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The gut microbiome plays a critical role in human health through its influence on numerous physiological functions such as metabolism and immunity, with disruptions in microbial communities increasingly linked to metabolic disorders. In a large-scale cohort study in Japan, we investigated the association between gut microbiome profiles and metabolic health. Using 16S rRNA gene sequencing, four-enterotype clustering revealed that the Bacteroides 2 (B2) enterotype was associated with lower alpha-diversity and increased risk of metabolic diseases, particularly obesity (OR = 1.51) and hypertension (OR = 1.49). Refined seven-enterotype clustering further stratified the Ruminococcus, Prevotella, and Bacteroides enterotypes into distinct subtypes, uncovering a novel high-risk Prevotella 2 (P2) enterotype associated with nearly two-fold increased risk of obesity and diabetes mellitus. The B2 and P2 enterotypes were characterized by reduced abundance of beneficial short-chain fatty acid (SCFA) producers (Faecalibacterium, Anaerostipes) and enrichment of opportunistic pathogens (Fusobacterium and Veillonella for B2, Megamonas and Megasphaera for P2). Microbial metabolic influence network analysis revealed enterotype-specific interaction patterns, with R1, R2, and P1 enterotypes demonstrating cooperative production of SCFAs and other metabolites, while B enterotypes displayed synergy in the production of a range of sugar compounds. These findings underscore the utility of refined enterotype clustering as a powerful tool to reveal previously unrecognized gut microbial patterns linked to metabolic risk. By identifying B2 and the newly characterized P2 enterotypes as high-risk microbial profiles, this study opens new avenues for microbiome-based stratification and early intervention in metabolic disease management.