How circadian disruption causes gut dysbiosis

Gut dysbiosis is an imbalance in the bacterial communities that live in the gut. Dysbiosis plays a big role in the increase of gut disorders such as IBS, IBD, and SIBO. This is due, in large part, to the fact that most of the genes in the gut belong to our microbiome, not us.

Circadian rhythms are biological processes that follow a 24 hour pattern and persist in the absence of environmental cues. Processes not under our conscious control, such as digestion, are under heavy circadian control.

For optimal digestion, circadian rhythms help the gut tell what time it is. This helps the gut prepare for food when it comes, fight bacteria when it enters the gut, and repair the gut when there’s a break. Environmental cues called zeitgebers link our digestion to the day/night cycle and when we normally eat.

I cannot emphasize enough how important circadian rhythms are to optimal digestion. In fact, the best way to mess up your digestion is to ignore your circadian rhythms. Two studies published this year give us a glimpse in to why this happens.

ILC3 Gut Dysbiosis

Circadian rhythms and dysbiosis

Circadian rhythms control every aspect of your digestion. Digestive enzymes, absorption, motility, and even the microbiome are under circadian control. Anticipating the arrival of food allows your gut to be ready for what comes and to know when it’s time to repair the damage.

The immune system plays a starring role in the gut. It helps regulate the microbiome, tamps down inflammation, and prevents autoimmune attack on our own cells. We don’t want too much inflammation, but we also don’t want bad guys getting into our bloodstream. Both would be bad.

Type 3 innate lymphoid cells(ILC3) are in charge of maintaining intestinal homeostasis. They’re a part of the antimicrobial defense system and help maintain the gut via secretion of the cytokines IL-17 and IL-22.

Since ILC3 cells are in charge of shaping a healthy gut, it’s not hard to see why circadian rhythms may play a role in their function. To determine if they are under circadian control, researchers knocked out circadian proteins in mice.

Lo and behold, knocking out circadian proteins altered the expression of cytokines secreted from ILC3 cells. Specifically, IL-17 levels increased and IL-22 levels decreased. The enhanced IL-17 secretion increases inflammation while the decreased IL-22 affects other aspects of digestion and absorption. To quote:

Thus, disruption of circadian fluctuations may impair the capacity of ILC3s to preserve homeostatic interactions with nutrients and commensal bacteria (47, 48), thereby facilitating malabsorption and dysbiosis.

IL-22 secreted from ILC3 cells helps promote fat and fat soluble vitamin absorption. It also helps prevent Candida albicans overgrowth. This helps explain how circadian disruption is a major player in functional gut disorders such as IBS and SIBO.

Shedding some light on gut dysbiosis

The next study on the docket dug a little deeper. They also found that ILC3 exhibit circadian rhythms. And disrupting circadian rhythms altered fat transporter expression and caused dysbiosis via altered IL-17 and IL-22 levels.

They found something else that may pique your interest. It turns out that the feeding/fasting cycle and microbiome rhythms help fine tune the circadian rhythms of ILC3 cells. Other circadian variables may also play a role.

But, the primary entraining cue is the light/dark cycle. And knocking out one of the core circadian clock proteins solely in the master clock of the brain disrupted ILC3 rhythm.

Therefore, proper light exposure as well as feeding cues and other cues help set the rhythm of ILC3 cells to maintain gut homeostasis. Without addressing light, the gut will be imbalanced and you’ll be primed for dysbiosis and C. albicans overgrowth.

This is a concept that I’ve tried to get across to people. You don’t control C. albicans by restricting diets. You control it by optimizing gut function via circadian rhythms.


The circadian system creates a synergy within and between organ systems to optimize function. Circadian rhythms play a large role in shaping the environment of the gut via the autonomic nervous system.

But the gut is a unique organ system in that most of the genes that regulate it’s function aren’t our own. They belong to the trillions of bacteria that make up our microbiome. When the synergy between us and our microbial tag team partners is lost, dysfunction ensues.

Because of this, our circadian rhythms need to be on point for our digestion to function properly. Loss of a robust circadian rhythm leads to dysbiosis, and ILC3 cells appear to be a driver of this. This leads to a vicious cycle of inflammation, malabsorption, and further dysbiosis.

Light appears to be the primary environmental cue for ILC3 cell circadian rhythm. But other factors including the feeding/fasting cycle and microbiome rhythm help fine tune it. These factors, coupled with diet, promote intestinal homeostasis and efficient digestion and absorption.

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