-1911","article-title":"Molecular and evolutionary relationships among enteric bacteria","volume":"137","author":"Lawrence","year":"1991","journal-title":"J Gen Microbiol"},{"key":"2022070111263263700_bib155","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1007\/PL00006158","article-title":"Amelioration of bacterial genomes: rates of change and exchange","volume":"44","author":"Lawrence","year":"1997","journal-title":"J Mol Evol"},{"key":"2022070111263263700_bib156","doi-asserted-by":"crossref","first-page":"9413","DOI":"10.1073\/pnas.95.16.9413","article-title":"Molecular archaeology of the Escherichiacoli genome","volume":"95","author":"Lawrence","year":"1998","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022070111263263700_bib157","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0966-842X(01)02282-X","article-title":"Reconciling the many faces of lateral gene transfer","volume":"10","author":"Lawrence","year":"2002","journal-title":"Trends Microbiol"},{"key":"2022070111263263700_bib158","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/cid\/ciu785","article-title":"Do human extraintestinal Escherichiacoli infections resistant to expanded-spectrum cephalosporins originate from food-producing animals? A systematic review","volume":"60","author":"Lazarus","year":"2015","journal-title":"Clin Infect Dis"},{"key":"2022070111263263700_bib159","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ijmm.2010.04.021","article-title":"Sugar metabolism, an additional virulence factor in enterobacteria","volume":"301","author":"Le\u00a0Bougu\u00e9nec","year":"2011","journal-title":"Int J Med Microbiol"},{"key":"2022070111263263700_bib160","doi-asserted-by":"crossref","first-page":"2876","DOI":"10.1128\/IAI.00059-09","article-title":"Precolonized human commensal Escherichiacoli strains serve as a barrier to E. coli O157:H7 growth in the streptomycin-treated mouse intestine","volume":"77","author":"Leatham","year":"2009","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib161","doi-asserted-by":"crossref","first-page":"8039","DOI":"10.1128\/IAI.73.12.8039-8049.2005","article-title":"Mouse intestine selects nonmotile flhDC mutants of Escherichiacoli MG1655 with increased colonizing ability and better utilization of carbon sources","volume":"73","author":"Leatham","year":"2005","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib162","doi-asserted-by":"crossref","first-page":"1716","DOI":"10.1128\/IAI.06193-11","article-title":"The streptomycin-treated mouse intestine selects Escherichiacoli envZ missense mutants that interact with dense and diverse intestinal microbiota","volume":"80","author":"Leatham-Jensen","year":"2012","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib319_1645529662395","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1128\/jb.63.3.399-406.1952","article-title":"Replica plating and indirect selection of bacterial mutants","volume":"63","author":"Lederberg","year":"1952","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib163","doi-asserted-by":"crossref","first-page":"E2774","DOI":"10.1073\/pnas.1210309109","article-title":"Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichiacoli as determined by whole-genome sequencing","volume":"109","author":"Lee","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022070111263263700_bib164","doi-asserted-by":"crossref","first-page":"1564","DOI":"10.1016\/j.mex.2019.05.022","article-title":"Protocol measuring horizontal gene transfer from algae to non-photosynthetic organisms","volume":"6","author":"Lee","year":"2019","journal-title":"MethodsX"},{"key":"2022070111263263700_bib303_1645526279736","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/S0021-9258(19)68048-8","article-title":"Enzymatic synthesis of deoxyribonucleic acid. I. Preparation of substrates and partial purification of an enzyme from\u00a0 Escherichia coli","volume":"233","author":"Lehman","year":"1958","journal-title":"J Biol Chem"},{"key":"2022070111263263700_bib165","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/82_2012_303","article-title":"E. coli as an all-rounder: the thin line between commensalism and pathogenicity","volume-title":"Between Pathogenicity and Commensalism","author":"Leimbach","year":"2013"},{"key":"2022070111263263700_bib322_1645530174099","first-page":"425","article-title":"Experimental studies of pleiotropy and epistasis in Escherichia coli. I. Variation in competitive fitness among mutants resistant to virus T4","volume":"42","author":"Lenski","year":"1988","journal-title":"Evolution"},{"key":"2022070111263263700_bib166","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1111\/j.1758-2229.2012.00374.x","article-title":"Commensal Escherichiacoli strains in Guiana reveal a high genetic diversity with host-dependant population structure","volume":"5","author":"Lescat","year":"2013","journal-title":"Environ Microbiol Rep"},{"key":"2022070111263263700_bib167","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1126\/science.1155725","article-title":"Evolution of mammals and their gut microbes","volume":"320","author":"Ley","year":"2008","journal-title":"Science"},{"key":"2022070111263263700_bib168","doi-asserted-by":"crossref","DOI":"10.1128\/MMBR.00062-18","article-title":"Deciphering within-host microevolution of Mycobacteriumtuberculosis through whole-genome sequencing: the phenotypic impact and way forward","volume":"83","author":"Ley","year":"2019","journal-title":"Microbiol Mol Biol Rev"},{"key":"2022070111263263700_bib169","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1038\/s41396-018-0283-x","article-title":"Niche and fitness differences determine invasion success and impact in laboratory bacterial communities","volume":"13","author":"Li","year":"2019","journal-title":"ISME J"},{"key":"2022070111263263700_bib170","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1007\/BF02125493","article-title":"The homogeneity of the faecal coliform flora of normal school-girls, characterized by serological and biochemical properties","volume":"164","author":"Lidin-Janson","year":"1978","journal-title":"Med Microbiol Immunol (Berl)"},{"key":"2022070111263263700_bib308_1645527133979","doi-asserted-by":"crossref","first-page":"1300","DOI":"10.1073\/pnas.59.4.1300","article-title":"Host specificity of DNA produced by Escherichia coli, X. In vitro restriction of phage fd replicative form","volume":"59","author":"Linn","year":"1968","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022070111263263700_bib171","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1017\/S0022172400022130","article-title":"Antibiotic resistance and transmissible R-factors in the intestinal coliform flora of healthy adults and children in an urban and a rural community","volume":"70","author":"Linton","year":"1972","journal-title":"J Hyg"},{"key":"2022070111263263700_bib172","doi-asserted-by":"crossref","first-page":"10619","DOI":"10.1038\/s41598-019-46831-3","article-title":"Genomic and molecular characterisation of Escherichiamarmotae from wild rodents in Qinghai-Tibetplateau as a potential pathogen","volume":"9","author":"Liu","year":"2019","journal-title":"Sci Rep"},{"key":"2022070111263263700_bib173","doi-asserted-by":"crossref","first-page":"2130","DOI":"10.1099\/ijs.0.000228","article-title":"Escherichia marmotae sp. nov., isolated from faeces of Marmotahimalayana","volume":"65","author":"Liu","year":"2015","journal-title":"Int J Syst Evol Microbiol"},{"key":"2022070111263263700_bib327_1645531381817","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1146\/annurev-genet-102209-163440","article-title":"Genetic engineering of Escherichia coli for biofuel production","volume":"44","author":"Liu","year":"2010","journal-title":"Annu Rev Genet"},{"key":"2022070111263263700_bib174","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1159\/000244421","article-title":"Effect of preventive administration of a nonpathogenic Escherichiacoli strain on the colonization of the intestine with microbial pathogens in newborn infants","volume":"71","author":"Lodinov\u00e1-Z\u00e1dnikov\u00e1","year":"1997","journal-title":"Biol Neonate"},{"key":"2022070111263263700_bib175","doi-asserted-by":"crossref","first-page":"e122","DOI":"10.1038\/emi.2016.122","article-title":"Insights into the evolution of pathogenicity of Escherichiacoli from genomic analysis of intestinal E. coli of Marmotahimalayana in Qinghai-Tibet plateau of China","volume":"5","author":"Lu","year":"2016","journal-title":"Emerg Microbes Infect"},{"key":"2022070111263263700_bib176","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1007\/s00248-010-9717-3","article-title":"Comparison of 61 sequenced Escherichiacoli genomes","volume":"60","author":"Lukjancenko","year":"2010","journal-title":"Microb Ecol"},{"key":"2022070111263263700_bib318_1645529513711","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1093\/genetics\/28.6.491","article-title":"Mutations of bacteria from virus sensitivity to virus resistance","volume":"28","author":"Luria","year":"1943","journal-title":"Genetics"},{"key":"2022070111263263700_bib306_1645526838063","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1128\/br.17.4.269-337.1953","article-title":"Lysogeny","volume":"17","author":"Lwoff","year":"1953","journal-title":"Bacteriol Rev"},{"key":"2022070111263263700_bib177","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1097\/ACI.0000000000000255","article-title":"The microbiome and development of allergic disease","volume":"16","author":"Lynch","year":"2016","journal-title":"Curr Opin Allergy Clin Immunol"},{"key":"2022070111263263700_bib178","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1080\/00365521.1997.11720708","article-title":"Human colonic microbiota: ecology, physiology and metabolic potential of intestinal bacteria","volume":"222","author":"Macfarlane","year":"1997","journal-title":"Scand J Gastroenterol"},{"key":"2022070111263263700_bib329_1645541027050","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1016\/j.vetimm.2012.09.032","article-title":"Escherichia coli virulence factors","volume":"152","author":"Mainil","year":"2013","journal-title":"Vet Immunol Immunopathol"},{"key":"2022070111263263700_bib179","doi-asserted-by":"crossref","first-page":"e53957","DOI":"10.1371\/journal.pone.0053957","article-title":"Nutritional basis for colonization resistance by human commensal Escherichiacoli strains HS and Nissle 1917 against E. coli O157:H7 in the mouse intestine","volume":"8","author":"Maltby","year":"2013","journal-title":"PLoS ONE"},{"key":"2022070111263263700_bib180","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1080\/23744235.2016.1177199","article-title":"Fecal microbiota transplantation for the intestinal decolonization of extensively antimicrobial-resistant opportunistic pathogens: a review","volume":"48","author":"Manges","year":"2016","journal-title":"Infect Dis"},{"key":"2022070111263263700_bib181","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1002\/nmi2.49","article-title":"Haemolytic-uraemic syndrome with bacteraemia caused by a new hybrid Escherichiacoli pathotype","volume":"2","author":"Mariani-Kurkdjian","year":"2014","journal-title":"New Microbes New Infect"},{"key":"2022070111263263700_bib182","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.mrrev.2010.05.001","article-title":"DNA methylation and mutator genes in Escherichiacoli K-12","volume":"705","author":"Marinus","year":"2010","journal-title":"Mutat Res"},{"key":"2022070111263263700_bib183","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":"2022070111263263700_bib184","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/ecosalplus.ESP-0003-2020","article-title":"Residency in the gut of healthy human adults","volume":"9","author":"Martinson","year":"2020","journal-title":"EcoSal Plus"},{"key":"2022070111263263700_bib185","doi-asserted-by":"crossref","first-page":"e1003741","DOI":"10.1371\/journal.pgen.1003741","article-title":"Genome analysis of a transmissible lineage of Pseudomonasaeruginosa reveals pathoadaptive mutations and distinct evolutionary paths of hypermutators","volume":"9","author":"Marvig","year":"2013","journal-title":"PLos Genet"},{"key":"2022070111263263700_bib186","doi-asserted-by":"crossref","first-page":"642","DOI":"10.1099\/mic.0.000242","article-title":"Phylogenetic, virulence and antibiotic resistance characteristics of commensal strain populations of Escherichiacoli from community subjects in the Paris area in 2010 and evolution over 30 years","volume":"162","author":"Massot","year":"2016","journal-title":"Microbiology"},{"key":"2022070111263263700_bib187","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1038\/nrmicro3164","article-title":"Playing fast and loose with mutation","volume":"11","author":"Mather","year":"2013","journal-title":"Nat Rev Microbiol"},{"key":"2022070111263263700_bib188","doi-asserted-by":"crossref","first-page":"R44","DOI":"10.1186\/gb-2006-7-5-r44","article-title":"Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichiacoli","volume":"7","author":"Mau","year":"2006","journal-title":"Genome Biol"},{"key":"2022070111263263700_bib189","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.00644-19","article-title":"Diversification of colonization factors in a multidrug-resistant Escherichiacoli lineage evolving under negative frequency-dependent selection","volume":"10","author":"McNally","year":"2019","journal-title":"Mbio"},{"key":"2022070111263263700_bib190","doi-asserted-by":"crossref","first-page":"e1006280","DOI":"10.1371\/journal.pgen.1006280","article-title":"Combined analysis of variation in cre, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations","volume":"12","author":"McNally","year":"2016","journal-title":"PLos Genet"},{"key":"2022070111263263700_bib191","doi-asserted-by":"crossref","first-page":"1931","DOI":"10.1128\/IAI.01435-13","article-title":"Escherichia coli pathotypes occupy distinct niches in the mouse intestine","volume":"82","author":"Meador","year":"2014","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib309_1645527304401","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1038\/2171110a0","article-title":"DNA restriction enzyme from E. coli","volume":"217","author":"Meselson","year":"1968","journal-title":"Nature"},{"key":"2022070111263263700_bib192","first-page":"219","article-title":"[The fecal flora of man. IV. Communication: comparison of the newly developed method with the old conventional method for the analysis of intestinal flora (author's transl)]","volume":"234","author":"Mitsuoka","year":"1976","journal-title":"Zentralbl Bakteriol Orig A"},{"key":"2022070111263263700_bib193","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1007\/s00394-013-0568-9","article-title":"Anti-obesity effect of Lactobacillusgasseri SBT2055 accompanied by inhibition of pro-inflammatory gene expression in the visceral adipose tissue in diet-induced obese mice","volume":"53","author":"Miyoshi","year":"2014","journal-title":"Eur J Nutr"},{"key":"2022070111263263700_bib194","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1016\/j.chest.2016.10.006","article-title":"Blurred lines: dysbiosis and probiotics in the ICU","volume":"151","author":"Morrow","year":"2017","journal-title":"Chest"},{"key":"2022070111263263700_bib195","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1126\/science.1198719","article-title":"Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans","volume":"332","author":"Muegge","year":"2011","journal-title":"Science"},{"key":"2022070111263263700_bib196","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.molmed.2014.12.002","article-title":"The infant microbiome development: mom matters","volume":"21","author":"Mueller","year":"2015","journal-title":"Trends Mol Med"},{"key":"2022070111263263700_bib197","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1073\/pnas.84.1.166","article-title":"The guanine and cytosine content of genomic DNA and bacterial evolution","volume":"84","author":"Muto","year":"1987","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022070111263263700_bib198","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1128\/IAI.71.3.1505-1512.2003","article-title":"Lymphoid follicle-dense mucosa at the terminal rectum is the principal site of colonization of enterohemorrhagic Escherichiacoli O157:H7 in the bovine host","volume":"71","author":"Naylor","year":"2003","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib199","volume-title":"Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology","author":"Neidhardt","year":"1996"},{"key":"2022070111263263700_bib200","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1038\/nature12503","article-title":"Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens","volume":"502","author":"Ng","year":"2013","journal-title":"Nature"},{"key":"2022070111263263700_bib201","doi-asserted-by":"crossref","first-page":"e0147757","DOI":"10.1371\/journal.pone.0147757","article-title":"Genetic characterization of expec-like virulence plasmids among a subset of NMEC","volume":"11","author":"Nicholson","year":"2016","journal-title":"PLoS ONE"},{"key":"2022070111263263700_bib202","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1126\/science.1223813","article-title":"Host-gut microbiota metabolic interactions","volume":"336","author":"Nicholson","year":"2012","journal-title":"Science"},{"key":"2022070111263263700_bib203","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1099\/jmm.0.068783-0","article-title":"Faecal Escherichiacoli from patients with E. coli urinary tract infection and healthy controls who have never had a urinary tract infection","volume":"63","author":"Nielsen","year":"2014","journal-title":"J Med Microbiol"},{"key":"2022070111263263700_bib204","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1093\/jac\/37.6.1141","article-title":"In-vitro transfer of antibiotic resistance between faecal Escherichiacoli strains isolated from pig farmers and pigs","volume":"37","author":"Nijsten","year":"1996","journal-title":"J Antimicrob Chemother"},{"key":"2022070111263263700_bib206","first-page":"1017","article-title":"[Explanations of the significance of colonic dysbacteria & the mechanism of action of E. coli therapy (mutaflor)]","volume":"4","author":"Nissle","year":"1959","journal-title":"Medizinische"},{"key":"2022070111263263700_bib205","first-page":"68","article-title":"[Mutaflor and its medical significance]","volume":"2","author":"Nissle","year":"1951","journal-title":"Z Klin Med"},{"key":"2022070111263263700_bib207","first-page":"1519","article-title":"[Old and new experiences on therapeutic successes by restoration of the colonic flora with mutaflor in gastrointestinal diseases]","volume":"29-30","author":"Nissle","year":"1961","journal-title":"Med Welt"},{"key":"2022070111263263700_bib208","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1017\/S0950268801005118","article-title":"P fimbriae, capsule and aerobactin characterize colonic resident Escherichiacoli","volume":"126","author":"Nowrouzian","year":"2001","journal-title":"Epidemiol Infect"},{"key":"2022070111263263700_bib209","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1016\/j.ijmm.2018.05.007","article-title":"Genetic characterization of Shiga toxin producing Escherichiacoli belonging to the emerging hybrid pathotype O80:H2 isolated from humans 2010-2017 in Switzerland","volume":"308","author":"N\u00fcesch-Inderbinen","year":"2018","journal-title":"Int J Med Microbiol"},{"key":"2022070111263263700_bib210","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/j.jegh.2013.11.002","article-title":"Nosocomial pathogens associated with the mobile phones of healthcare workers in a hospital in Anyigba, Kogi state, Nigeria","volume":"4","author":"Nwankwo","year":"2014","journal-title":"J Epidemiol Glob Health"},{"key":"2022070111263263700_bib211","doi-asserted-by":"crossref","first-page":"e00739","DOI":"10.1128\/MRA.00739-20","article-title":"Draft genome sequence of Escherichiamarmotae E690, isolated from beef cattle","volume":"9","author":"Ocejo","year":"2020","journal-title":"Microbiol Resour Announc"},{"key":"2022070111263263700_bib212","doi-asserted-by":"crossref","first-page":"6637","DOI":"10.1093\/emboj\/19.24.6637","article-title":"Evolutionary dynamics of full genome content in Escherichiacoli","volume":"19","author":"Ochman","year":"2000","journal-title":"EMBO J"},{"key":"2022070111263263700_bib213","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/35012500","article-title":"Lateral gene transfer and the nature of bacterial innovation","volume":"405","author":"Ochman","year":"2000","journal-title":"Nature"},{"key":"2022070111263263700_bib214","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1139\/m92-115","article-title":"Escherichia coli serotyping and disease in man and animals","volume":"38","author":"Orskov","year":"1992","journal-title":"Can J Microbiol"},{"key":"2022070111263263700_bib215","doi-asserted-by":"crossref","first-page":"144","DOI":"10.4103\/2277-9175.161553","article-title":"Mobile phones: reservoirs for the transmission of nosocomial pathogens","volume":"4","author":"Pal","year":"2015","journal-title":"Adv Biomed Res"},{"key":"2022070111263263700_bib216","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/j.tim.2020.10.009","article-title":"The next million names for Archaea and Bacteria","volume":"29","author":"Pallen","year":"2020","journal-title":"Trends Microbiol"},{"key":"2022070111263263700_bib217","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1126\/science.aad9382","article-title":"Resurrecting the intestinal microbiota to combat antibiotic-resistant pathogens","volume":"352","author":"Pamer","year":"2016","journal-title":"Science"},{"key":"2022070111263263700_bib218","doi-asserted-by":"crossref","first-page":"2272","DOI":"10.1128\/IAI.01333-08","article-title":"The plasmid of Escherichiacoli strain S88 (O45:K1:H7) that causes neonatal meningitis is closely related to avian pathogenic E. coli plasmids and is associated with high-level bacteremia in a neonatal rat meningitis model","volume":"77","author":"Peigne","year":"2009","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib219","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1542\/peds.2005-2824","article-title":"Factors influencing the composition of the intestinal microbiota in early infancy","volume":"118","author":"Penders","year":"2006","journal-title":"Pediatrics"},{"key":"2022070111263263700_bib220","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1126\/science.277.5331.1432","article-title":"Laboratory workhorse decoded","volume":"277","author":"Pennisi","year":"1997","journal-title":"Science"},{"key":"2022070111263263700_bib221","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":"2022070111263263700_bib222","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/bioinformatics\/btu600","article-title":"Insights into structural variations and genome rearrangements in prokaryotic genomes","volume":"31","author":"Periwal","year":"2015","journal-title":"Bioinformatics"},{"key":"2022070111263263700_bib223","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/35054089","article-title":"Genome sequence of enterohaemorrhagic Escherichiacoli O157:H7","volume":"409","author":"Perna","year":"2001","journal-title":"Nature"},{"key":"2022070111263263700_bib224","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1128\/IAI.67.2.546-553.1999","article-title":"The link between phylogeny and virulence in Escherichiacoli extraintestinal infection","volume":"67","author":"Picard","year":"1999","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib225","doi-asserted-by":"crossref","first-page":"9","DOI":"10.3389\/fmicb.2012.00009","article-title":"Extraintestinal pathogenic Escherichiacoli: a combination of virulence with antibiotic resistance","volume":"3","author":"Pitout","year":"2012","journal-title":"Front Microbiol"},{"key":"2022070111263263700_bib226","doi-asserted-by":"crossref","first-page":"5191","DOI":"10.1128\/iai.62.11.5191-5194.1994","article-title":"Spatial distribution of Escherichiacoli in the mouse large intestine inferred from rRNA in situ hybridization","volume":"62","author":"Poulsen","year":"1994","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib227","doi-asserted-by":"crossref","first-page":"5840","DOI":"10.1128\/jb.177.20.5840-5845.1995","article-title":"Physiological state of Escherichiacoli BJ4 growing in the large intestines of streptomycin-treated mice","volume":"177","author":"Poulsen","year":"1995","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib228","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1099\/ijs.0.013458-0","article-title":"Gram-negative bacteria associated with brewery yeasts: reclassification of Obesumbacteriumproteus biogroup 2 as Shimwelliapseudoproteus gen. nov., sp. nov., and transfer of Escherichiablattae to Shimwelliablattae comb. nov","volume":"60","author":"Priest","year":"2010","journal-title":"Int J Syst Evol Microbiol"},{"key":"2022070111263263700_bib229","doi-asserted-by":"crossref","first-page":"10567","DOI":"10.1073\/pnas.180094797","article-title":"Multiple independent origins of Shigella clones of Escherichiacoli and convergent evolution of many of their characteristics","volume":"97","author":"Pupo","year":"2000","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022070111263263700_bib230","doi-asserted-by":"crossref","first-page":"1718","DOI":"10.1038\/ajg.2015.357","article-title":"Extensive modulation of the fecal metagenome in children with Crohn's disease during exclusive enteral nutrition","volume":"110","author":"Quince","year":"2015","journal-title":"Am J Gastroenterol"},{"key":"2022070111263263700_bib231","doi-asserted-by":"crossref","first-page":"e01377","DOI":"10.1128\/mBio.01377-14","article-title":"Large chromosomal rearrangements during a long-term evolution experiment with Escherichiacoli","volume":"5","author":"Raeside","year":"2014","journal-title":"Mbio"},{"key":"2022070111263263700_bib232","doi-asserted-by":"crossref","first-page":"6881","DOI":"10.1128\/JB.00619-08","article-title":"The pangenome structure of Escherichiacoli: comparative genomic analysis of E. coli commensal and pathogenic isolates","volume":"190","author":"Rasko","year":"2008","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib233","first-page":"e000293","article-title":"Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients","volume":"5","author":"Ravi","year":"2019","journal-title":"Microb Genom"},{"key":"2022070111263263700_bib234","doi-asserted-by":"crossref","first-page":"e26907","DOI":"10.1371\/journal.pone.0026907","article-title":"Rates of mutation and host transmission for an Escherichiacoli clone over 3 years","volume":"6","author":"Reeves","year":"2011","journal-title":"PLoS ONE"},{"key":"2022070111263263700_bib235","doi-asserted-by":"crossref","first-page":"2544","DOI":"10.1021\/acsinfecdis.0c00036","article-title":"Effects of antibiotic treatment on gut microbiota and how to overcome its negative impacts on human health","volume":"6","author":"Ribeiro","year":"2020","journal-title":"ACS Infect Dis"},{"key":"2022070111263263700_bib236","doi-asserted-by":"crossref","first-page":"19126","DOI":"10.1073\/pnas.0906412106","article-title":"Shifting the genomic gold standard for the prokaryotic species definition","volume":"106","author":"Richter","year":"2009","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022070111263263700_bib237","doi-asserted-by":"crossref","first-page":"e00558","DOI":"10.1128\/mSphere.00558-18","article-title":"Temporal variability of Escherichia coli diversity in the gastrointestinal tracts of Tanzanian children with and without exposure to antibiotics","volume":"3","author":"Richter","year":"2018","journal-title":"mSphere"},{"key":"2022070111263263700_bib238","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00047-18","article-title":"Responses of the human gut Escherichia coli population to pathogen and antibiotic disturbances","volume-title":"mSystems","author":"Richter","year":"2018"},{"key":"2022070111263263700_bib239","doi-asserted-by":"crossref","first-page":"33385193","DOI":"10.1128\/microbiolspec.AME-0014-2020","article-title":"Distinguishing pathovars from nonpathovars: Escherichiacoli","volume":"8","author":"Riley","year":"2020","journal-title":"Microbiol Spectr"},{"key":"2022070111263263700_bib240","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1128\/jb.84.5.896-901.1962","article-title":"Relationship of host antibody to fluctuations of Escherichiacoli serotypes in the human intestine","volume":"84","author":"Robinet","year":"1962","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib241","doi-asserted-by":"crossref","first-page":"141","DOI":"10.3389\/fcimb.2016.00141","article-title":"Are Escherichiacoli pathotypes still relevant in the era of whole-genome sequencing?","volume":"6","author":"Robins-Browne","year":"2016","journal-title":"Front Cell Infect Microbiol"},{"key":"2022070111263263700_bib242","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1002\/jcp.25053","article-title":"Error-prone repair of DNA double-strand breaks","volume":"231","author":"Rodgers","year":"2016","journal-title":"J Cell Physiol"},{"key":"2022070111263263700_bib243","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nri2515","article-title":"The gut microbiota shapes intestinal immune responses during health and disease","volume":"9","author":"Round","year":"2009","journal-title":"Nat Rev Immunol"},{"key":"2022070111263263700_bib244","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1128\/IAI.70.3.1225-1229.2002","article-title":"Clonal diversity of Escherichiacoli colonizing stools and urinary tracts of young girls","volume":"70","author":"Schlager","year":"2002","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib245","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1128\/jb.59.2.293-301.1950","article-title":"Persistence of individual strains of Escherichiacoli in the intestinal tract of man","volume":"59","author":"Sears","year":"1950","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib246","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1128\/jb.63.1.47-57.1952","article-title":"Further observations on the persistence of individual strains of Escherichiacoli in the intestinal tract of man","volume":"63","author":"Sears","year":"1952","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib247","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1126\/science.6999623","article-title":"Genetic diversity and structure in Escherichiacoli populations","volume":"210","author":"Selander","year":"1980","journal-title":"Science"},{"key":"2022070111263263700_bib328_1645540715802","doi-asserted-by":"crossref","first-page":"e9192","DOI":"10.1371\/journal.pone.0009192","article-title":"Specific strains of Escherichia coli are pathogenic for the endometrium of cattle and cause pelvic inflammatory disease in cattle and mice","volume":"5","author":"Sheldon","year":"2010","journal-title":"PLoS One"},{"key":"2022070111263263700_bib248","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1017\/S0022172400055972","article-title":"Escherichia coli serotypes in the faeces of healthy adults over a period of several months","volume":"78","author":"Shooter","year":"1977","journal-title":"J Hyg"},{"key":"2022070111263263700_bib249","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1086\/521946","article-title":"Theodor Escherich: the first pediatric infectious diseases physician?","volume":"45","author":"Shulman","year":"2007","journal-title":"Clin Infect Dis"},{"key":"2022070111263263700_bib250","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1126\/science.aac4255","article-title":"Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy","volume":"350","author":"Sivan","year":"2015","journal-title":"Science"},{"key":"2022070111263263700_bib251","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1099\/00207713-30-1-225","article-title":"Approved lists of bacterial names","volume":"30","author":"Skerman","year":"1980","journal-title":"Int J Syst Evol Microbiol"},{"key":"2022070111263263700_bib252","doi-asserted-by":"crossref","first-page":"2132","DOI":"10.1111\/j.1462-2920.2008.01636.x","article-title":"Characteristics of human intestinal Escherichiacoli with changing environments","volume":"10","author":"Skurnik","year":"2008","journal-title":"Environ Microbiol"},{"key":"2022070111263263700_bib253","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1128\/jb.74.5.591-595.1957","article-title":"Numbers of enterococci in water, sewage, and feces determined by the membrane filter technique with an improved medium","volume":"74","author":"Slanetz","year":"1957","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib254","first-page":"689","article-title":"Zur kenntnis der colibacillen des sa\u0308uglingsstuhles","volume":"25","author":"Smith","year":"1899","journal-title":"Zentr Bakt Parasitenk I Orig"},{"key":"2022070111263263700_bib255","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":"2022070111263263700_bib256","doi-asserted-by":"crossref","first-page":"1604","DOI":"10.3201\/eid2209.160304","article-title":"Enterohemorrhagic Escherichiacoli hybrid pathotype O80:H2 as a new therapeutic challenge","volume":"22","author":"Soysal","year":"2016","journal-title":"Emerg Infect Dis"},{"key":"2022070111263263700_bib257","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1186\/s12879-016-1737-2","article-title":"Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients","volume":"16","author":"Ssengooba","year":"2016","journal-title":"BMC Infect Dis"},{"key":"2022070111263263700_bib258","doi-asserted-by":"crossref","first-page":"151401","DOI":"10.1016\/j.ijmm.2020.151401","article-title":"A snapshot of diversity: intraclonal variation of Escherichiacoli clones as commensals and pathogens","volume":"310","author":"Stegger","year":"2020","journal-title":"Int J Med Microbiol"},{"key":"2022070111263263700_bib259","doi-asserted-by":"crossref","first-page":"2916","DOI":"10.1128\/JCM.02432-09","article-title":"Ancestral lineages of human enterotoxigenic Escherichiacoli","volume":"48","author":"Steinsland","year":"2010","journal-title":"J Clin Microbiol"},{"key":"2022070111263263700_bib304_1645526472425","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/0006-291X(60)90110-8","article-title":"Incorporation of the adenine ribonucleotide into RNA by cell fractions from E. coli","volume":"3","author":"Stevens","year":"1960","journal-title":"Biochem Biophys Res Commun"},{"key":"2022070111263263700_bib260","doi-asserted-by":"crossref","first-page":"2122","DOI":"10.1128\/JCM.00378-15","article-title":"Extensive within-host diversity in fecally carried extended-spectrum-beta-lactamase-producing Escherichiacoli isolates: implications for transmission analyses","volume":"53","author":"Stoesser","year":"2015","journal-title":"J Clin Microbiol"},{"key":"2022070111263263700_bib261","doi-asserted-by":"crossref","first-page":"e02162","DOI":"10.1128\/mBio.02162-15","article-title":"Evolutionary history of the global emergence of the Escherichiacoli epidemic clone ST131","volume":"7","author":"Stoesser","year":"2016","journal-title":"Mbio"},{"key":"2022070111263263700_bib262","doi-asserted-by":"crossref","first-page":"2782","DOI":"10.1128\/JB.180.10.2782-2787.1998","article-title":"Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menA gene from Escherichiacoli","volume":"180","author":"Suvarna","year":"1998","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib314_1645528305381","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/S0958-1669(00)00199-3","article-title":"Advances in Escherichia coli production of therapeutic proteins","volume":"12","author":"Swartz","year":"2001","journal-title":"Curr Opin Biotechnol"},{"key":"2022070111263263700_bib263","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1128\/iai.2.4.376-386.1970","article-title":"Efficiency of various intestinal bacteria in assuming normal functions of enteric flora after association with germ-free mice","volume":"2","author":"Syed","year":"1970","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib264","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/j.alit.2017.07.010","article-title":"Development of the gut microbiota in infancy and its impact on health in later life","volume":"66","author":"Tanaka","year":"2017","journal-title":"Allergol Int"},{"key":"2022070111263263700_bib265","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1099\/jmm.0.025874-0","article-title":"Testing probiotic strain Escherichiacoli Nissle 1917 (Mutaflor) for its ability to reduce carriage of multidrug-resistant E. coli by elderly residents in long-term care facilities","volume":"60","author":"Tannock","year":"2011","journal-title":"J Med Microbiol"},{"key":"2022070111263263700_bib266","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":"2022070111263263700_bib267","doi-asserted-by":"crossref","first-page":"13950","DOI":"10.1073\/pnas.0506758102","article-title":"Genome analysis of multiple pathogenic isolates of Streptococcusagalactiae: implications for the microbial \u201cpan-genome\u201d","volume":"102","author":"Tettelin","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022070111263263700_bib268","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-030-38281-0","volume-title":"The Pangenome: Diversity, Dynamics and Evolution of Genomes","author":"Tettelin","year":"2020"},{"key":"2022070111263263700_bib269","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1007\/s000180050022","article-title":"Spread of antibiotic resistance with food-borne pathogens","volume":"56","author":"Teuber","year":"1999","journal-title":"Cell Mol Life Sci"},{"key":"2022070111263263700_bib270","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1038\/nrmicro.2016.10","article-title":"The genomic signatures of Shigella evolution, adaptation and geographical spread","volume":"14","author":"The","year":"2016","journal-title":"Nat Rev Microbiol"},{"key":"2022070111263263700_bib271","doi-asserted-by":"crossref","first-page":"2093","DOI":"10.3201\/eid2312.170450","article-title":"Enteropathogenic Escherichiacoli O80:H2 in young calves with diarrhea, Belgium","volume":"23","author":"Thiry","year":"2017","journal-title":"Emerg Infect Dis"},{"key":"2022070111263263700_bib272","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1016\/j.clnu.2007.04.008","article-title":"Design of a multispecies probiotic mixture to prevent infectious complications in critically ill patients","volume":"26","author":"Timmerman","year":"2007","journal-title":"Clin Nutr"},{"key":"2022070111263263700_bib273","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01613-20","article-title":"Carriage of extended-spectrum-beta-lactamase- and AmpC beta-lactamase-producing Escherichiacoli strains from humans and pets in the same households","volume":"86","author":"Toombs-Ruane","year":"2020","journal-title":"Appl Environ Microbiol"},{"key":"2022070111263263700_bib274","first-page":"115","article-title":"Studien \u00fcber Bacteriumcoli","volume":"45","author":"Totsuka","year":"1902","journal-title":"Z Hyg Infektionskrankh"},{"key":"2022070111263263700_bib275","doi-asserted-by":"crossref","first-page":"e1000344","DOI":"10.1371\/journal.pgen.1000344","article-title":"Organised genome dynamics in the Escherichiacoli species results in highly diverse adaptive paths","volume":"5","author":"Touchon","year":"2009","journal-title":"PLos Genet"},{"key":"2022070111263263700_bib276","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/s13059-017-1196-0","article-title":"The within-host population dynamics of Mycobacteriumtuberculosis vary with treatment efficacy","volume":"18","author":"Trauner","year":"2017","journal-title":"Genome Biol"},{"key":"2022070111263263700_bib277","doi-asserted-by":"crossref","first-page":"e01068","DOI":"10.1128\/mBio.01068-17","article-title":"Reciprocal prioritization to dietary glycans by gut bacteria in a competitive environment promotes stable coexistence","volume":"8","author":"Tuncil","year":"2017","journal-title":"Mbio"},{"key":"2022070111263263700_bib278","doi-asserted-by":"crossref","first-page":"6ra14","DOI":"10.1126\/scitranslmed.3000322","article-title":"The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice","volume":"1","author":"Turnbaugh","year":"2009","journal-title":"Sci Transl Med"},{"key":"2022070111263263700_bib279","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1017\/S0950268800049232","article-title":"The population structure and transmission of Escherichiacoli in an isolated human community; studies on an Antarctic base","volume":"107","author":"Tzabar","year":"1991","journal-title":"Epidemiol Infect"},{"key":"2022070111263263700_bib280","doi-asserted-by":"crossref","first-page":"5649","DOI":"10.1073\/pnas.1503141112","article-title":"Global trends in antimicrobial use in food animals","volume":"112","author":"Van\u00a0Boeckel","year":"2015","journal-title":"Proc Natl Acad Sci"},{"key":"2022070111263263700_bib281","first-page":"004609","article-title":"Escherichia ruysiae sp. nov., a novel Gram-stain-negative bacterium, isolated from a faecal sample of an international traveller","volume":"71","author":"van\u00a0der\u00a0Putten","year":"2021","journal-title":"Int J Syst Evol Microbiol"},{"key":"2022070111263263700_bib282","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/ismej.2010.80","article-title":"Survival of Escherichiacoli in the environment: fundamental and public health aspects","volume":"5","author":"van\u00a0Elsas","year":"2011","journal-title":"ISME J"},{"key":"2022070111263263700_bib283","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":"2022070111263263700_bib284","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1046\/j.1365-2036.1999.00560.x","article-title":"Impact on the composition of the faecal flora by a new probiotic preparation: preliminary data on maintenance treatment of patients with ulcerative colitis","volume":"13","author":"Venturi","year":"1999","journal-title":"Aliment Pharmacol Ther"},{"key":"2022070111263263700_bib285","doi-asserted-by":"crossref","first-page":"6534","DOI":"10.1128\/AEM.01262-09","article-title":"Cryptic lineages of the genus Escherichia","volume":"75","author":"Walk","year":"2009","journal-title":"Appl Environ Microbiol"},{"key":"2022070111263263700_bib286","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1128\/jb.45.2.121-126.1943","article-title":"Antigenic relationships of Escherichiacoli isolated from one individual","volume":"45","author":"Wallick","year":"1943","journal-title":"J Bacteriol"},{"key":"2022070111263263700_bib287","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1016\/j.vetmic.2013.04.009","article-title":"Hypermutable Staphylococcusaureus strains present at high frequency in subclinical bovine mastitis isolates are associated with the development of antibiotic resistance","volume":"165","author":"Wang","year":"2013","journal-title":"Vet Microbiol"},{"key":"2022070111263263700_bib288","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/S0140-6736(05)65257-9","article-title":"Outbreaks of enterohaemorrhagic Escherichiacoli O157:H7 infection by two different genotype strains in Japan, 1996","volume":"348","author":"Watanabe","year":"1996","journal-title":"Lancet"},{"key":"2022070111263263700_bib289","first-page":"374","volume-title":"Frontiers in Antimicrobial Resistance: a Tribute to Stuart B Levy","author":"Webber","year":"2005"},{"key":"2022070111263263700_bib290","doi-asserted-by":"crossref","first-page":"5750","DOI":"10.1128\/IAI.72.10.5750-5758.2004","article-title":"NF-kappaB- and AP-1-mediated induction of human beta defensin-2 in intestinal epithelial cells by Escherichiacoli Nissle 1917: a novel effect of a probiotic bacterium","volume":"72","author":"Wehkamp","year":"2004","journal-title":"Infect Immun"},{"key":"2022070111263263700_bib291","doi-asserted-by":"crossref","first-page":"17020","DOI":"10.1073\/pnas.252529799","article-title":"Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichiacoli","volume":"99","author":"Welch","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022070111263263700_bib292","first-page":"581","article-title":"[Stablility of Escherichiacoli-flora in healthy men. 3. Occurrence of permanent and transitory strains in infants]","volume":"154","author":"Wiedemann","year":"1971","journal-title":"Arch Hyg Bakteriol"},{"key":"2022070111263263700_bib320_1645529882797","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1126\/science.1243357","article-title":"Long-term dynamics of adaptation in asexual populations","volume":"342","author":"Wiser","year":"2013","journal-title":"Science"},{"key":"2022070111263263700_bib293","doi-asserted-by":"crossref","first-page":"e1003549","DOI":"10.1371\/journal.pcbi.1003549","article-title":"Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data","volume":"10","author":"Worby","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"2022070111263263700_bib294","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1126\/science.1208344","article-title":"Linking long-term dietary patterns with gut microbial enterotypes","volume":"334","author":"Wu","year":"2011","journal-title":"Science"},{"key":"2022070111263263700_bib295","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1093\/molbev\/msx304","article-title":"PHYLOSCANNER: inferring transmission from within- and between-host pathogen genetic diversity","volume":"35","author":"Wymant","year":"2018","journal-title":"Mol Biol Evol"},{"key":"2022070111263263700_bib296","doi-asserted-by":"crossref","first-page":"1713","DOI":"10.1111\/j.1365-294X.2006.02882.x","article-title":"Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances","volume":"15","author":"Xu","year":"2006","journal-title":"Mol Ecol"},{"key":"2022070111263263700_bib297","doi-asserted-by":"crossref","first-page":"8833757","DOI":"10.1155\/2020\/8833757","article-title":"Bacterial contaminants and antibiogram of Ghana paper currency notes in circulation and their associated health risks in asante-mampong, Ghana","volume":"2020","author":"Yar","year":"2020","journal-title":"Int J Microbiol"},{"key":"2022070111263263700_bib298","doi-asserted-by":"crossref","first-page":"1772","DOI":"10.1001\/jama.2014.13875","article-title":"Oral, capsulized, frozen fecal microbiota transplantation for relapsing Clostridiumdifficile infection","volume":"312","author":"Youngster","year":"2014","journal-title":"JAMA"},{"key":"2022070111263263700_bib299","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1101\/gr.251678.119","article-title":"The enterobase user's guide, with case studies on Salmonella transmission, Yersiniapestis phylogeny, and Escherichia core genomic diversity","volume":"30","author":"Zhou","year":"2020","journal-title":"Genome Res"},{"key":"2022070111263263700_bib300","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.vetmic.2018.02.011","article-title":"Antimicrobial resistance, multilocus sequence types and virulence profiles of ESBL producing and non-ESBL producing uropathogenic Escherichia coli isolated from cats and dogs in Switzerland","volume":"216","author":"Zogg","year":"2018","journal-title":"Vet Microbiol"},{"key":"2022070111263263700_bib301","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1111\/j.1462-5822.2006.00836.x","article-title":"Molecular mechanisms underlying the probiotic effects of Escherichiacoli Nissle 1917 involve ZO-2 and PKCzeta redistribution resulting in tight junction and epithelial barrier repair","volume":"9","author":"Zyrek","year":"2007","journal-title":"Cell Microbiol"}],"container-title":["FEMS Microbiology Reviews"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/femsre\/advance-article-pdf\/doi\/10.1093\/femsre\/fuac008\/43258017\/fuac008.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/femsre\/article-pdf\/46\/3\/fuac008\/44362840\/fuac008.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/femsre\/article-pdf\/46\/3\/fuac008\/44362840\/fuac008.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,9,17]],"date-time":"2024-09-17T15:45:19Z","timestamp":1726587919000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/femsre\/article\/doi\/10.1093\/femsre\/fuac008\/6522174"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,4]]},"references-count":331,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2022,5,6]]}},"URL":"https:\/\/doi.org\/10.1093\/femsre\/fuac008","relation":{},"ISSN":["1574-6976"],"issn-type":[{"value":"1574-6976","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,5]]},"published":{"date-parts":[[2022,2,4]]},"article-number":"fuac008"}}