{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T09:31:55Z","timestamp":1789464715738,"version":"build-2803163510"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2022,10,14]],"date-time":"2022-10-14T00:00:00Z","timestamp":1665705600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Irish Health Research Board","award":["ILP-POR-2019-030"],"award-info":[{"award-number":["ILP-POR-2019-030"]}]},{"name":"National Children\u2019s Research Centre, Dublin","award":["J\/15\/1"],"award-info":[{"award-number":["J\/15\/1"]}]},{"name":"National Children\u2019s Research Centre, Dublin","award":["C\/18\/2"],"award-info":[{"award-number":["C\/18\/2"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,4,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>There is a limited literature describing the oral microbiome and its diagnostic potential in paediatric inflammatory bowel disease [IBD].<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We examined the dorsum tongue microbiome by V1\u2013V2 sequencing in a cohort of 156 treatment-na\u00efve children diagnosed with IBD compared to 102 healthy control children. Microbiome changes over time following treatment were examined in a subset of patients and associations between IBD diagnosis and dysbiosis were explored.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Analysis of community structure of the microbiome in tongue samples revealed that IBD samples diverged significantly from healthy control samples [PERMANOVA p\u2005=\u20050.0009] and exhibited a reduced abundance of Clostridia in addition to several major oral genera [Veillonella, Prevotella and Fusobacterium species] with an increased abundance of streptococci. This dysbiosis was more marked in patients with severe disease. Higher levels of the potential pathobionts Klebsiella and Pseudomonas spp. were also associated with IBD. In terms of predicted functions, the IBD oral microbiome was potentially more acidogenic and exhibited reduced capacity for B vitamin biosynthesis. We used a machine learning approach to develop a predictive model of IBD which exhibited a mean-prediction AUC [area under the ROC curve] of 0.762. Finally, we examined a subset of 53 patients following 12 months of therapy and could show resolution of oral dysbiosis as demonstrated by a shift towards a healthy community structure and a significant reduction in oral dysbiosis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>Oral dysbiosis found in children with IBD is related to disease severity and resolves over time following successful IBD treatment.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/ecco-jcc\/jjac155","type":"journal-article","created":{"date-parts":[[2022,10,14]],"date-time":"2022-10-14T21:18:08Z","timestamp":1665782288000},"page":"553-564","source":"Crossref","is-referenced-by-count":24,"title":["The Oral Microbiome in Treatment-Na\u00efve Paediatric IBD Patients Exhibits Dysbiosis Related to Disease Severity that Resolves Following Therapy"],"prefix":"10.1093","volume":"17","author":[{"given":"Khalid","family":"Elmaghrawy","sequence":"first","affiliation":[{"name":"School of Dental Science, Trinity College Dublin and Dublin Dental University Hospital , Dublin 2 , Republic of Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paddy","family":"Fleming","sequence":"additional","affiliation":[{"name":"School of Dental Science, Trinity College Dublin and Dublin Dental University Hospital , Dublin 2 , Republic of Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kirsten","family":"Fitzgerald","sequence":"additional","affiliation":[{"name":"School of Dental Science, Trinity College Dublin and Dublin Dental University Hospital , Dublin 2 , Republic of Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Cooper","sequence":"additional","affiliation":[{"name":"DOCHAS Study, Children\u2019s Health Ireland, Crumlin, Dublin, Republic of Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Dominik","sequence":"additional","affiliation":[{"name":"DOCHAS Study, Children\u2019s Health Ireland, Crumlin, Dublin, Republic of Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9362-0465","authenticated-orcid":false,"given":"S\u00e9amus","family":"Hussey","sequence":"additional","affiliation":[{"name":"DOCHAS Study, Children\u2019s Health Ireland, Crumlin, Dublin, Republic of Ireland"},{"name":"Department of Paediatrics, University of Medicine and Health Sciences, RCSI, Dublin and University College Dublin , Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0469-1788","authenticated-orcid":false,"given":"Gary P","family":"Moran","sequence":"additional","affiliation":[{"name":"School of Dental Science, Trinity College Dublin and Dublin Dental University Hospital , Dublin 2 , Republic of Ireland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,10,14]]},"reference":[{"key":"2023041916524419100_CIT0001","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1111\/apm.12609","article-title":"The human gastrointestinal tract and oral microbiota in inflammatory bowel disease: a state of the science review","volume":"125","author":"L\u00f3pez","year":"2016","journal-title":"APMIS"},{"key":"2023041916524419100_CIT0002","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1038\/ng.549","article-title":"Genome-wide association identifies multiple ulcerative colitis susceptibility loci","volume":"42","author":"McGovern","year":"2010","journal-title":"Nat Genet"},{"key":"2023041916524419100_CIT0003","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases","volume":"569","author":"Lloyd-Price","year":"2019","journal-title":"Nature"},{"key":"2023041916524419100_CIT0004","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1186\/s13073-014-0107-1","article-title":"Complex host genetics influence the microbiome in inflammatory bowel disease","volume":"6","author":"Knights","year":"2014","journal-title":"Genome Med"},{"key":"2023041916524419100_CIT0005","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\u2019s disease.","volume":"15","author":"Gevers","year":"2014","journal-title":"Cell Host Microbe"},{"key":"2023041916524419100_CIT0006","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s13073-016-0331-y","article-title":"Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease","volume":"8","author":"Shaw","year":"2016","journal-title":"Genome Med"},{"key":"2023041916524419100_CIT0007","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1016\/j.chom.2018.09.009","article-title":"Compositional and temporal changes in the gut microbiome of pediatric ulcerative colitis patients are linked to disease course","volume":"24","author":"Schirmer","year":"2018","journal-title":"Cell Host Microbe"},{"key":"2023041916524419100_CIT0008","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1016\/j.celrep.2015.12.088","article-title":"Detecting microbial dysbiosis associated with pediatric Crohn disease despite the high variability of the gut microbiota","volume":"14","author":"Wang","year":"2016","journal-title":"Cell Rep"},{"key":"2023041916524419100_CIT0009","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1126\/science.aan4526","article-title":"Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation","volume":"358","author":"Atarashi","year":"2017","journal-title":"Science"},{"key":"2023041916524419100_CIT0010","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/BF03262800","article-title":"Disease outcome for children who present with oral manifestations of Crohn\u2019s disease.","volume":"12","author":"Hussey","year":"2012","journal-title":"Eur Arch Paediatr Dent"},{"key":"2023041916524419100_CIT0011","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1002\/ibd.20983","article-title":"Looking in the mouth for Crohn\u2019s disease","volume":"16","author":"Rowland","year":"2010","journal-title":"Inflamm Bowel Dis"},{"key":"2023041916524419100_CIT0012","doi-asserted-by":"crossref","first-page":"S431","DOI":"10.4103\/0975-7406.100322","article-title":"Oral Crohn\u2019s disease without intestinal manifestations","volume":"4","author":"Harikishan","year":"2012","journal-title":"J Pharm Bioallied Sci"},{"key":"2023041916524419100_CIT0013","doi-asserted-by":"crossref","first-page":"8571","DOI":"10.3748\/wjg.v19.i46.8571","article-title":"Oral manifestation in inflammatory bowel disease: a review.","volume":"19","author":"Lankarani","year":"2013","journal-title":"World J Gastroenterol"},{"key":"2023041916524419100_CIT0014","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1111\/j.1468-3083.2009.03304.x","article-title":"Oral manifestations of inflammatory bowel disease: a review based on the observation of six cases.","volume":"24","author":"Louren\u00e7o","year":"2009","journal-title":"J Eur Acad Dermatol Venereol"},{"key":"2023041916524419100_CIT0015","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1111\/apt.13217","article-title":"Review article: non-malignant oral manifestations in inflammatory bowel diseases.","volume":"42","author":"Katsanos","year":"2015","journal-title":"Aliment Pharmacol Ther"},{"key":"2023041916524419100_CIT0016","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/dnares\/dst037","article-title":"Dysbiosis of salivary microbiota in inflammatory bowel disease and its association with oral immunological biomarkers","volume":"21","author":"Said","year":"2014","journal-title":"DNA Res"},{"key":"2023041916524419100_CIT0017","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.3389\/fmicb.2018.01136","article-title":"Dysbiosis and ecotypes of the salivary microbiome associated with inflammatory bowel diseases and the assistance in diagnosis of diseases using oral bacterial profiles","volume":"9","author":"Xun","year":"2018","journal-title":"Front Microbiol"},{"key":"2023041916524419100_CIT0018","doi-asserted-by":"crossref","first-page":"544704","DOI":"10.3389\/fcimb.2020.544704","article-title":"Dynamics of the salivary microbiome during different phases of Crohn\u2019s disease.","volume":"10","author":"Zhang","year":"2020","journal-title":"Front Cell Infect Microbiol"},{"key":"2023041916524419100_CIT0019","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1016\/j.ygeno.2020.09.063","article-title":"High-throughput sequencing provides insights into oral microbiota dysbiosis in association with inflammatory bowel disease","volume":"113","author":"Qi","year":"2021","journal-title":"Genomics"},{"key":"2023041916524419100_CIT0020","article-title":"Oral","author":"Hu","year":"2022","journal-title":"J Crohns Colitis"},{"key":"2023041916524419100_CIT0021","doi-asserted-by":"crossref","first-page":"1889","DOI":"10.1093\/ibd\/izab082","article-title":"Site- and taxa-specific disease-associated oral microbial structures distinguish inflammatory bowel diseases","volume":"27","author":"Somineni","year":"2021","journal-title":"Inflamm Bowel Dis"},{"key":"2023041916524419100_CIT0022","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1093\/ibd\/izz022","article-title":"Streptococcus salivarius: a potential salivary biomarker for orofacial granulomatosis and Crohn\u2019s disease?","volume":"25","author":"Goel","year":"2019","journal-title":"Inflamm Bowel Dis"},{"key":"2023041916524419100_CIT0023","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1097\/MPG.0000000000000239","article-title":"ESPGHAN revised porto criteria for the diagnosis of inflammatory bowel disease in children and adolescents.","volume":"58","author":"Levine","year":"2014","journal-title":"J Pediatr Gastr Nutr"},{"key":"2023041916524419100_CIT0024","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1002\/ibd.21493","article-title":"Pediatric modification of the Montreal classification for inflammatory bowel disease: the Paris classification","volume":"17","author":"Levine","year":"2011","journal-title":"Inflamm Bowel Dis"},{"key":"2023041916524419100_CIT0025","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1097\/00005176-199105000-00005","article-title":"Development and validation of a pediatric Crohn\u2019s disease activity index.","volume":"12","author":"Hyams","year":"1991","journal-title":"J Pediatr Gastr Nutr"},{"key":"2023041916524419100_CIT0026","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":"2023041916524419100_CIT0027","doi-asserted-by":"crossref","first-page":"2391","DOI":"10.3389\/fmicb.2017.02391","article-title":"The microbiome of potentially malignant oral leukoplakia exhibits enrichment for Fusobacterium, Leptotrichia, Campylobacter, and Rothia species","volume":"8","author":"Amer","year":"2017","journal-title":"Front Microbiol"},{"key":"2023041916524419100_CIT0028","doi-asserted-by":"crossref","first-page":"2461","DOI":"10.1128\/AEM.02272-07","article-title":"Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes.","volume":"74","author":"Frank","year":"2008","journal-title":"Appl Environ Microb"},{"key":"2023041916524419100_CIT0029","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1111\/j.2041-1014.2012.00642.x","article-title":"Using high throughput sequencing to explore the biodiversity in oral bacterial communities","volume":"27","author":"Diaz","year":"2012","journal-title":"Mol Oral Microbiol"},{"key":"2023041916524419100_CIT0030","first-page":"1","author":"Illumina","year":"2013"},{"key":"2023041916524419100_CIT0031","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat Methods"},{"key":"2023041916524419100_CIT0032","doi-asserted-by":"crossref","first-page":"5002","DOI":"10.1128\/JB.00542-10","article-title":"The human oral microbiome","volume":"192","author":"Dewhirst","year":"2010","journal-title":"J Bacteriol"},{"key":"2023041916524419100_CIT0033","doi-asserted-by":"crossref","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLoS One"},{"key":"2023041916524419100_CIT0034","doi-asserted-by":"crossref","first-page":"3201","DOI":"10.21105\/joss.03201","article-title":"microViz: an R package for microbiome data visualization and statistics","volume":"6","author":"Barnett","year":"2021","journal-title":"J Open Source Softw"},{"key":"2023041916524419100_CIT0035","doi-asserted-by":"crossref","first-page":"e1009442","DOI":"10.1371\/journal.pcbi.1009442","article-title":"Multivariable association discovery in population-scale meta-omics studies","volume":"17","author":"Mallick","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"2023041916524419100_CIT0036","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023041916524419100_CIT0037","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1186\/s13059-021-02306-1","article-title":"Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox","volume":"22","author":"Wirbel","year":"2021","journal-title":"Genome Biol"},{"key":"2023041916524419100_CIT0038","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random forests","volume":"45","author":"Breiman","year":"2001","journal-title":"Mach Learn"},{"key":"2023041916524419100_CIT0039","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol"},{"key":"2023041916524419100_CIT0040","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences","volume":"31","author":"Langille","year":"2013","journal-title":"Nat Biotechnol"},{"key":"2023041916524419100_CIT0041","doi-asserted-by":"crossref","first-page":"935","DOI":"10.1002\/ibd.21874","article-title":"Alterations in diversity of the oral microbiome in pediatric inflammatory bowel disease","volume":"18","author":"Docktor","year":"2012","journal-title":"Inflamm Bowel Dis"},{"key":"2023041916524419100_CIT0042","first-page":"1","article-title":"Dynamic immunoglobulin responses to gut bacteria during inflammatory bowel disease","volume":"11","author":"Rengarajan","year":"2019","journal-title":"Gut Microbes"},{"key":"2023041916524419100_CIT0043","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/j.freeradbiomed.2012.11.013","article-title":"Physiological role for nitrate-reducing oral bacteria in blood pressure control.","volume":"55","author":"Kapil","year":"2013","journal-title":"Free Radical Bio Med"},{"key":"2023041916524419100_CIT0044","doi-asserted-by":"crossref","first-page":"e3578","DOI":"10.1371\/journal.pone.0003578","article-title":"Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn\u2019s disease","volume":"3","author":"Wagner","year":"2008","journal-title":"PLoS One"},{"key":"2023041916524419100_CIT0045","doi-asserted-by":"crossref","first-page":"E58","DOI":"10.1002\/ibd.23017","article-title":"Pseudomonas infection in children with early-onset crohn\u2019s disease: an association with a mutation close to PSMG1","volume":"19","author":"Wagner","year":"2012","journal-title":"Inflamm Bowel Dis"},{"key":"2023041916524419100_CIT0046","doi-asserted-by":"crossref","first-page":"4418","DOI":"10.3748\/wjg.v19.i27.4418","article-title":"Crohn\u2019s disease complicated by intestinal infection with methicillin-resistant Staphylococcus aureus.","volume":"19","author":"Bettenworth","year":"2013","journal-title":"World J Gastroenterol"},{"key":"2023041916524419100_CIT0047","doi-asserted-by":"crossref","first-page":"620254","DOI":"10.3389\/fped.2020.620254","article-title":"The oral microbiome in pediatric IBD: a source of pathobionts or biomarkers?","volume":"8","author":"Elmaghrawy","year":"2021","journal-title":"Front Pediatr"}],"container-title":["Journal of Crohn's and Colitis"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ecco-jcc\/advance-article-pdf\/doi\/10.1093\/ecco-jcc\/jjac155\/49253916\/jjac155.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ecco-jcc\/article-pdf\/17\/4\/553\/50033734\/jjac155.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ecco-jcc\/article-pdf\/17\/4\/553\/50033734\/jjac155.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,19]],"date-time":"2023-04-19T16:56:49Z","timestamp":1681923409000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ecco-jcc\/article\/17\/4\/553\/6761098"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,10,14]]},"references-count":47,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2022,10,14]]},"published-print":{"date-parts":[[2023,4,19]]}},"URL":"https:\/\/doi.org\/10.1093\/ecco-jcc\/jjac155","relation":{},"ISSN":["1873-9946","1876-4479"],"issn-type":[{"value":"1873-9946","type":"print"},{"value":"1876-4479","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,4,1]]},"published":{"date-parts":[[2022,10,14]]}}}