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Exclusive enteral nutrition (EEN) and the specific carbohydrate diet (SCD) have been demonstrated as effective anti-inflammatory treatments for children with Crohn\u2019s disease. We have previously shown an anti-inflammatory effect from these nutritional treatments in children with juvenile idiopathic arthritis (JIA). The aim of this study was to investigate if improved clinical symptoms after EEN or SCD treatment in children with JIA could be linked to changes in faecal microbiota. We included sixteen patients with JIA (age 7\u201317\u00a0years), six for treatment with EEN and ten with SCD. EEN was given for 3\u20135\u00a0weeks and SCD for 4\u20135\u00a0weeks, with clinical and laboratory status assessed before and after treatment. Faecal samples were analysed for microbiota diversity and composition using 16S rRNA gene sequencing. Analyses of the faecal microbiota showed an effect on the overall composition with both interventions; the most striking result was a decreased relative abundance of the genus <jats:italic>Faecalibacterium<\/jats:italic> from EEN and of <jats:italic>Bifidobacterium<\/jats:italic> from SCD. The \u03b1-diversity decreased significantly from SCD (<jats:italic>P<\/jats:italic>\u2009=\u20090.04), but not from EEN (<jats:italic>P<\/jats:italic>\u2009=\u20090.22). Despite the study cohorts being small, both EEN and SCD were shown to impact the faecal microbiota. Future larger studies with a focus on metagenomics or metabolomics could possibly reveal a link and clarify the clinical effects of those nutritional regimens.<\/jats:p>","DOI":"10.1007\/s00284-022-02899-1","type":"journal-article","created":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T17:03:56Z","timestamp":1654621436000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["A Pilot Study Investigating Faecal Microbiota After Two Dietary Interventions in Children with Juvenile Idiopathic Arthritis"],"prefix":"10.1007","volume":"79","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3962-0453","authenticated-orcid":false,"given":"Lillemor","family":"Berntson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8462-327X","authenticated-orcid":false,"given":"Anders","family":"\u00d6man","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7713-2373","authenticated-orcid":false,"given":"Lars","family":"Engstrand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7515-4480","authenticated-orcid":false,"given":"Johan","family":"Dicksved","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,6,7]]},"reference":[{"issue":"2","key":"2899_CR1","first-page":"390","volume":"31","author":"RE Petty","year":"2004","unstructured":"Petty RE, Southwood TR, Manners P, Baum J, Glass DN, Goldenberg J, He X, Maldonado-Cocco J, Orozco-Alcala J, Prieur AM, Suarez-Almazor ME, Woo P, International League of Associations for R (2004) International League of Associations for Rheumatology classification of juvenile idiopathic arthritis: second revision, Edmonton, 2001. 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