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 multiomics 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 wk. 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: proinflammatory 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.NEW & NOTEWORTHY Using a phase-stratified multiomics framework in a murine MASLD model, we show that chronic FPC feeding is associated with altered temporal coordination between the gut and liver, beyond compositional dysbiosis. FPC reduces phase-dependent differences in hepatic clock and lipogenic gene expression, attenuates microbiome phase organization, and is associated with misaligned cecal and systemic metabolite profiles. Covariance networks reveal alteration of microbiome-metabolome-transcriptional connectivity, implicating disruption of phase-dependent gut-liver integration as an underappreciated axis of MASLD pathogenesis.