Defined Microbiota Modulates Host Metabolome and Skeletal Adaptation to Diet-Induced Obesity

The gut microbiota is increasingly recognized as a regulator of host metabolism and bone physiology. However, how microbial colonization integrates systemic metabolic cues with skeletal remodeling under metabolic stress remains unclear. We used germ-free (GF) and gnotobiotic C57BL/6J mice colonized with the defined 12-member Oligo-Mouse-Microbiota (Oligo-MM¹²) to dissect microbiota-dependent bone adaptation during high-fat diet (HFD)-induced obesity. Micro-CT analysis revealed that only colonized mice exhibited structural adaptations, namely increased cortical thickness and trabecular area, in response to HFD, whereas GF mice failed to remodel their skeleton despite broadly comparable weight gain trajectories and adiposity. Serum metabolomics uncovered distinct microbiota-specific metabolic signatures. GF mice accumulated bone-relevant metabolites including lysine, uridine, DHA, and pyruvate, suggesting altered systemic handling of bone-relevant metabolites, whereas colonized mice displayed reduced circulating levels associated with skeletal remodeling. These metabolic patterns correlated with reduced β-CTX levels in colonized mice, indicative of microbiota-mediated suppression of bone resorption. Our findings identify the gut microbiota as a key determinant of skeletal adaptation to diet-induced obesity, presumably acting through systemic metabolic reprogramming and modulation of bone turnover. The defined-microbiota mouse model provides a powerful framework to disentangle the gut-bone axis at a systems and metabolic level.