{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T02:07:34Z","timestamp":1780538854802,"version":"3.54.1"},"reference-count":53,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T00:00:00Z","timestamp":1780012800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Background: Crohn\u2019s disease (CD) is characterized by gut microbiota alterations including reduced microbial diversity, loss of commensal species, and increased abundance of opportunistic taxa. Methods: This prospective study was conducted between 2022 and 2024 at the Emergency Clinical Hospital for Children, Cluj-Napoca. Children with CD and healthy controls were evaluated. The gut microbiota was analyzed using shotgun metagenomics. Bioinformatic processing assessed alpha and beta diversity, core microbiome composition, and differential taxa. Results: Ten patients with CD and eight healthy children were included; five patients were re-evaluated after a median interval of 14 weeks. The Shannon index was significantly lower in CD patients compared with controls (p = 0.037). Beta diversity analysis suggested partial separation between CD at diagnosis and controls (p = 0.041). An inverse correlation was observed between the Shannon index and the clinical score (p = 0.028). Ruminococcus gnavus was among the taxa contributing to group separation. At follow-up, all patients were in clinical remission, while 80% had achieved biological remission and mucosal healing. They showed persistently reduced alpha diversity and distinct microbial communities compared with controls (p = 0.028 and p = 0.005, respectively). Conclusions: Pediatric CD was correlated with dysbiosis that persisted despite remission. Reduced alpha diversity was associated with greater disease severity at diagnosis.<\/jats:p>","DOI":"10.3390\/biom16060801","type":"journal-article","created":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T01:08:02Z","timestamp":1780535282000},"page":"801","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Persistent Gut Microbiota Dysbiosis in Pediatric Crohn\u2019s Disease: A Next-Generation Sequencing Pilot Study"],"prefix":"10.3390","volume":"16","author":[{"given":"Georgia Valentina","family":"Tita","sequence":"first","affiliation":[{"name":"3rd Medical Discipline, Department of Internal Medicine, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina Rebeca","family":"Fogas","sequence":"additional","affiliation":[{"name":"3rd Medical Discipline, Department of Internal Medicine, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kinga Cristina","family":"Slavescu","sequence":"additional","affiliation":[{"name":"Department of Mother and Child, 2nd Clinic of Pediatrics, Emergency Clinical Hospital for Children, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400177 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasile Marcel","family":"Tantau","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine and Gastroenterology, \u201cProf. Dr. Octavian Fodor\u201d Regional Institute of Gastroenterology and Hepatology, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefana Arlinda","family":"Medan","sequence":"additional","affiliation":[{"name":"Department of Anatomy and Embryology, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400006 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0906-1232","authenticated-orcid":false,"given":"Daniela Elena","family":"Serban","sequence":"additional","affiliation":[{"name":"Department of Mother and Child, 2nd Clinic of Pediatrics, Emergency Clinical Hospital for Children, \u201cIuliu Hatieganu\u201d University of Medicine and Pharmacy, 400177 Cluj-Napoca, Romania"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1093\/ecco-jcc\/jjaa161","article-title":"The Medical Management of Paediatric Crohn\u2019s Disease: An ECCO-ESPGHAN Guideline Update","volume":"15","author":"Aloi","year":"2021","journal-title":"J. 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