Circadian Control of Host–Microbiome Symbioses

Life on Earth has evolved under the predictable rotation of the planet, giving rise to intrinsic timing mechanisms that synchronize physiology and behavior with the 24-h day-night cycle. These molecular timing systems organize metabolism, immunity, and cellular renewal into recurring daily programs that optimize energy use and defense. Increasing evidence now reveals that circadian logic extends beyond the host to include its microbial partners. Host feeding rhythms, epithelial renewal, and immune activity impose temporal order on the microbiota, while microbial metabolites and immune signaling feedback to reinforce host circadian oscillations. When this temporal coordination is lost, through genetic disruption of clock genes, high-fat diet, or behavioral desynchrony, microbial and host rhythms collapse, leading to metabolic syndrome, obesity, and impaired xenobiotic detoxification. Thus, temporal order emerges as a coevolved property of host–microbe symbiosis, linking planetary rotation to cellular physiology across kingdoms and defining a chronobiological foundation for health and disease.