Cho I, Blaser MJ: The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012, 13: 260-270.
PubMed Central
CAS
PubMed
Google Scholar
Tenaillon O, Skurnik D, Picard B, Denamur E: The population genetics of commensal Escherichia coli. Nat Rev Microbiol. 2010, 8: 207-217. 10.1038/nrmicro2298.
Article
CAS
PubMed
Google Scholar
Lukjancenko O, Wassenaar TM, Ussery DW: Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol. 2010, 60: 708-720. 10.1007/s00248-010-9717-3.
Article
PubMed Central
CAS
PubMed
Google Scholar
Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW: Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray. Genome Biol. 2007, 8: R267-10.1186/gb-2007-8-12-r267.
Article
PubMed Central
PubMed
Google Scholar
Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O: Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 2009, 5: e1000344-10.1371/journal.pgen.1000344.
Article
PubMed Central
PubMed
Google Scholar
Luo C, Walk ST, Gordon DM, Feldgarden M, Tiedje JM, Konstantinidis KT: Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci U S A. 2011, 108: 7200-7205. 10.1073/pnas.1015622108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Storro O, Oien T, Dotterud CK, Jenssen JA, Johnsen R: A primary health-care intervention on pre- and postnatal risk factor behavior to prevent childhood allergy. The Prevention of Allergy among Children in Trondheim (PACT) study. BMC Public Health. 2010, 10: 443-10.1186/1471-2458-10-443.
Article
PubMed Central
PubMed
Google Scholar
Storro O, Oien T, Langsrud O, Rudi K, Dotterud C, Johnsen R: Temporal variations in early gut microbial colonization are associated with allergen-specific immunoglobulin E but not atopic eczema at 2 years of age. Clin Exp Allergy. 2011, 41: 1545-1554. 10.1111/j.1365-2222.2011.03817.x.
Article
CAS
PubMed
Google Scholar
Rudi K, Storro O, Oien T, Johnsen R: Modelling bacterial transmission in human allergen-specific IgE sensitization. Lett Appl Microbiol. 2012, 54: 447-454. 10.1111/j.1472-765X.2012.03229.x.
Article
CAS
PubMed
Google Scholar
de Muinck EJ, Oien T, Storro O, Johnsen R, Stenseth NC, Ronningen KS, Rudi K: Diversity, transmission and persistence of Escherichia coli in a cohort of mothers and their infants. Environmental Microbiology Reports. 2011, 3: 352-359. 10.1111/j.1758-2229.2010.00231.x.
Article
PubMed
Google Scholar
Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R: Diversity, stability and resilience of the human gut microbiota. Nature. 2012, 489: 220-230. 10.1038/nature11550.
Article
PubMed Central
CAS
PubMed
Google Scholar
Delmont TO, Robe P, Cecillon S, Clark IM, Constancias F, Simonet P, Hirsch PR, Vogel TM: Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol. 2011, 77: 1315-1324. 10.1128/AEM.01526-10.
Article
PubMed Central
CAS
PubMed
Google Scholar
Oien T, Storro O, Johnsen R: Intestinal microbiota and its effect on the immune system–a nested case-cohort study on prevention of atopy among small children in Trondheim: the IMPACT study. Contemp Clin Trials. 2006, 27: 389-395. 10.1016/j.cct.2006.02.009.
Article
PubMed
Google Scholar
Afset JE, Anderssen E, Bruant G, Harel J, Wieler L, Bergh K: Phylogenetic backgrounds and virulence profiles of atypical enteropathogenic Escherichia coli strains from a case–control study using multilocus sequence typing and DNA microarray analysis. J Clin Microbiol. 2008, 46: 2280-2290. 10.1128/JCM.01752-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Elliott SJ, Wainwright LA, McDaniel TK, Jarvis KG, Deng YK, Lai LC, McNamara BP, Donnenberg MS, Kaper JB: The complete sequence of the locus of enterocyte effacement (LEE) from enteropathogenic Escherichia coli E2348/69. Mol Microbiol. 1998, 28: 1-4.
Article
CAS
PubMed
Google Scholar
Ramer SW, Schoolnik GK, Wu CY, Hwang J, Schmidt SA, Bieber D: The type IV pilus assembly complex: biogenic interactions among the bundle-forming pilus proteins of enteropathogenic Escherichia coli. J Bacteriol. 2002, 184: 3457-3465. 10.1128/JB.184.13.3457-3465.2002.
Article
PubMed Central
CAS
PubMed
Google Scholar
Vieira-Silva S, Rocha EP: The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet. 2010, 6: e1000808-10.1371/journal.pgen.1000808.
Article
PubMed Central
PubMed
Google Scholar
Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF: The complete genome sequence of Escherichia coli K-12. Science. 1997, 277: 1453-1462. 10.1126/science.277.5331.1453.
Article
CAS
PubMed
Google Scholar
Chaudhuri RR, Sebaihia M, Hobman JL, Webber MA, Leyton DL, Goldberg MD, Cunningham AF, Scott-Tucker A, Ferguson PR, Thomas CM: Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042. PLoS One. 2010, 5: e8801-10.1371/journal.pone.0008801.
Article
PubMed Central
PubMed
Google Scholar
Hochhut B, Wilde C, Balling G, Middendorf B, Dobrindt U, Brzuszkiewicz E, Gottschalk G, Carniel E, Hacker J: Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536. Mol Microbiol. 2006, 61: 584-595. 10.1111/j.1365-2958.2006.05255.x.
Article
CAS
PubMed
Google Scholar
Welch RA, Burland V, Plunkett G, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J: Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci U S A. 2002, 99: 17020-17024. 10.1073/pnas.252529799.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rasko DA, Rosovitz MJ, Myers GS, Mongodin EF, Fricke WF, Gajer P, Crabtree J, Sebaihia M, Thomson NR, Chaudhuri R: The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol. 2008, 190: 6881-6893. 10.1128/JB.00619-08.
Article
PubMed Central
CAS
PubMed
Google Scholar
Crossman LC, Chaudhuri RR, Beatson SA, Wells TJ, Desvaux M, Cunningham AF, Petty NK, Mahon V, Brinkley C, Hobman JL: A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407. J Bacteriol. 2010, 192: 5822-5831. 10.1128/JB.00710-10.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen SL, Hung CS, Xu J, Reigstad CS, Magrini V, Sabo A, Blasiar D, Bieri T, Meyer RR, Ozersky P: Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci U S A. 2006, 103: 5977-5982. 10.1073/pnas.0600938103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Krause DO, Little AC, Dowd SE, Bernstein CN: Complete genome sequence of adherent invasive Escherichia coli UM146 isolated from Ileal Crohn's disease biopsy tissue. J Bacteriol. 2011, 193: 583-10.1128/JB.01290-10.
Article
PubMed Central
CAS
PubMed
Google Scholar
Toh H, Oshima K, Toyoda A, Ogura Y, Ooka T, Sasamoto H, Park SH, Iyoda S, Kurokawa K, Morita H: Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2. J Bacteriol. 2010, 192: 1165-1166. 10.1128/JB.01543-09.
Article
PubMed Central
CAS
PubMed
Google Scholar
Oshima K, Toh H, Ogura Y, Sasamoto H, Morita H, Park SH, Ooka T, Iyoda S, Taylor TD, Hayashi T: Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Res. 2008, 15: 375-386. 10.1093/dnares/dsn026.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T: Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 2001, 8: 11-22. 10.1093/dnares/8.1.11.
Article
CAS
PubMed
Google Scholar
Iguchi A, Thomson NR, Ogura Y, Saunders D, Ooka T, Henderson IR, Harris D, Asadulghani M, Kurokawa K, Dean P: Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J Bacteriol. 2009, 191: 347-354. 10.1128/JB.01238-08.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ahmed SA, Awosika J, Baldwin C, Bishop-Lilly KA, Biswas B, Broomall S, Chain PS, Chertkov O, Chokoshvili O, Coyne S: Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2. PLoS One. 2012, 7: e48228-10.1371/journal.pone.0048228.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nash JH, Villegas A, Kropinski AM, Aguilar-Valenzuela R, Konczy P, Mascarenhas M, Ziebell K, Torres AG, Karmali MA, Coombes BK: Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes. BMC Genomics. 2010, 11: 667-10.1186/1471-2164-11-667.
Article
PubMed Central
PubMed
Google Scholar
Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M, Oshima K, Kodama T, Abe H, Nakayama K, Kurokawa K: Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci U S A. 2009, 106: 17939-17944. 10.1073/pnas.0903585106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lu S, Zhang X, Zhu Y, Kim KS, Yang J, Jin Q: Complete genome sequence of the neonatal-meningitis-associated Escherichia coli strain CE10. J Bacteriol. 2011, 193: 7005-10.1128/JB.06284-11.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wetzel J, Kingsford C, Pop M: Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics. 2011, 12: 95-10.1186/1471-2105-12-95.
Article
PubMed Central
PubMed
Google Scholar
Brzuszkiewicz E, Bruggemann H, Liesegang H, Emmerth M, Olschlager T, Nagy G, Albermann K, Wagner C, Buchrieser C, Emody L: How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc Natl Acad Sci U S A. 2006, 103: 12879-12884. 10.1073/pnas.0603038103.
Article
PubMed Central
PubMed
Google Scholar
Diard M, Garry L, Selva M, Mosser T, Denamur E, Matic I: Pathogenicity-associated islands in extraintestinal pathogenic Escherichia coli are fitness elements involved in intestinal colonization. J Bacteriol. 2010, 192: 4885-4893. 10.1128/JB.00804-10.
Article
PubMed Central
CAS
PubMed
Google Scholar
Le GT, Clermont O, Gouriou S, Picard B, Nassif X, Denamur E, Tenaillon O: Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains. Mol Biol Evol. 2007, 24: 2373-2384. 10.1093/molbev/msm172.
Article
Google Scholar
Kamada N, Kim YG, Sham HP, Vallance BA, Puente JL, Martens EC, Nunez G: Regulated virulence controls the ability of a pathogen to compete with the gut microbiota. Science. 2012, 336: 1325-1329. 10.1126/science.1222195.
Article
PubMed Central
CAS
PubMed
Google Scholar
Alteri CJ, Mobley HL: Escherichia coli physiology and metabolism dictates adaptation to diverse host microenvironments. Curr Opin Microbiol. 2012, 15: 3-9. 10.1016/j.mib.2011.12.004.
Article
PubMed Central
CAS
PubMed
Google Scholar
Read AF: The evolution of virulence. Trends Microbiol. 1994, 2: 73-76. 10.1016/0966-842X(94)90537-1.
Article
CAS
PubMed
Google Scholar
Meric G, Kemsley EK, Falush D, Saggers EJ, Lucchini S: Phylogenetic distribution of traits associated with plant colonization in Escherichia coli. Environ Microbiol. 2012, 15: 487-501.
Article
PubMed
Google Scholar
Koch AL: The adaptive responses of Escherichia coli to a feast and famine existence. Adv Microb Physiol. 1971, 6: 147-217.
Article
CAS
PubMed
Google Scholar
Button DK: Biochemical basis for whole-cell uptake kinetics: specific affinity, oligotrophic capacity, and the meaning of the michaelis constant. Appl Environ Microbiol. 1991, 57: 2033-2038.
PubMed Central
CAS
PubMed
Google Scholar
Adlerberth I: Factors influencing the establishment of the intestinal microbiota in infancy. Nestle Nutr Workshop Ser Pediatr Program. 2008, 62: 13-29.
Article
PubMed
Google Scholar
Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO: Development of the human infant intestinal microbiota. PLoS Biol. 2007, 5: e177-10.1371/journal.pbio.0050177.
Article
PubMed Central
PubMed
Google Scholar
Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE: Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A. 2011, 108 (Suppl 1): 4578-4585.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE: Metagenomic analysis of the human distal gut microbiome. Science. 2006, 312: 1355-1359. 10.1126/science.1124234.
Article
PubMed Central
CAS
PubMed
Google Scholar
Koren O, Goodrich JK, Cullender TC, Spor A, Laitinen K, Kling BH, Gonzalez A, Werner JJ, Angenent LT, Knight R: Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell. 2012, 150: 470-480. 10.1016/j.cell.2012.07.008.
Article
PubMed Central
CAS
PubMed
Google Scholar
Buckling A, Craig MR, Brockhurst MA, Colegrave N: The Beagle in a bottle. Nature. 2009, 457: 824-829. 10.1038/nature07892.
Article
CAS
PubMed
Google Scholar
Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, Mohaideen N, Ioerger TR, Sacchettini JC, Lipsitch M: Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection. Nat Genet. 2011, 43: 482-486. 10.1038/ng.811.
Article
PubMed Central
CAS
PubMed
Google Scholar
Okoro CK, Kingsley RA, Quail MA, Kankwatira AM, Feasey NA, Parkhill J, Dougan G, Gordon MA: High-resolution single nucleotide polymorphism analysis distinguishes recrudescence and reinfection in recurrent invasive nontyphoidal Salmonella typhimurium disease. Clin Infect Dis. 2012, 54: 955-963. 10.1093/cid/cir1032.
Article
PubMed Central
CAS
PubMed
Google Scholar
Morowitz MJ, Denef VJ, Costello EK, Thomas BC, Poroyko V, Relman DA, Banfield JF: Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci U S A. 2011, 108: 1128-1133. 10.1073/pnas.1010992108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Taylor DE: Bacterial tellurite resistance. Trends Microbiol. 1999, 7: 111-115. 10.1016/S0966-842X(99)01454-7.
Article
CAS
PubMed
Google Scholar
Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP: Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 2007, 14: 169-181. 10.1093/dnares/dsm018.
Article
PubMed Central
CAS
PubMed
Google Scholar
Martens EC, Chiang HC, Gordon JI: Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe. 2008, 4: 447-457. 10.1016/j.chom.2008.09.007.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kim DH, Konishi L, Kobashi K: Purification, characterization and reaction mechanism of novel arylsulfotransferase obtained from an anaerobic bacterium of human intestine. Biochim Biophys Acta. 1986, 872: 33-41. 10.1016/0167-4838(86)90144-5.
Article
CAS
PubMed
Google Scholar
Kurihara S, Oda S, Kumagai H, Suzuki H: Gamma-glutamyl-gamma-aminobutyrate hydrolase in the putrescine utilization pathway of Escherichia coli K-12. FEMS Microbiol Lett. 2006, 256: 318-323. 10.1111/j.1574-6968.2006.00137.x.
Article
CAS
PubMed
Google Scholar
Kurihara S, Oda S, Tsuboi Y, Kim HG, Oshida M, Kumagai H: Suzuki H: gamma-Glutamylputrescine synthetase in the putrescine utilization pathway of Escherichia coli K-12. J Biol Chem. 2008, 283: 19981-19990. 10.1074/jbc.M800133200.
Article
CAS
PubMed
Google Scholar
Skibinski DA, Golby P, Chang YS, Sargent F, Hoffman R, Harper R, Guest JR, Attwood MM, Berks BC, Andrews SC: Regulation of the hydrogenase-4 operon of Escherichia coli by the sigma(54)-dependent transcriptional activators FhlA and HyfR. J Bacteriol. 2002, 184: 6642-6653. 10.1128/JB.184.23.6642-6653.2002.
Article
PubMed Central
CAS
PubMed
Google Scholar
Didelot X, Meric G, Falush D, Darling AE: Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. BMC Genomics. 2012, 13: 256-10.1186/1471-2164-13-256.
Article
PubMed Central
PubMed
Google Scholar
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M: The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008, 9: 75-10.1186/1471-2164-9-75.
Article
PubMed Central
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410.
Article
CAS
PubMed
Google Scholar
Darling AE, Mau B: Perna NT: progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One. 2010, 5: e11147-10.1371/journal.pone.0011147.
Article
PubMed Central
PubMed
Google Scholar
Didelot X, Falush D: Inference of bacterial microevolution using multilocus sequence data. Genetics. 2007, 175: 1251-1266.
Article
PubMed Central
CAS
PubMed
Google Scholar
R Foundation for Statistical Computing: R:A language and environment for statistical computing. Vienna, Austria, URL http://www.R-project.org.ISBN3-900051-07-01.
Nenadic O, Greenacre M: Correspondence analysis in R, with two- and three-dimensional graphics: The ca package. J Stat Software. 2007, 20: 1-13.
Google Scholar
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 2005, 21: 3674-3676. 10.1093/bioinformatics/bti610.
Article
CAS
PubMed
Google Scholar
Wright F: The ‘effective number of codons’ used in a gene. Gene. 1990, 87: 23-29. 10.1016/0378-1119(90)90491-9.
Article
CAS
PubMed
Google Scholar