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The gut microbiota plays a pivotal role in human health by modulating physiological homeostasis and influencing the pathogenesis of various diseases. Recent studies have underscored the close relationship between neurotransmitters, which act as communication mediators between the gut and brain, and the development and treatment of multiple brain disorders. Despite these advances, the intricate interactions between gut microbiota and brain diseases remain largely unexplored in the extensive biomedical literature. There is a notable absence of a structured database focusing on gut microbiota-brain disease associations. Introducing BGMDB (Brain Disease Gut Microbiota Database), a meticulously curated database designed to provide experimentally supported connections between gut microbiota and brain diseases. The current version of BGMDB extensively covers 1,419 associations involving 609 gut microbiota and 43 brain diseases, including 184 specific association triplets linking brain diseases, neurotransmitters, and gut microbiota among six neurotransmitters. Noteworthy is that BGMDB integrates gene data related to gut microbiota from the gutMGene database. Brain region and disease microbial networks are introduced to investigate potential common genetic relationships between brain diseases and brain region changes. Each entry in BGMDB offers detailed insights into specific associations, including the particular brain disease implicated, the involved gut microbiota, neurotransmitter, and a concise description of the relationship supported by relevant literature references. To facilitate easier access to relevant information for specific brain diseases, BGMDB provides enhanced graphical query options to address various biologically pertinent inquiries. Additionally, a user-friendly interface allows users to browse, retrieve, and download entries conveniently. BGMDB serves as a valuable resource for investigating microbes associated with human brain disorders. Access BGMDB through http://43.139.38.118:8080/demo02/ .