Phase-dependent Disruption of Microbiome-Metabolome Coordination Is Associated with Diet-Induced MASLD

Metabolic-dysfunction-associated steatotic liver disease (MASLD) is typically attributed to caloric overload, lipotoxicity, and static gut dysbiosis, but how chronic diet alters the temporal organization of gut-liver communication remains unclear. We combined a phase stratified multi omics framework, cecal 16S rRNA profiling, dual compartment (cecum and serum) metabolomics, and hepatic clock and lipogenic gene expression in C57BL/6J male mice fed a high fat, palmitate and cholesterol enriched (FPC) diet containing high sucrose for 22 weeks. FPC feeding was associated with severe MASLD and markedly attenuated homeostatic phase dependent differences in hepatic clock and lipogenic transcripts, consistent with a persistently lipogenic transcriptional state across the light-dark cycle. This temporal disruption coincided with reduced phase structured ecological organization in the cecal microbiome and the emergence of a constrained, dysbiotic community dominated by a few taxa. Dual-compartment metabolomics revealed that, despite retaining overall phase structure, local (cecal) and systemic (serum) metabolite pools showed misalignment: pro inflammatory and bile acid species showed exaggerated luminal variations but flattened, persistently elevated profiles in serum. High-stringency covariance network analysis identified diet-associated differences in microbiome-metabolome covariance patterns. These findings are consistent with a model in which diet-induced MASLD is associated with altered spatial and phase-dependent coordination across microbiome-host metabolic and transcriptional networks, suggesting disruption of integrated microbiome-host organization beyond static dysbiosis and lipotoxic stress.