• Host circadian clocks regulate gut microbial diurnal oscillations via rhythmic behaviors, establishing a bidirectional temporal dialogue.
• Disruption of this crosstalk by modern lifestyle factors leads to loss of microbial rhythms, impaired intestinal barrier, and systemic metabolic dysregulation.
• Microbial metabolites such as butyrate and propionate oscillate rhythmically and directly modulate host metabolic processes.
• Targeting microbial rhythms offers promising therapeutic strategies to reset host immunity and metabolism in immunometabolic diseases.