{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T00:08:42Z","timestamp":1792454922566,"version":"4.5.0"},"reference-count":81,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2020,9,1]],"date-time":"2020-09-01T00:00:00Z","timestamp":1598918400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2020,9,1]],"date-time":"2020-09-01T00:00:00Z","timestamp":1598918400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,9,9]],"date-time":"2021-09-09T00:00:00Z","timestamp":1631145600000},"content-version":"vor","delay-in-days":373,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"}],"funder":[{"DOI":"10.13039\/100004897","name":"Pennsylvania Department of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004897","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Host &amp; Microbe"],"published-print":{"date-parts":[[2020,9]]},"DOI":"10.1016\/j.chom.2020.07.020","type":"journal-article","created":{"date-parts":[[2020,8,20]],"date-time":"2020-08-20T10:44:58Z","timestamp":1597920298000},"page":"422-433.e7","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":77,"title":["Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease"],"prefix":"10.1016","volume":"28","author":[{"given":"Frederic D.","family":"Bushman","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maire","family":"Conrad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunyu","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Gu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Petucci","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min-Soo","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arwa","family":"Abbas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kevin J.","family":"Downes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nina","family":"Devas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa M.","family":"Mattei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Breton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Judith","family":"Kelsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Marakos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alissa","family":"Galgano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kelly","family":"Kachelries","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessi","family":"Erlichman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica L.","family":"Hart","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Moraskie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dorothy","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huanjia","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Casey E.","family":"Hofstaedter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gary D.","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James D.","family":"Lewis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph P.","family":"Zackular","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongzhe","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kyle","family":"Bittinger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Baldassano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.chom.2020.07.020_bib1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.mib.2020.01.016","article-title":"Microbe-microbe interactions during Clostridioides difficile infection","volume":"53","author":"Abbas","year":"2020","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/j.chom.2020.07.020_bib2","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1038\/nrmicro.2016.108","article-title":"Clostridium difficile colitis: pathogenesis and host defence","volume":"14","author":"Abt","year":"2016","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.chom.2020.07.020_bib3","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J.\u00a0Mol. Biol."},{"key":"10.1016\/j.chom.2020.07.020_bib4","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aam7019","article-title":"Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea","volume":"10","author":"Battaglioli","year":"2018","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.chom.2020.07.020_bib5","first-page":"1","article-title":"Genetic manipulation of Clostridium difficile","volume":"2","author":"Bouillaut","year":"2011","journal-title":"Curr Protoc microbiol"},{"key":"10.1016\/j.chom.2020.07.020_bib6","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1128\/JB.01492-12","article-title":"Proline-dependent regulation of Clostridium difficile Stickland metabolism","volume":"195","author":"Bouillaut","year":"2013","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.chom.2020.07.020_bib7","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.14309\/ajg.0000000000000136","article-title":"Individualized dynamics in the gut microbiota precede Crohn's disease flares","volume":"114","author":"Braun","year":"2019","journal-title":"Am. J. Gastroenterol."},{"key":"10.1016\/j.chom.2020.07.020_bib8","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/nature13828","article-title":"Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile","volume":"517","author":"Buffie","year":"2015","journal-title":"Nature"},{"key":"10.1016\/j.chom.2020.07.020_bib9","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1056\/NEJM197807062990117","article-title":"Pseudomembranous colitis caused by Clostridia","volume":"299","author":"Burdon","year":"1978","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.chom.2020.07.020_bib10","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1128\/AEM.02525-09","article-title":"A mariner-based transposon system for in\u00a0vivo random mutagenesis of Clostridium difficile","volume":"76","author":"Cartman","year":"2010","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.chom.2020.07.020_bib11","doi-asserted-by":"crossref","first-page":"1948","DOI":"10.1097\/MIB.0000000000000454","article-title":"Fungal signature in the gut microbiota of pediatric patients with inflammatory bowel disease","volume":"21","author":"Chehoud","year":"2015","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.chom.2020.07.020_bib12","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1001\/jamainternmed.2013.7056","article-title":"Epidemiology of community-associated Clostridium difficile infection, 2009 through 2011","volume":"173","author":"Chitnis","year":"2013","journal-title":"JAMA Intern. Med."},{"key":"10.1016\/j.chom.2020.07.020_bib13","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s40168-019-0658-x","article-title":"Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments","volume":"7","author":"Clarke","year":"2019","journal-title":"Microbiome"},{"key":"10.1016\/j.chom.2020.07.020_bib14","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1038\/s41564-017-0072-8","article-title":"Enterotypes in the landscape of gut microbial community composition","volume":"3","author":"Costea","year":"2018","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2020.07.020_bib15","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"Edgar","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.chom.2020.07.020_bib16","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1016\/j.chom.2014.11.003","article-title":"Gut microbiota-produced succinate promotes C. difficile infection after antibiotic treatment or motility disturbance","volume":"16","author":"Ferreyra","year":"2014","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2020.07.020_bib17","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00089-18","article-title":"Shifts in the gut metabolome and Clostridium difficile transcriptome throughout colonization and infection in a mouse model","volume":"3","author":"Fletcher","year":"2018","journal-title":"mSphere"},{"key":"10.1016\/j.chom.2020.07.020_bib18","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41564-018-0306-4","article-title":"Gut microbiome structure and metabolic activity in inflammatory bowel disease","volume":"4","author":"Franzosa","year":"2019","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.chom.2020.07.020_bib19","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1136\/bmj.1.6114.695","article-title":"Identification of Clostridium difficile as a cause of pseudomembranous colitis","volume":"1","author":"George","year":"1978","journal-title":"Br. Med. J."},{"key":"10.1016\/j.chom.2020.07.020_bib20","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.idc.2014.11.004","article-title":"The epidemiology of Clostridium difficile infection inside and outside health care institutions","volume":"29","author":"Gerding","year":"2015","journal-title":"Infect. Dis. Clin. North Am."},{"key":"10.1016\/j.chom.2020.07.020_bib21","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1016\/j.chom.2014.02.005","article-title":"The treatment-naive microbiome in new-onset Crohn's disease","volume":"15","author":"Gevers","year":"2014","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2020.07.020_bib22","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1126\/science.1124234","article-title":"Metagenomic analysis of the human distal gut microbiome","volume":"312","author":"Gill","year":"2006","journal-title":"Science"},{"key":"10.1016\/j.chom.2020.07.020_bib23","doi-asserted-by":"crossref","first-page":"1162","DOI":"10.1086\/592257","article-title":"Emergence of Clostridium difficile infection due to a new hypervirulent strain, polymerase chain reaction ribotype 078","volume":"47","author":"Goorhuis","year":"2008","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.chom.2020.07.020_bib24","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1128\/JCM.01796-09","article-title":"Multilocus sequence typing of Clostridium difficile","volume":"48","author":"Griffiths","year":"2010","journal-title":"J.\u00a0Clin. Microbiol."},{"key":"10.1016\/j.chom.2020.07.020_bib25","doi-asserted-by":"crossref","first-page":"3617","DOI":"10.1172\/JCI75436","article-title":"Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature","volume":"124","author":"Haberman","year":"2014","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.chom.2020.07.020_bib26","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1084\/jem.180.2.525","article-title":"Ionizing radiation acts on cellular membranes to generate ceramide and initiate apoptosis","volume":"180","author":"Haimovitz-Friedman","year":"1994","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.chom.2020.07.020_bib27","doi-asserted-by":"crossref","first-page":"2222","DOI":"10.1007\/s10620-014-3169-4","article-title":"The prevalence of Clostridium difficile infection in pediatric and adult patients with inflammatory bowel disease","volume":"59","author":"Hourigan","year":"2014","journal-title":"Dig. Dis. Sci."},{"key":"10.1016\/j.chom.2020.07.020_bib28","first-page":"439","article-title":"Development and validation of a pediatric Crohn's disease activity index","volume":"12","author":"Hyams","year":"1991","journal-title":"J.\u00a0Pediatr. Gastroenterol. Nutr."},{"key":"10.1016\/j.chom.2020.07.020_bib29","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1080\/10618600.1996.10474713","article-title":"R: a language for data analysis and graphics","volume":"5","author":"Ihaka","year":"1996","journal-title":"J.\u00a0Comp. Graph. Stat."},{"key":"10.1016\/j.chom.2020.07.020_bib30","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005945","article-title":"Identifying human diamine sensors for death related putrescine and cadaverine molecules","volume":"14","author":"Izquierdo","year":"2018","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.chom.2020.07.020_bib31","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00063-17","article-title":"Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut microbiomes","volume":"2","author":"Jenior","year":"2017","journal-title":"mSystems"},{"key":"10.1016\/j.chom.2020.07.020_bib32","doi-asserted-by":"crossref","first-page":"2471","DOI":"10.1038\/s41467-020-16274-w","article-title":"Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels","volume":"11","author":"Johnson","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2020.07.020_bib33","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1002\/ibd.21421","article-title":"Recurrence rate of clostridium difficile infection in hospitalized pediatric patients with inflammatory bowel disease","volume":"17","author":"Kelsen","year":"2011","journal-title":"Inflamm. Bowel Dis."},{"key":"10.1016\/j.chom.2020.07.020_bib34","doi-asserted-by":"crossref","first-page":"6062","DOI":"10.1128\/AEM.00772-06","article-title":"Characterization of (R)-2-hydroxyisocaproate dehydrogenase and a family III coenzyme A transferase involved in reduction of L-leucine to isocaproate by Clostridium difficile","volume":"72","author":"Kim","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.chom.2020.07.020_bib35","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.1542\/peds.2008-0469","article-title":"Epidemiological features of Clostridium difficile-associated disease among inpatients at children's hospitals in the United States, 2001\u20132006","volume":"122","author":"Kim","year":"2008","journal-title":"Pediatrics"},{"key":"10.1016\/j.chom.2020.07.020_bib36","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1007486","article-title":"Heme sensing and detoxification by HatRT contributes to pathogenesis during Clostridium difficile infection","volume":"14","author":"Knippel","year":"2018","journal-title":"PLoS Pathog"},{"key":"10.1016\/j.chom.2020.07.020_bib37","first-page":"321","article-title":"Faecal and serum metabolomics in paediatric inflammatory bowel disease","volume":"11","author":"Kolho","year":"2017","journal-title":"J.\u00a0Crohns Colitis"},{"key":"10.1016\/j.chom.2020.07.020_bib38","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res"},{"key":"10.1016\/j.chom.2020.07.020_bib39","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake--a scalable bioinformatics workflow engine","volume":"28","author":"K\u00f6ster","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2020.07.020_bib40","doi-asserted-by":"crossref","first-page":"1489","DOI":"10.1053\/j.gastro.2014.02.009","article-title":"The microbiome in inflammatory bowel disease: current status and the future ahead","volume":"146","author":"Kostic","year":"2014","journal-title":"Gastroenterology"},{"key":"10.1016\/j.chom.2020.07.020_bib41","doi-asserted-by":"crossref","first-page":"2369","DOI":"10.1056\/NEJMoa1408913","article-title":"Burden of Clostridium difficile infection in the United States","volume":"372","author":"Lessa","year":"2015","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.chom.2020.07.020_bib42","doi-asserted-by":"crossref","first-page":"1428","DOI":"10.1016\/j.cell.2015.10.048","article-title":"Microbiota-modulated metabolites shape the intestinal microenvironment by regulating NLRP6 inflammasome signaling","volume":"163","author":"Levy","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.chom.2020.07.020_bib43","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00885-17","article-title":"Pathogenicity locus, core genome, and accessory gene contributions to Clostridium difficile virulence","volume":"8","author":"Lewis","year":"2017","journal-title":"mBio"},{"key":"10.1016\/j.chom.2020.07.020_bib44","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1016\/j.chom.2015.09.008","article-title":"Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn's disease","volume":"18","author":"Lewis","year":"2015","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.chom.2020.07.020_bib45","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2020.07.020_bib46","first-page":"18","article-title":"Classification and regression by randomForest","volume":"2\/3","author":"Liaw","year":"2002","journal-title":"R News"},{"key":"10.1016\/j.chom.2020.07.020_bib47","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1128\/JCM.01983-10","article-title":"Rapid stool-based diagnosis of Clostridium difficile infection by real-time PCR in a children's hospital","volume":"49","author":"Luna","year":"2011","journal-title":"J.\u00a0Clin. Microbiol."},{"key":"10.1016\/j.chom.2020.07.020_bib48","doi-asserted-by":"crossref","first-page":"308","DOI":"10.7326\/L17-0602","article-title":"Increasing incidence of multiply recurrent Clostridium difficile infection","volume":"168","author":"Ma","year":"2018","journal-title":"Ann. Intern. Med."},{"key":"10.1016\/j.chom.2020.07.020_bib49","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1007\/s00726-012-1361-4","article-title":"Taurine and inflammatory diseases","volume":"46","author":"Marcinkiewicz","year":"2014","journal-title":"Amino Acids"},{"key":"10.1016\/j.chom.2020.07.020_bib50","doi-asserted-by":"crossref","first-page":"153","DOI":"10.3390\/toxins8050153","article-title":"The regulatory networks that control Clostridium difficile toxin synthesis","volume":"8","author":"Martin-Verstraete","year":"2016","journal-title":"Toxins (Basel)"},{"key":"10.1016\/j.chom.2020.07.020_bib51","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00031-18","article-title":"American gut: an open platform for citizen science microbiome research","volume":"3","author":"McDonald","year":"2018","journal-title":"mSystems"},{"key":"10.1016\/j.chom.2020.07.020_bib52","doi-asserted-by":"crossref","first-page":"2433","DOI":"10.1056\/NEJMoa051590","article-title":"An epidemic, toxin gene-variant strain of Clostridium difficile","volume":"353","author":"McDonald","year":"2005","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.chom.2020.07.020_bib53","doi-asserted-by":"crossref","first-page":"1644","DOI":"10.1038\/s41590-019-0504-0","article-title":"Control of CD1d-restricted antigen presentation and inflammation by sphingomyelin","volume":"20","author":"Melum","year":"2019","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.chom.2020.07.020_bib54","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1038\/s41591-020-0764-0","article-title":"Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota","volume":"26","author":"Nagao-Kitamoto","year":"2020","journal-title":"Nat. Med."},{"key":"10.1016\/j.chom.2020.07.020_bib55","doi-asserted-by":"crossref","first-page":"219","DOI":"10.3389\/fmicb.2019.00219","article-title":"Metabolism the difficile way: the key to the success of the pathogen Clostridioides difficile","volume":"10","author":"Neumann-Schaal","year":"2019","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.chom.2020.07.020_bib56","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aah6888","article-title":"A role for bacterial urease in gut dysbiosis and Crohn's disease","volume":"9","author":"Ni","year":"2017","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.chom.2020.07.020_bib57","doi-asserted-by":"crossref","first-page":"2864","DOI":"10.1038\/ismej.2017.126","article-title":"dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication","volume":"11","author":"Olm","year":"2017","journal-title":"ISME J"},{"key":"10.1016\/j.chom.2020.07.020_bib58","doi-asserted-by":"crossref","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":"10.1016\/j.chom.2020.07.020_bib59","article-title":"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments","volume":"2","author":"Page","year":"2016","journal-title":"Microb. Genom."},{"key":"10.1016\/j.chom.2020.07.020_bib60","doi-asserted-by":"crossref","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":"10.1016\/j.chom.2020.07.020_bib61","doi-asserted-by":"crossref","first-page":"1641","DOI":"10.1093\/molbev\/msp077","article-title":"FastTree: computing large minimum evolution trees with profiles instead of a distance matrix","volume":"26","author":"Price","year":"2009","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.chom.2020.07.020_bib62","doi-asserted-by":"crossref","first-page":"3792","DOI":"10.1172\/JCI126905","article-title":"Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections","volume":"129","author":"Robinson","year":"2019","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.chom.2020.07.020_bib63","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/j.cgh.2006.12.027","article-title":"Incidence of Clostridium difficile infection in inflammatory bowel disease","volume":"5","author":"Rodemann","year":"2007","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"10.1016\/j.chom.2020.07.020_bib64","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1097\/MPG.0000000000000636","article-title":"Disproportionate rise in Clostridium difficile-associated hospitalizations among US youth with inflammatory bowel disease, 1997\u20132011","volume":"60","author":"Sandberg","year":"2015","journal-title":"J.\u00a0Pediatr. Gastroenterol. Nutr."},{"key":"10.1016\/j.chom.2020.07.020_bib65","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/S0378-1097(03)00611-6","article-title":"Taurine: new implications for an old amino acid","volume":"226","author":"Schuller-Levis","year":"2003","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.chom.2020.07.020_bib66","doi-asserted-by":"crossref","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":"10.1016\/j.chom.2020.07.020_bib67","doi-asserted-by":"crossref","first-page":"4983","DOI":"10.1128\/JB.00610-10","article-title":"Inhibiting the initiation of Clostridium difficile spore germination using analogs of chenodeoxycholic acid, a bile acid","volume":"192","author":"Sorg","year":"2010","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.chom.2020.07.020_bib68","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1038\/ajg.2013.4","article-title":"Guidelines for diagnosis, treatment, and prevention of Clostridium difficile infections","volume":"108","author":"Surawicz","year":"2013","journal-title":"Am. J. Gastroenterol."},{"key":"10.1016\/j.chom.2020.07.020_bib69","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/S0070-2153(03)01010-X","article-title":"Plasmid and chromosome traffic control: how ParA and ParB drive partition","volume":"56","author":"Surtees","year":"2003","journal-title":"Curr. Top. Dev. Biol."},{"key":"10.1016\/j.chom.2020.07.020_bib70","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.anaerobe.2017.03.004","article-title":"Inhibition of spore germination, growth, and toxin activity of clinically relevant C. difficile strains by gut microbiota derived secondary bile acids","volume":"45","author":"Thanissery","year":"2017","journal-title":"Anaerobe"},{"key":"10.1016\/j.chom.2020.07.020_bib71","doi-asserted-by":"crossref","first-page":"3114","DOI":"10.1038\/ncomms4114","article-title":"Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection","volume":"5","author":"Theriot","year":"2014","journal-title":"Nat. Commun."},{"key":"10.1016\/j.chom.2020.07.020_bib72","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1093\/cid\/cit581","article-title":"Distinguishing community-associated from hospital-associated Clostridium difficile infections in children: implications for public health surveillance","volume":"57","author":"Tschudin-Sutter","year":"2013","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.chom.2020.07.020_bib73","doi-asserted-by":"crossref","first-page":"2085","DOI":"10.1038\/ajg.2010.143","article-title":"Appraisal of the pediatric Crohn's disease activity index on four prospectively collected datasets: recommended cutoff values and clinimetric properties","volume":"105","author":"Turner","year":"2010","journal-title":"Am. J. Gastroenterol."},{"key":"10.1016\/j.chom.2020.07.020_bib74","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1053\/j.gastro.2007.05.029","article-title":"Development, validation, and evaluation of a pediatric ulcerative colitis activity index: a prospective multicenter study","volume":"133","author":"Turner","year":"2007","journal-title":"Gastroenterology"},{"key":"10.1016\/j.chom.2020.07.020_bib75","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aap8914","article-title":"Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome","volume":"10","author":"Vich Vila","year":"2018","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.chom.2020.07.020_bib76","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"Walker","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.chom.2020.07.020_bib77","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: resolving bacterial genome assemblies from short and long sequencing reads","volume":"13","author":"Wick","year":"2017","journal-title":"PLOS Comput. Biol."},{"key":"10.1016\/j.chom.2020.07.020_bib78","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol"},{"key":"10.1016\/j.chom.2020.07.020_bib79","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":"10.1016\/j.chom.2020.07.020_bib80","doi-asserted-by":"crossref","first-page":"2271","DOI":"10.1042\/BCJ20190486","article-title":"A gene cluster for taurine sulfur assimilation in an anaerobic human gut bacterium","volume":"476","author":"Xing","year":"2019","journal-title":"Biochem. J."},{"key":"10.1016\/j.chom.2020.07.020_bib81","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1086\/519265","article-title":"A comparison of vancomycin and metronidazole for the treatment of Clostridium difficile-associated diarrhea, stratified by disease severity","volume":"45","author":"Zar","year":"2007","journal-title":"Clin. Infect. Dis."}],"container-title":["Cell Host &amp; Microbe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312820304236?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1931312820304236?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T12:22:43Z","timestamp":1761826963000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1931312820304236"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,9]]},"references-count":81,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2020,9]]}},"alternative-id":["S1931312820304236"],"URL":"https:\/\/doi.org\/10.1016\/j.chom.2020.07.020","relation":{},"ISSN":["1931-3128"],"issn-type":[{"value":"1931-3128","type":"print"}],"subject":[],"published":{"date-parts":[[2020,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease","name":"articletitle","label":"Article Title"},{"value":"Cell Host & Microbe","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.chom.2020.07.020","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2020 Elsevier Inc.","name":"copyright","label":"Copyright"}]}}