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Despite extensive research, these factors have largely been investigated as separate entities, with limited integrative insights into their interplay. This review is the first comprehensive synthesis of physicochemical, mechanical, and microbial parameters shaping SIMO pathogenesis. By reviewing both clinical and experimental data, we reveal how alterations in pH, transit time, digestive secretion dynamics, bile acid composition and impaired intestinal absorption collectively reshape microbial load, diversity, and metabolic output, establishing a self-perpetuating loop of dysfunction. We further discuss the limitations of current diagnostic tools and the transformative potential of emerging approaches, from sampling capsules enabling molecular analyses, to in vitro models simulating human small intestinal ecosystem. This integrative perspective shifts the paradigm from a microbe-centered to an ecosystem-based understanding of SIMO, outlining key challenges and opportunities for personalized diagnostics, mechanistic research, and microbiota-targeted next-generation therapeutics including pre-, pro-, postbiotics and faecal transplantation.<\/jats:p>","DOI":"10.1093\/femsre\/fuag016","type":"journal-article","created":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T11:49:11Z","timestamp":1775735351000},"source":"Crossref","is-referenced-by-count":0,"title":["Small intestinal microbiome, the underrated maestro of SIMO disease"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5461-1195","authenticated-orcid":false,"given":"Charlotte","family":"Deschamps","sequence":"first","affiliation":[{"name":"UMR 454 MEDIS, Microbiologie Environnement Digestif et Sant\u00e9, Universit\u00e9 Clermont Auvergne-INRAE , 63001 Clermont-Ferrand 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