This review investigates the hypothesis that the composition of gut microbiota influences central nervous system (CNS) functions and cognition, playing a crucial role in the pathogenesis of various CNS diseases. To explore this hypothesis, we reviewed data from existing literature and analyzed its implications for clinical medicine. We also propose potential therapeutic strategies based on current clinical research. Our methodology involved an extensive literature search in databases such as PubMed/Medline and the Frontiers archive, using key terms like “microbiome,” “nervous system,” and “gut-brain axis.” After screening 35,873 publications, we identified and analyzed 160 full-text papers and reviews, based on their relevance. Additional keywords explored included “short-chain fatty acids,” “microbiome metabolites,” “immune system,” “multiple sclerosis,” “autism,” “anxiety,” “depression,” “Alzheimer’s disease,” “Parkinson’s disease,” and “probiotics.” Our findings suggest that a gut microbiota composition rich in short-chain fatty acid-producing strains has a generally positive effect on CNS health. These insights were drawn from preclinical animal models and early clinical studies. The review further discusses the potential of microbiota modulation as a therapeutic approach for CNS disorders.