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Thus, human microbiome data holds significant potential as a source of information for diagnosing and characterizing diseases\u2014such as phenotypes, disease course, and therapeutic response\u2014associated with dysbiotic microbiota communities. However, multiple attempts to leverage gut microbiota taxonomic data for diagnostic and disease characterization have failed due to significant inter-individual variability of microbiota community and overlap of disrupted microbiota communities among multiple diseases. One potential approach is to look at the microbiota community pattern and response to microbiota modifiers like dietary fiber in different disease states. This approach has become feasible with the advent of machine learning, which can uncover hidden patterns in human microbiome data and enable disease prediction. Accordingly, the aim of our study was to test the hypothesis that  machine learning algorithms can distinguish\u00a0stool microbiota patterns\u2014and their responses to fiber\u2014across diseases with previously reported overlapping dysbiotic microbiota profiles. Here, we applied machine learning algorithms to distinguish between Parkinson's disease, Crohn's disease (CD), ulcerative colitis (UC), human immune deficiency virus (HIV), and healthy control (HC) subjects in the presence and absence of fiber treatments. We demonstrated that machine learning algorithms can classify diseases with accuracy as high as 95%. Furthermore, applying machine learning to microbiome data to distinguish UC from CD yielded a prediction accuracy of up to 90%.<\/jats:p>","DOI":"10.1186\/s12866-025-04072-7","type":"journal-article","created":{"date-parts":[[2025,6,5]],"date-time":"2025-06-05T22:14:05Z","timestamp":1749161645000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Machine learning based gut microbiota pattern and response to fiber as a diagnostic tool for chronic inflammatory diseases"],"prefix":"10.1186","volume":"25","author":[{"given":"Miad","family":"Boodaghidizaji","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thaisa","family":"Jungles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tingting","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianming","family":"Yao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan","family":"Landay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Keshavarzian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruce","family":"Hamaker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arezoo","family":"Ardekani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,6,6]]},"reference":[{"key":"4072_CR1","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1136\/bmj.k2179","volume":"361","author":"AM Valdes","year":"2018","unstructured":"Valdes AM, Walter J, Segal E, Spector TD. 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All participants signed the Rush University Medical Center (RUMC) Institutional Review Board approved informed consent forms (ORA#: 07100403; 12020204; 07092603; L04092807). The study was approved by the Rush University Medical Center (RUMC) Institutional Review Board.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and Consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interest"}}],"article-number":"353"}}