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Although stent-based diverting technique (SDT) and conventional ileostomy exert divergent impacts on gut microbial balance, high-quality comparative microbiome data from randomized trials are lacking. We report a 16S rRNA amplicon dataset from 80 patients randomized to SDT (n\u2009=\u200937) or ileostomy (n\u2009=\u200943), with fecal samples collected preoperatively and on postoperative day 90. We characterized phylum-level taxonomic composition, \u03b1-diversity and intergroup \u03b2-diversity across four subgroups, and identified discriminatory taxa via LEfSe. Functional prediction detected differential metabolic pathways after surgery. We additionally performed correlation analyses to link clinical covariates with microbial signatures. This public dataset enables independent reprocessing and cross-study comparisons, facilitating exploration of diversion-strategy-specific microbial remodeling and validation of SDT\u2019s gut microbiota-preserving capacity.<\/jats:p>","DOI":"10.1038\/s41597-026-08247-3","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T15:53:22Z","timestamp":1790783602000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["16S rRNA Datasets of Gut Microbiota in Stent-Based Diverting Technique and Ileostomy from A Prospective, Open-Label, Multicenter Randomized Controlled Trial"],"prefix":"10.1038","volume":"13","author":[{"given":"Zhongyu","family":"Wu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifan","family":"Tong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiping","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenbin","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingfei","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5990-3720","authenticated-orcid":false,"given":"Diyu","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zheyong","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhangfa","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6457-0577","authenticated-orcid":false,"given":"Xiujun","family":"Cai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"key":"8247_CR1","first-page":"209","volume":"71","author":"H Sung","year":"2021","unstructured":"Sung, H. et al. 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