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This study provides the first integrated multi\u2010omics analysis in a CCHS group and matched controls, combining fecal DNA\u2010based gut taxonomic profiling with targeted quantification of fatty acids and aromatic carboxylic acids. While overall microbial diversity and community structure remained largely preserved, significant alterations were observed in specific taxa within the CCHS group. Notably, the control group exhibited an enrichment of short\u2010chain fatty acid (SCFA)\u2010producing genera, which are associated with eubiotic gut ecosystems, whereas the CCHS group showed higher abundance of taxa commonly linked to inflammatory contexts. Consistently, fecal levels of beneficial SCFAs\u2014particularly valeric acid, and to a lesser extent butyric acid\u2014were reduced in CCHS group. These findings point to a dysbiotic gut microbiota in patients with CCHS, likely supporting putative inflammatory processes that would further worsen overall health status if confirmed. Furthermore, this work provides exploratory functional signatures for future studies aimed at understanding systemic consequences, guiding mechanistic investigations, and informing strategies to improve supportive care and long\u2010term health outcomes in this rare patient population.<\/jats:p>","DOI":"10.1155\/ijm\/7551500","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T04:23:15Z","timestamp":1788841395000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Microbiota\u2013Metabolome Alterations Suggest Pro\u2010Inflammatory Phenotype in Congenital Central Hypoventilation Syndrome"],"prefix":"10.1155","volume":"2026","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8630-8166","authenticated-orcid":false,"given":"Leandro","family":"Di 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