{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T01:14:44Z","timestamp":1788311684656,"version":"build-2803163510"},"reference-count":83,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2018,10,30]],"date-time":"2018-10-30T00:00:00Z","timestamp":1540857600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000009","name":"Foundation for the National Institutes of Health","doi-asserted-by":"publisher","award":["1-U01-AI124316-01"],"award-info":[{"award-number":["1-U01-AI124316-01"]}],"id":[{"id":"10.13039\/100000009","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Fonden","doi-asserted-by":"publisher","award":["NNF10CC1016517"],"award-info":[{"award-number":["NNF10CC1016517"]}],"id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007911","name":"University of California, San Diego","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007911","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"DOI":"10.3389\/fmicb.2018.02559","type":"journal-article","created":{"date-parts":[[2018,10,30]],"date-time":"2018-10-30T06:20:36Z","timestamp":1540880436000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":47,"title":["Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient"],"prefix":"10.3389","volume":"9","author":[{"given":"Xin","family":"Fang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan M.","family":"Monk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergey","family":"Nurk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margarita","family":"Akseshina","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiyun","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Gemmell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Connor","family":"Gianetto-Hill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nelly","family":"Leung","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Szubin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jon","family":"Sanders","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul L.","family":"Beck","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weizhong","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William J.","family":"Sandborn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott D.","family":"Gray-Owen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rob","family":"Knight","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"Allen-Vercoe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernhard O.","family":"Palsson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Larry","family":"Smarr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2018,10,30]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/j.imlet.2014.05.014","article-title":"Fusobacterium and enterobacteriaceae: important players for CRC?","volume":"162","author":"Allen-Vercoe","year":"2014","journal-title":"Immunol. Lett."},{"key":"B2","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1126\/science.1224820","article-title":"Intestinal inflammation targets cancer-inducing activity of the microbiota","volume":"338","author":"Arthur","year":"2012","journal-title":"Science"},{"key":"B3","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"B4","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1566","DOI":"10.1172\/JCI30504","article-title":"CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in crohn disease","volume":"117","author":"Barnich","year":"2007","journal-title":"J. Clin. Invest."},{"key":"B6","doi-asserted-by":"publisher","first-page":"6151","DOI":"10.1128\/IAI.72.10.6151-6156.2004","article-title":"Use of deoxyribose by intestinal and extraintestinal pathogenic escherichia coli strains: a metabolic adaptation involved in competitiveness","volume":"72","author":"Bernier-F\u00e9breau","year":"2004","journal-title":"Infect. Immun."},{"key":"B7","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/1745-6150-7-12","article-title":"Domain enhanced lookup time accelerated BLAST","volume":"7","author":"Boratyn","year":"2012","journal-title":"Biol. Direct"},{"key":"B8","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/s40168-017-0244-z","article-title":"Proteobacteria explain significant functional variability in the human gut microbiome","volume":"5","author":"Bradley","year":"2017","journal-title":"Microbiome"},{"key":"B9","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":"B10","doi-asserted-by":"publisher","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: a reference database for bacterial virulence factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1904","DOI":"10.1128\/IAI.03003-14","article-title":"The IbeA invasin of adherent-invasive Escherichia coli mediates interaction with intestinal epithelia and macrophages","volume":"83","author":"Cieza","year":"2015","journal-title":"Infect. Immun."},{"key":"B12","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1016\/S0140-6736(15)00465-1","article-title":"Inherited determinants of crohn's disease and ulcerative colitis phenotypes: a genetic association study","volume":"387","author":"Cleynen","year":"2016","journal-title":"Lancet"},{"key":"B13","doi-asserted-by":"publisher","first-page":"11117","DOI":"10.1021\/ja903322w","article-title":"The building blocks of cellulose: the intrinsic conformational structures of cellobiose, its epimer, lactose, and their singly hydrated complexes","volume":"131","author":"Cocinero","year":"2009","journal-title":"J. Am. Chem. Soc."},{"key":"B14","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1136\/gut.25.8.805","article-title":"Cellulose and the human gut","volume":"25","author":"Cummings","year":"1984","journal-title":"Gut"},{"key":"B15","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1078\/1438-4221-00201","article-title":"Adherent-invasive escherichia coli: a putative new E. coli pathotype associated with crohn's disease","volume":"292","author":"Darfeuille-Michaud","year":"2002","journal-title":"Int. J. Med. Microbiol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1053\/j.gastro.2004.04.061","article-title":"High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in crohn's disease","volume":"127","author":"Darfeuille-Michaud","year":"2004","journal-title":"Gastroenterology"},{"key":"B17","doi-asserted-by":"publisher","first-page":"1405","DOI":"10.1016\/S0016-5085(98)70019-8","article-title":"Presence of adherent escherichia coli strains in ileal mucosa of patients with crohn's disease","volume":"115","author":"Darfeuille-Michaud","year":"1998","journal-title":"Gastroenterology"},{"key":"B18","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1097\/MIB.0000000000000574","article-title":"Genome-based definition of an inflammatory bowel disease-associated Adherent-Invasive Escherichia coli pathovar","volume":"22","author":"Desilets","year":"2016","journal-title":"Inflamm. Bowel Dis."},{"key":"B19","doi-asserted-by":"publisher","first-page":"1919","DOI":"10.1097\/MIB.0000000000000183","article-title":"Inflammation-associated adherent-invasive Escherichia coli are enriched in pathways for use of propanediol and iron and m-cell translocation","volume":"20","author":"Dogan","year":"2014","journal-title":"Inflamm. Bowel Dis."},{"key":"B20","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1128\/JCM.02562-14","article-title":"Rapid identification of major Escherichia coli sequence types causing urinary tract and bloodstream infections","volume":"53","author":"Doumith","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1016\/j.ijmm.2007.05.011","article-title":"Escherichia coli isolated from a crohn's disease patient adheres, invades, and induces inflammatory responses in polarized intestinal epithelial cells","volume":"298","author":"Eaves-Pyles","year":"2008","journal-title":"Int. J. Med. Microbiol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1186\/1752-0509-7-74","article-title":"COBRApy: COnstraints-based reconstruction and analysis for python","volume":"7","author":"Ebrahim","year":"2013","journal-title":"BMC Syst. Biol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"4068","DOI":"10.1128\/IAI.00904-15","article-title":"Adherent-Invasive escherichia coli production of cellulose influences Iron-Induced bacterial aggregation, phagocytosis, and induction of colitis","volume":"83","author":"Ellermann","year":"2015","journal-title":"Infect. Immun."},{"key":"B24","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/s12918-018-0587-5","article-title":"Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa","volume":"12","author":"Fang","year":"2018","journal-title":"BMC Syst. Biol."},{"key":"B25","doi-asserted-by":"publisher","first-page":"i124","DOI":"10.1093\/bioinformatics\/btx237","article-title":"Abundance estimation and differential testing on strain level in metagenomics data","volume":"33","author":"Fischer","year":"2017","journal-title":"Bioinformatics"},{"key":"B26","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1111\/cmi.12539","article-title":"The Vat-AIEC protease promotes crossing of the intestinal mucus layer by crohn's disease-associated Escherichia coli","volume":"18","author":"Gibold","year":"2016","journal-title":"Cell. Microbiol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"765","DOI":"10.1053\/j.gastro.2013.11.033","article-title":"Endotoxicity of lipopolysaccharide as a determinant of t-cell-mediated colitis induction in mice","volume":"146","author":"Gronbach","year":"2014","journal-title":"Gastroenterology"},{"key":"B28","doi-asserted-by":"publisher","first-page":"17004","DOI":"10.1038\/nmicrobiol.2017.4","article-title":"Dynamics of the human gut microbiome in inflammatory bowel disease","volume":"2","author":"Halfvarson","year":"2017","journal-title":"Nat. Microbiol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"963","DOI":"10.1097\/MIB.0000000000000332","article-title":"Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases","volume":"21","author":"Huang","year":"2015","journal-title":"Inflamm. Bowel Dis."},{"key":"B30","doi-asserted-by":"publisher","first-page":"994","DOI":"10.1126\/science.1183605","article-title":"A catalog of reference genomes from the human microbiome","volume":"328","author":"Nelson","year":"2010","journal-title":"Science"},{"key":"B31","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","year":"2012","journal-title":"Nature"},{"key":"B32","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1186\/1471-2105-15-182","article-title":"Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads","volume":"15","author":"Jiang","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"B33","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1002\/biot.201200267","article-title":"Metabolic costs of amino acid and protein production in Escherichia coli","volume":"8","author":"Kaleta","year":"2013","journal-title":"Biotechnol. J."},{"key":"B34","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1136\/gut.2006.099796","article-title":"High prevalence of escherichia coli belonging to the B2+D phylogenetic group in inflammatory bowel disease","volume":"56","author":"Kotlowski","year":"2007","journal-title":"Gut"},{"key":"B35","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1186\/s13073-016-0294-z","article-title":"The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation","volume":"8","author":"Langdon","year":"2016","journal-title":"Genome Med."},{"key":"B36","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"B37","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1038\/nbt.3319","article-title":"ConStrains identifies microbial strains in metagenomic datasets","volume":"33","author":"Luo","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"B38","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet. J."},{"key":"B39","doi-asserted-by":"publisher","first-page":"1442","DOI":"10.1128\/IAI.01039-08","article-title":"Role of deoxyribose catabolism in colonization of the murine intestine by pathogenic Escherichia coli strains","volume":"77","author":"Martinez-J\u00e9hanne","year":"2009","journal-title":"Infect. Immun."},{"key":"B40","doi-asserted-by":"publisher","first-page":"213","DOI":"10.4291\/wjgp.v5.i3.213","article-title":"Escherichia coli in chronic inflammatory bowel diseases: an update on adherent invasive escherichia coli pathogenicity","volume":"5","author":"Martinez-Medina","year":"2014","journal-title":"World J. Gastrointest. Pathophysiol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"3968","DOI":"10.1128\/JCM.01484-09","article-title":"Similarity and divergence among adherent-invasive Escherichia coli and extraintestinal pathogenic E. coli strains","volume":"47","author":"Martinez-Medina","year":"2009","journal-title":"J. Clin. Microbiol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1007\/s00281-014-0454-4","article-title":"The gut microbiota and inflammatory bowel disease","volume":"37","author":"Matsuoka","year":"2015","journal-title":"Semin. Immunopathol."},{"key":"B43","unstructured":"mca2018"},{"key":"B44","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/msb.2013.18","article-title":"Basic and applied uses of genome\u2013scale metabolic network reconstructions of Escherichia coli","volume":"9","author":"McCloskey","year":"2013","journal-title":"Mol. Syst. Biol."},{"key":"B45","doi-asserted-by":"publisher","first-page":"W20","DOI":"10.1093\/nar\/gkh435","article-title":"BLAST: at the core of a powerful and diverse set of sequence analysis tools","volume":"32","author":"McGinnis","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"B46","doi-asserted-by":"publisher","first-page":"e12714","DOI":"10.1371\/journal.pone.0012714","article-title":"Complete genome sequence of crohn's disease-associated adherent-invasive E. coli strain LF82","volume":"5","author":"Miquel","year":"2010","journal-title":"PLoS ONE"},{"key":"B47","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1038\/nbt.2870","article-title":"Optimizing genome-scale network reconstructions","volume":"32","author":"Monk","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"B48","doi-asserted-by":"publisher","first-page":"20338","DOI":"10.1073\/pnas.1307797110","article-title":"Genome-scale metabolic reconstructions of multiple escherichia coli strains highlight strain-specific adaptations to nutritional environments","volume":"110","author":"Monk","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B49","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1038\/nbt.3956","article-title":"iML1515, a knowledgebase that computes escherichia coli traits","volume":"35","author":"Monk","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"R79","DOI":"10.1186\/gb-2012-13-9-r79","article-title":"Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment","volume":"13","author":"Morgan","year":"2012","journal-title":"Genome Biol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1038\/ajg.2015.120","article-title":"C-Reactive protein, fecal calprotectin, and stool lactoferrin for detection of endoscopic activity in symptomatic inflammatory bowel disease patients: a systematic review and Meta-Analysis","volume":"110","author":"Mosli","year":"2015","journal-title":"Am. J. Gastroenterol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1038\/nrgastro.2012.14","article-title":"IBD\u2014what role do proteobacteria play?","volume":"9","author":"Mukhopadhya","year":"2012","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"B53","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1186\/1471-2164-11-667","article-title":"Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes","volume":"11","author":"Nash","year":"2010","journal-title":"BMC Genomics"},{"key":"B54","doi-asserted-by":"publisher","first-page":"1612","DOI":"10.1101\/gr.201863.115","article-title":"An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography","volume":"26","author":"Nayfach","year":"2016","journal-title":"Genome Res."},{"key":"B55","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1002\/ibd.21899","article-title":"Characterization of adherent-invasive Escherichia coli isolated from pediatric patients with inflammatory bowel disease","volume":"18","author":"Negroni","year":"2012","journal-title":"Inflamm. Bowel Dis."},{"key":"B56","volume-title":"Escherichia coli and Salmonella: Cellular and Molecular Biology","author":"Neidhardt","year":"1999"},{"key":"B57","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1038\/nrgastro.2017.88","article-title":"Gut microbiota and IBD: causation or correlation?","volume":"14","author":"Ni","year":"2017","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"B58","doi-asserted-by":"publisher","first-page":"1382","DOI":"10.1136\/gutjnl-2015-311059","article-title":"Comparative genomics of crohn's disease-associated adherent-invasive Escherichia coli","volume":"66","author":"O'Brien","year":"2016","journal-title":"Gut"},{"key":"B59","doi-asserted-by":"publisher","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"B60","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1136\/gutjnl-2017-314903","article-title":"Adherent-invasive Escherichia coli in inflammatory bowel disease","volume":"67","author":"Palmela","year":"2017","journal-title":"Gut"},{"key":"B61","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"B62","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1136\/gutjnl-2016-313235","article-title":"A microbial signature for crohn's disease","volume":"66","author":"Pascal","year":"2017","journal-title":"Gut"},{"key":"B63","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1186\/1471-2180-9-171","article-title":"A phylogenetic group of Escherichia coli associated with active left-sided inflammatory bowel disease","volume":"9","author":"Petersen","year":"2009","journal-title":"BMC Microbiol."},{"key":"B64","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1186\/s13059-017-1309-9","article-title":"DESMAN: a new tool for de novo extraction of strains from metagenomes","volume":"18","author":"Quince","year":"2017","journal-title":"Genome Biol."},{"key":"B65","doi-asserted-by":"publisher","first-page":"6881","DOI":"10.1128\/JB.00619-08","article-title":"The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates","volume":"190","author":"Rasko","year":"2008","journal-title":"J. Bacteriol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"111","DOI":"10.3389\/fgene.2017.00111","article-title":"Comparative genomic analysis of the human gut microbiome reveals a broad distribution of metabolic pathways for the degradation of Host-Synthetized mucin glycans and utilization of Mucin-Derived monosaccharides","volume":"8","author":"Ravcheev","year":"2017","journal-title":"Front. Genet."},{"key":"B67","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1136\/gut.2006.111872","article-title":"The role of Escherichia coli in inflammatory bowel disease","volume":"56","author":"Rhodes","year":"2007","journal-title":"Gut"},{"key":"B68","doi-asserted-by":"publisher","first-page":"D682","DOI":"10.1093\/nar\/gkv1004","article-title":"BacWGSTdb, a database for genotyping and source tracking bacterial pathogens","volume":"44","author":"Ruan","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"B69","doi-asserted-by":"publisher","first-page":"1042","DOI":"10.1038\/labinvest.3700661","article-title":"Invasive Escherichia coli are a feature of crohn's disease","volume":"87","author":"Sasaki","year":"2007","journal-title":"Lab. Invest."},{"key":"B70","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1038\/s41564-017-0089-z","article-title":"Dynamics of metatranscription in the inflammatory bowel disease gut microbiome","volume":"3","author":"Schirmer","year":"2018","journal-title":"Nat. Microbiol."},{"key":"B71","unstructured":"scikit-bio.2018"},{"key":"B72","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B73","doi-asserted-by":"publisher","first-page":"2304","DOI":"10.1038\/ncomms3304","article-title":"PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes","volume":"4","author":"Segata","year":"2013","journal-title":"Nat. Commun."},{"key":"B74","doi-asserted-by":"publisher","first-page":"e00036","DOI":"10.1128\/mSystems.00036-17","article-title":"Development of inflammatory bowel disease is linked to a longitudinal restructuring of the gut metagenome in mice","volume":"2","author":"Sharpton","year":"2017","journal-title":"mSystems"},{"key":"B75","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1186\/1471-2164-10-385","article-title":"Microbial comparative pan-genomics using binomial mixture models","volume":"10","author":"Snipen","year":"2009","journal-title":"BMC Genomics"},{"key":"B76","doi-asserted-by":"publisher","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B77","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1038\/nprot.2009.203","article-title":"A protocol for generating a high-quality genome-scale metabolic reconstruction","volume":"5","author":"Thiele","year":"2010","journal-title":"Nat. Protoc."},{"key":"B78","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1101\/gr.216242.116","article-title":"Microbial strain-level population structure and genetic diversity from metagenomes","volume":"27","author":"Truong","year":"2017","journal-title":"Genome Res."},{"key":"B79","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1097\/MIB.0000000000000609","article-title":"GipA factor supports colonization of peyer's patches by crohn's disease-associated Escherichia coli","volume":"22","author":"Vazeille","year":"2016","journal-title":"Inflamm. Bowel Dis."},{"key":"B80","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1186\/1471-2164-12-316","article-title":"Comparative genomics of Escherichia coli isolated from patients with inflammatory bowel disease","volume":"12","author":"Vejborg","year":"2011","journal-title":"BMC Genomics"},{"key":"B81","doi-asserted-by":"crossref","DOI":"10.1145\/2484762.2484828","article-title":"Large memory high performance computing enables comparison across human gut microbiome of patients with autoimmune diseases and healthy subjects","volume-title":"Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery","author":"Wu","year":"2013"},{"key":"B82","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1093\/bioinformatics\/btv638","article-title":"MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets","volume":"32","author":"Wu","year":"2016","journal-title":"Bioinformatics"},{"key":"B83","doi-asserted-by":"publisher","first-page":"e0130902","DOI":"10.1371\/journal.pone.0130902","article-title":"Identification of candidate adherent-invasive E. coli signature transcripts by genomic\/transcriptomic analysis","volume":"10","author":"Zhang","year":"2015","journal-title":"PLoS ONE"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2018.02559\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,4]],"date-time":"2022-09-04T21:47:18Z","timestamp":1662328038000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmicb.2018.02559\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,10,30]]},"references-count":83,"alternative-id":["10.3389\/fmicb.2018.02559"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2018.02559","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,10,30]]},"article-number":"2559"}}