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Accumulating evidence supports an organ\u2010like conceptual framework in which the gut microbiome exhibits spatially structured organization, extensive metabolic capacity, and continuous bidirectional communication with host systems. Through the production of bioactive metabolites with endocrine\u2010like, immunomodulatory, and neuromodulatory properties, the microbiome contributes to metabolic, immune, and neuroendocrine regulation, thereby influencing systemic homeostasis and disease susceptibility. Recent advances in multi\u2010omics, spatial biology, and computational modeling are moving the field from taxonomic association toward functional interpretation, mechanistic insight, and causal inference. These approaches are beginning to reveal microbiome\u2010derived functional modules and host\u2013microbe signaling networks that are shaped by host genetics, diet, medications, feeding patterns, circadian rhythms, and environmental exposures. In this review, we synthesize current mechanistic and translational evidence to conceptualize the gut microbiome as an organ\u2010like functional system, delineate its structural and functional organization, and propose a framework for mapping, modeling, and therapeutically targeting microbiome\u2010derived circuits to support precision medicine in metabolic, inflammatory, and selected gut\u2013brain axis\u2010related disorders.<\/jats:p>","DOI":"10.1002\/imt2.70144","type":"journal-article","created":{"date-parts":[[2026,8,21]],"date-time":"2026-08-21T14:28:32Z","timestamp":1787322512000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["The gut microbiome organ"],"prefix":"10.1002","volume":"5","author":[{"given":"Yang","family":"Bi","sequence":"first","affiliation":[{"name":"Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Children and Adolescents' Health and 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