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It highlights microbiota roles in regulating the immune system, metabolism, and overall health, and summarizes contributions of diverse microbial populations across body regions. Molecular mechanisms governing microbiota-host interactions are discussed, alongside how dysbiosis can heighten disease susceptibility. 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The microbiota plays a crucial role in regulating the immune system, metabolism, and overall health. We explore the diverse microbial populations inhabiting different body regions and their essential contributions to maintaining balance within the host. Recent research has uncovered molecular mechanisms that govern microbiota-host interactions, offering new insights into how these microbes support health and, conversely, how imbalances known as dysbiosis can increase susceptibility to diseases. While much attention has been given to the gut microbiota, this review also explores the influence of microbes in other parts of the body, including their effects on various organs and tissues. Additionally, we discuss emerging evidence on the gut-brain axis, illustrating how the microbiota can impact brain function and behavior. Understanding this connection could open new possibilities for treating neurological and psychological disorders. Finally, we evaluate microbiota-based therapies such as probiotics and fecal microbiota transplantation, emphasizing the importance of personalized approaches. By integrating findings from multiple disciplines, this review provides a comprehensive perspective on the microbiota’s vital role in human health and its potential as a therapeutic target.  \nKey Words: Gut microbiota; Microbiota-host relationship; Immune system; Faecal microbiome transplantation; Probiotics; Gut dysbiosis; Chronic disorders; Gastrointestinal tract; Metabolic disorders; Gut-organ axis  \n©The Author(s) 2025. Published by Baishideng Publishing Group Inc. All rights reserved.  \n WJEM  [https://www.wjgnet.com](https://www.wjgnet.com) 1 September 20, 2025  Volume 15  Issue 3   \nKhan AS et al. Microbiota-host interactions  \nCore Tip: This review article explores the crucial role of gut microbiota and their metabolites in immune regulation, gene expression, and disease progression. It introduces the gut-organ axis hypothesis, linking systemic genetic factors with inflammatory bowel disease progression and treatment response. The study emphasizes microbiota-targeted therapies, such as probiotics, fecal microbiota transplantation, and dietary interventions, as promising strategies in precision medicine. Future research should focus on personalized microbiome-based treatments, leveraging machine learning and advanced analytics to optimize therapie","cbCaioNlkdZYt6Js","https://ap.wps.com/l/cbCaioNlkdZYt6Js","pdf",1700157,17,"English","# Abstract\n# Core Tip\n# Introduction","[{\"question\":\"What is the focus of this review on microbiota and the host?\",\"answer\":\"The review focuses on how microbiota-host interactions regulate physiological functions and influence health beyond simple coexistence.\"},{\"question\":\"Which major biological systems are affected by the microbiota?\",\"answer\":\"The microbiota is discussed as influencing the immune system, metabolism, and overall health, with additional effects extending to organs and tissues.\"},{\"question\":\"What therapies related to microbiota are evaluated?\",\"answer\":\"The review evaluates microbiota-based therapies such as probiotics and fecal microbiota transplantation, emphasizing personalized therapeutic strategies.\"}]","Understanding the intricate interactions between microbiota and host | PDF",1790746143,43]