{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T14:15:07Z","timestamp":1788531307620,"version":"build-2803163510"},"reference-count":145,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T00:00:00Z","timestamp":1788480000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014103","name":"Key Technology Research and Development Program of Shandong Province","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014103","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>Colorectal cancer (CRC) is one of the most common malignancies worldwide and a leading cause of cancer-related mortality. The gut microbiome has attracted growing attention because of its involvement in CRC initiation and progression, early detection, prognostic evaluation, and therapeutic response. However, CRC microbiome studies continue to face inconsistent findings and limited reproducibility, partly because of differences in specimen type. Directly comparing microbial signals from fecal, mucosal, and intratumoral samples may therefore bias mechanistic interpretation and mislead clinical translation. From a spatial-niche perspective, this review summarizes the distinct characteristics, formation mechanisms, interrelationships, and clinical implications of fecal, mucosal, and intratumoral microbiota during CRC progression. We further propose a \u201cseed bank\u2013colonizers\u2013specialized populations\u201d model to conceptualize the continuous but non-equivalent hierarchy among these niches. By providing a clearer spatially stratified framework, this review aims to help move CRC microbiome research beyond descriptive associations toward precision-oriented applications supported by mechanistic interpretability, reproducible evidence, and clinical translatability.<\/jats:p>","DOI":"10.3389\/fcimb.2026.1904188","type":"journal-article","created":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T13:23:09Z","timestamp":1788528189000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Spatial niches of the colorectal cancer microbiome: differences, interrelationships, and clinical implications of fecal, mucosal, and intratumoral microbiota"],"prefix":"10.3389","volume":"16","author":[{"given":"Minghui","family":"Yu","sequence":"first","affiliation":[{"name":"Shuguang Hospital, Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]},{"name":"Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]},{"name":"Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Shi","sequence":"additional","affiliation":[{"name":"Shuguang Hospital, Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]},{"name":"Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]},{"name":"Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong","family":"Li","sequence":"additional","affiliation":[{"name":"Shuguang Hospital, Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]},{"name":"Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]},{"name":"Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuelin","family":"Li","sequence":"additional","affiliation":[{"name":"Shuguang Hospital, Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]},{"name":"Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]},{"name":"Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingyu","family":"Sun","sequence":"additional","affiliation":[{"name":"Shuguang Hospital, Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]},{"name":"Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]},{"name":"Key Laboratory of Liver and Kidney Diseases, Institute of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine","place":["Shanghai, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,4]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/j.chom.2016.07.006","article-title":"Fap2 mediates Fusobacterium nucleatum colorectal adenocarcinoma enrichment by binding to tumor-expressed Gal-GalNAc","volume":"20","author":"Abed","year":"2016","journal-title":"Cell Host Microbe"},{"key":"B2","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1158\/1940-6207.Capr-23-0091","article-title":"Early-onset colon cancer shows a distinct intestinal microbiome and a host-microbe interaction","volume":"17","author":"Adnan","year":"2024","journal-title":"Cancer Prev. 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