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Intestinal stem cell (ISC) differentiation is pivotal in sustaining epithelial renewal and mucosal homeostasis. Huangqin decoction (HQD), a classical herbal formulation comprising\n                      <jats:italic>Scutellaria baicalensis, Ziziphus jujuba, Paeonia lactiflora,<\/jats:italic>\n                      and\n                      <jats:italic>Glycyrrhiza uralensis,<\/jats:italic>\n                      is clinically used for inflammatory bowel disease. Nevertheless, how HQD precisely regulates ISC differentiation to promote UC repair remains unclear.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Purpose<\/jats:title>\n                    <jats:p>This research sought to assess whether HQD ameliorates UC by concurrently modulating the gut microbiome, tryptophan metabolism, aryl hydrocarbon receptor (AhR) activation, and ISC differentiation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Mice developed colitis after drinking water with a 3.5% (w\/v) concentration of dextran sulfate sodium. We evaluated HQD effects on colon length, weight trajectory, disease activity index score, histological damage, and colonic inflammatory mediator abundance. Metagenomic sequencing resolved microbiota restructuring, while UPLC-MS\/MS quantified fecal tryptophan metabolites such as indole derivatives. AhR pathway activity (AhR, CYP1A1), its downstream cytokine IL-22, and ISC fate were mapped by combining immunofluorescence, ELISA, Western blot, and RT-qPCR, probing Lgr5 for stem-cell identity and MUC2, LYZ, and ChgA for lineage-specific differentiation. The involvement of AhR and gut microbiota was investigated using AhR inhibitors and broad-spectrum antibiotics.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>High-dose HQD significantly alleviated colitis symptoms, reduced colon damage, and corrected gut dysbiosis. HQD increased the abundance of related bacteria that elevated colonic levels of indole-3-propionic acid, indole-3-acetamide, and tryptamine, acting as AhR ligands that upregulate AhR and its downstream targets CYP1A1 and IL-22. Crucially, HQD promoted a shift in expression from the ISC marker Lgr5 toward differentiation markers MUC2, LYZ, and ChgA, indicating enhanced ISC differentiation and improved barrier function. These effects were effectively blocked by AhR inhibition or antibiotic treatment.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>HQD restores intestinal mucosal integrity and attenuates colonic inflammation by modulating gut microbiota composition, increasing microbial tryptophan metabolites with AhR-agonist activity, activating the AhR signaling pathway, and promoting ISC differentiation into functional epithelial cells. This work reveals a novel \u201cmicrobiota\u2013tryptophan metabolism\u2013AhR\u2013ISC differentiation\u201d axis underlying HQD\u2019s therapeutic efficacy in UC.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13020-025-01302-y","type":"journal-article","created":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T08:34:13Z","timestamp":1768293253000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Microbiota-driven tryptophan metabolism and AhR triggered intestinal stem cell differentiation: mechanisms of huangqin decoction in ulcerative colitis repair"],"prefix":"10.1186","volume":"21","author":[{"given":"Roude","family":"Li","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoxia","family":"Liao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Fu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoxin","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiyi","family":"Liao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuimei","family":"Cen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayang","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longyun","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Honggang","family":"Chi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Zou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,1,13]]},"reference":[{"key":"1302_CR1","doi-asserted-by":"publisher","DOI":"10.1038\/s41572-020-0205-x","volume":"6","author":"T Kobayashi","year":"2020","unstructured":"Kobayashi T, Siegmund B, Le Berre C, Wei SC, Ferrante M, Shen B, et al. 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