Shift work has become a major cause of circadian rhythm disruption in modern society. This study investigated the systemic consequences of shift schedules by subjecting mice to different light-dark (LD) cycles: non-24-hour cycles (rapidly rotating Groups A and B) and 24-hour cycles (Group C and Control group). We performed behavioral tests, serum hormone measurements, transcriptomic analysis of SCN genes, and gut microbiome analysis.  The results showed that the mice exhibited significant body weight gain after altering LD cycle compared with the control group. In groups exposed to non-24-hour cycles, the circadian expression rhythms of core clock genes (Per, Cry, Bmal1) in the SCN were lost. GO and KEGG enrichment analyses revealed that genes in the SCN losing rhythmicity were significantly enriched in metabolic and regulatory pathways, disrupting endocrine and metabolic rhythms and ultimately compromising health. The circadian rhythms of key hormones like melatonin (MT) and dopamine (DA) were also lost. Concurrently, these central disruptions drove peripheral pathology, including gut microbiota dysbiosis (altered Firmicutes/Bacteroidota ratio, reduced Verrucomicrobia) and a profound loss of gut microbial diurnal oscillations. Behaviorally, this multi-system discord manifested as significantly increased anxiety-like, depression-like behaviors and fatigue (P<0.05), while spatial memory remained intact, indicating selective affective vulnerability. SCN collapse together with hormonal chaos, desynchronizes the gut microbiome, potentially promoting inflammation and metabolic dysfunction that further disrupts central regulation. These findings provide a physiological foundation for understanding the health consequences of circadian disruption and may help guide the future design of healthier shift work schedules.
