{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,5]],"date-time":"2026-11-05T19:33:10Z","timestamp":1793907190470,"version":"4.8.0"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,9,15]],"date-time":"2022-09-15T00:00:00Z","timestamp":1663200000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Canadian Association of Gastroenterology-Crohn\u2019s Colitis Canada New Investigator","award":["2015\u20132019"],"award-info":[{"award-number":["2015\u20132019"]}]},{"name":"Canadian Association of Gastroenterology-Crohn\u2019s Colitis Canada New Investigator","award":["2018\u20132019"],"award-info":[{"award-number":["2018\u20132019"]}]},{"name":"Canadian Foundation of Innovation John R. Evans Leadership fund","award":["35235"],"award-info":[{"award-number":["35235"]}]},{"name":"Canadian Foundation of Innovation John R. Evans Leadership fund","award":["36764"],"award-info":[{"award-number":["36764"]}]},{"DOI":"10.13039\/501100000194","name":"Nova Scotia Health Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000194","id-type":"DOI","asserted-by":"publisher"}]},{"name":"IWK Health Centre Research Associateship"},{"name":"CIHR-SPOR-Chronic Diseases"},{"name":"Wetenschappelijke Adviesraad of Stichting Steun Emma kinderziekenhuis"},{"DOI":"10.13039\/100011684","name":"Crohn's and Colitis Foundation","doi-asserted-by":"publisher","award":["585718"],"award-info":[{"award-number":["585718"]}],"id":[{"id":"10.13039\/100011684","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background and aims<\/jats:title>\n                  <jats:p>Nutritional therapy with the Crohn\u2019s Disease Exclusion Diet + Partial Enteral Nutrition [CDED+PEN] or Exclusive Enteral Nutrition [EEN] induces remission and reduces inflammation in mild-to-moderate paediatric Crohn\u2019s disease [CD]. We aimed to assess if reaching remission with nutritional therapy is mediated by correcting compositional or functional dysbiosis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>We assessed metagenome sequences, short chain fatty acids [SCFA] and bile acids [BA] in 54 paediatric CD patients reaching remission after nutritional therapy [with CDED + PEN or EEN] [NCT01728870], compared to 26 paediatric healthy controls.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Successful dietary therapy decreased the relative abundance of Proteobacteria and increased Firmicutes towards healthy controls. CD patients possessed a mixture of two metabotypes [M1 and M2], whereas all healthy controls had metabotype M1. M1 was characterised by high Bacteroidetes and Firmicutes, low Proteobacteria, and higher SCFA synthesis pathways, and M2 was associated with high Proteobacteria and genes involved in SCFA degradation. M1 contribution increased during diet: 48%, 63%, up to 74% [Weeks 0, 6, 12, respectively.]. By Week 12, genera from Proteobacteria reached relative abundance levels of healthy controls with the exception of E. coli. Despite an increase in SCFA synthesis pathways, remission was not associated with increased SCFAs. Primary BA decreased with EEN but not with CDED+PEN, and secondary BA did not change during diet.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>Successful dietary therapy induced correction of both compositional and functional dysbiosis. However, 12 weeks of diet was not enough to achieve complete correction of dysbiosis. Our data suggests that composition and metabotype are important and change quickly during the early clinical response to dietary intervention. Correction of dysbiosis may therefore be an important future treatment goal for CD.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/ecco-jcc\/jjac105","type":"journal-article","created":{"date-parts":[[2022,9,15]],"date-time":"2022-09-15T14:11:35Z","timestamp":1663251095000},"page":"61-72","source":"Crossref","is-referenced-by-count":56,"title":["Successful Dietary Therapy in Paediatric Crohn\u2019s Disease is Associated with Shifts in Bacterial Dysbiosis and Inflammatory Metabotype Towards Healthy Controls"],"prefix":"10.1093","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7198-0603","authenticated-orcid":false,"given":"Charlotte M","family":"Verburgt","sequence":"first","affiliation":[{"name":"Department of Paediatric Gastroenterology and Nutrition, Amsterdam University Medical Centers, University of Amsterdam, Emma Children\u2019s Hospital , Amsterdam , The Netherlands"},{"name":"Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam , Amsterdam , The Netherlands"},{"name":"Amsterdam Reproduction & Development Research Institute, Emma Children\u2019s Hospital , Amsterdam , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine A","family":"Dunn","sequence":"additional","affiliation":[{"name":"Department of Biology, Dalhousie University , Halifax, NS , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammed","family":"Ghiboub","sequence":"additional","affiliation":[{"name":"Department of Paediatric Gastroenterology and Nutrition, Amsterdam University Medical Centers, University of Amsterdam, Emma Children\u2019s Hospital , Amsterdam , The Netherlands"},{"name":"Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam , Amsterdam , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James D","family":"Lewis","sequence":"additional","affiliation":[{"name":"Centre for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania , USA"},{"name":"Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eytan","family":"Wine","sequence":"additional","affiliation":[{"name":"Division of Paediatric Gastroenterology, Stollery Children\u2019s Hospital, University of Alberta , Edmonton, AB , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rotem","family":"Sigall Boneh","sequence":"additional","affiliation":[{"name":"Wolfson Medical Centre, Holon, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9432-2200","authenticated-orcid":false,"given":"Konstantinos","family":"Gerasimidis","sequence":"additional","affiliation":[{"name":"Department of Human Nutrition, School of Medicine, Dentistry & Nursing, University of Glasgow , Glasgow , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raanan","family":"Shamir","sequence":"additional","affiliation":[{"name":"Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children\u2019s Medical Centre, Petach-Tikva, Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanne","family":"Penny","sequence":"additional","affiliation":[{"name":"Human Health Therapeutics, National Research Council , Halifax, NS , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devanand M","family":"Pinto","sequence":"additional","affiliation":[{"name":"Human Health Therapeutics, National Research Council , Halifax, NS , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Cohen","sequence":"additional","affiliation":[{"name":"Proteomics and Mass Spectrometry Core Facility, Faculty of Medicine, Dalhousie University , Halifax, NS , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Bjorndahl","sequence":"additional","affiliation":[{"name":"Department of Mathematics & Statistics, Dalhousie University , Halifax, NS , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vaios","family":"Svolos","sequence":"additional","affiliation":[{"name":"Department of Human Nutrition, School of Medicine, Dentistry & Nursing, University of Glasgow , Glasgow , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph P","family":"Bielawski","sequence":"additional","affiliation":[{"name":"Centre for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania , USA"},{"name":"Department of Mathematics & Statistics, Dalhousie University , Halifax, NS , Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc A","family":"Benninga","sequence":"additional","affiliation":[{"name":"Department of Paediatric Gastroenterology and Nutrition, Amsterdam University Medical Centers, University of Amsterdam, Emma Children\u2019s Hospital , Amsterdam , The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wouter J","family":"de Jonge","sequence":"additional","affiliation":[{"name":"Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, University of Amsterdam , Amsterdam , The Netherlands"},{"name":"Department of Mathematics & Statistics, Dalhousie 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