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Conventional immunosuppressants such as azathioprine (AZA), commonly used in the treatment of IBD, can partially alleviate symptoms but fail to restore normal barrier and immune functions, while exhibiting non-negligible adverse effects. Here, we report an AZA-loaded microbiota-modulating and colon-targeted nanoparticle constructed from pectin, Zein, and Eudragit\n                      <jats:sup>\u00ae<\/jats:sup>\n                      S100 (APZE).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      APZE could effectively encapsulate AZA and enhance its cellular and intestinal uptake, thereby improving oral bioavailability in rats compared to AZA suspension. Additionally, its colon targeting ability and mucoadhesive properties prolonged colonic retention, leading to higher colonic accumulation, as indicated by the AUC of colon fluorescence intensity in rats after oral administration of the DiR-labeled formulation. Animal studies demonstrated that APZE significantly reduced inflammation in IBD mice, repaired the intestinal barrier, modulated the gut microbiota, and upregulated short-chain fatty acid levels, exhibiting significant therapeutic efficacy with good safety. The protective effect of APZE against colitis is largely microbiota-dependent. When co-administered with commercially available\n                      <jats:italic>Bifidobacterium<\/jats:italic>\n                      , APZE attenuated colitis effectively, demonstrating excellent therapeutic effects and favorable safety.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      In summary, our findings indicate that APZE and\n                      <jats:italic>Bifidobacterium<\/jats:italic>\n                      improved intestinal barrier repair and colitis-related outcomes in a DSS-induced model, supporting their potential as therapeutic agents for IBD.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Graphical abstract<\/jats:title>\n                  <\/jats:sec>","DOI":"10.1186\/s12951-026-04136-4","type":"journal-article","created":{"date-parts":[[2026,2,15]],"date-time":"2026-02-15T06:24:11Z","timestamp":1771136651000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Colon-targeted microbiota-modulating nanoparticles amplify azathioprine efficacy via gut microbiota axis remodeling in inflammatory bowel disease"],"prefix":"10.1186","volume":"24","author":[{"given":"Jingjing","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanni","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaqi","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luquan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yubin","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siyao","family":"Jin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yana","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangyu","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Bing","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong","family":"Mei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Libo","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,2,15]]},"reference":[{"issue":"8067","key":"4136_CR1","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1038\/s41586-025-08940-0","volume":"642","author":"L Hracs","year":"2025","unstructured":"Hracs L, Windsor JW, Gorospe J, Cummings M, Coward S, Buie MJ, et al. 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