Humans are creatures of habit – we tend to wake up, feel hungry, and fall asleep at the same time every day. We owe this tendency to our circadian rhythms – 24 hour cycles that are present in the biological processes of most living beings. These cycles are generated by “clock genes,” which influence most of our organs and cells, including those of the digestive tract. This daily rhythm of the gastrointestinal system influences digestion, absorption, gastric motility, and the gut microbiota.

Recent studies suggest that circadian rhythm and clock genes may also affect intestinal immune cells, of which the circadian pathways are disrupted in inflammatory bowel disease. While the underlying reason behind this observation has remained to be seen, now Teng et al. and Wang et al. have identified for the first time that the development and functions of a group of immune cells in the gut are controlled by clock genes in mice.

The cells that researchers identified are called type 3 innate lymphoid cells (ILC3), which appear to help regulate the daily rhythm of the gut and help our GI tracts defend against pathogenic microorganisms. They do this by secreting cytokines that help maintain proper balance of the intestinal barrier and gut microbiota.

Researchers found that clock genes are highly active in ILC3 cells, and that the production of specific cytokines correspond with the activity of certain clock genes. If scientists eliminated the key clock gene Nr1D1 (encoding REV-ERB) from the mice, ILC3 produced less IL-22 and more IL-17 cytokines compared to mice who still harbored the Nr1D1 gene. A second group led by Teng et al. report similar results, finding that mice lacking the clock gene BMAL1 has a reduced number of intestinal ILC3s.

The NR1D1 deficient mice were also less able to clear an infection caused by the dangerous pathogen Clostridium difficile. Previous reports have suggested that IL-17A is implicated in poorer disease outcomes for C. difficile infection. Authors suggest that hyperresponsive IL-17 secretion by the ILC3s of Nr1D1 deficient mice may contribute to more severe inflammation and bacterial burden.

Wang et al. wondered what would happen if they actively hindered the normal circadian rhythm of the mice, mimicking, for example, the schedule of a shift-worker. To achieve this, they disrupted the normal circadian rhythm of the mice by altering the conventional 12:12 (12 hours light: 12 hours dark) pattern to include an 8-hour phase advance every 2 days. In altering the pattern of light and dark that the mice were exposed to, certain clock genes were also disrupted, as was the secretion of 1L-17A and 1L-22 by both NKp46+ and NKp46− ILC3s. The researchers conclude that a disruption in the circadian rhythm might impair the ability of ILC3s to maintain normal interactions in the gut with nutrients and commensal bacteria, ultimately leading to malabsorption, changes in gut microbiota composition, and disease.

Teng et al. also analyzed ILC3 cells isolated from inflamed and noninflamed intestinal regions of patients with inflammatory bowel disease (IBD). They found far less ILC3s in the inflamed intestinal regions of IBD patients compared to the noninflamed regions, and noticed that the inflamed intestinal regions exhibited altered expression of circadian-rhythm genes. The authors suspected that the altered gene expression is the result of chronic inflammation or microbial dysbiosis, leading them to suggest that circadian gene expression may be an important pathway for boosting ILC3 responses in the context of inflammation and dysbiosis.

Collectively, these studies highlight how the circadian rhythm affects crucial immune cells in the gut that are needed for proper interactions with nutrients and commensal bacteria. Future studies will specify which intestinal functions are affected by ILC3 daily fluctuations. Overall, these studies are the first evidence in mice showing that host circadian rhythms don’t only affect the gut microbiota, but also have a drastic effect on gut immune cells.


Teng F, Goc J, Zhou L, et al. A circadian clock is essential for homeostasis of group 3 innate lymphoid cells in the gut. Sci Immunol. 4(40):eaax1215. doi: 10.1126/sciimmunol.aax1215.

Wang Q, Robinette ML, Billon C, et al. Circadian rhythm-dependent and circadian rhythm-independent impacts of the molecular clock on type 3 innate lymphoid cells. Sci Immunol. 4(40):eaay7501. doi: 10.1126/sciimmunol.aay7501.