Circadian Rhythm Entrainment of the Gut Microbiome via Time-Restricted Eating

The mammalian gut microbiome exhibits 24-hour oscillatory dynamics in both compositional and functional abundance, but whether this circadian rhythmicity is driven by host timing cues or intrinsic microbial clocks remained unresolved. This randomised crossover trial of 211 adults compared ad libitum feeding against a 10-hour time-restricted eating (TRE) protocol over 12 weeks, with 16S rRNA faecal microbiome sequencing performed at baseline, 4 weeks, and 12 weeks. Dietary composition and caloric intake were matched between conditions to isolate the effect of meal timing alone.

Under ad libitum feeding, microbial circadian oscillation amplitude was low and species diversity was stable but not dynamic. TRE amplified the microbial circadian rhythmicity index 2.3-fold (p<0.001) and significantly increased relative abundance of Akkermansia muciniphila (+31%), Lactobacillus reuteri (+24%), and Bifidobacterium adolescentis (+18%) — all species associated with mucosal integrity and immune homeostasis. Microbial beta-diversity diverged meaningfully between conditions by week 4 (Bray-Curtis PERMANOVA p=0.003) and was sustained through week 12. These results identify meal timing — independent of dietary composition or caloric restriction — as a potent microbiome-synchronising intervention with broad applications for metabolic and gut health management.