Assessment of nutrient intake by gut microbiota enterotype in Japanese subjects

Japanese gut microbiota forms community clusters and shares some compositional features with Western enterotypes, although the relationship between enterotypes and habitual nutrient intake in Japanese adults remains unclear. We analyzed data from 770 community-dwelling adults. Enterotypes were assigned based on 16S rRNA gene profiles using a support vector machine model, and taxonomic annotations were updated using the SILVA 138 database. Dietary intake and nutrient intake were assessed, and differences among enterotypes were examined. Candidate nutrients and food groups potentially associated with enterotypes were prioritized using a SHapley Additive explanation (SHAP)-based interpretation of the XGBoost models and were further evaluated using linear discriminant analysis. Five enterotypes (Types A–E) were identified and exhibited insufficient dietary fiber and excessive salt intake. Types A and C showed the highest and lowest overall nutrient intake scores, respectively. Although predictive performance for nutrient intake and food-group intake was modest, linear discriminant analysis based on SHAP-prioritized features revealed distinct but partially overlapping dietary signatures among enterotypes. Correlation analyses identified associations between key bacterial taxa and enterotype-specific dietary features, which reflect complex combinations of nutrients and food groups. These findings may contribute to the development of enterotype-aware dietary strategies to promote a healthy gut microbiota.