The Gut–Circadian Rhythm Connection

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In past articles, I’ve covered the importance of the circadian rhythm to good health. I’ve also written a lot about the gut microbiome. But you may be surprised to learn that gut bacteria can directly influence your circadian rhythm. Imbalances in your gut can disrupt your circadian rhythm and affect your sleep, hormones, and immune system. Read on to learn more about how these two systems are interconnected and how you can keep your gut and “body clock” happy.

What Is the Circadian Rhythm?

The term “circadian rhythm” refers to the internal organization of biochemical processes within our bodies that follows an approximately 24-hour cycle and regulates many aspects of our behavior and physiology. Our circadian rhythms are produced by collections of genes and proteins within our bodies that exhibit rhythmic activity and are referred to as “body clocks.”

The “master” body clock is a structure in the brain called the suprachiasmatic nucleus (SCN). Additional body clocks, called “peripheral body clocks,” are distributed throughout organs such as the liver and pancreas. The master clock in the SCN regulates the activities of peripheral clocks, and the peripheral clocks interact with one another and provide feedback to the master clock. Together, these internal timekeepers generate our circadian rhythms, which affect many important aspects of our health such as our sleep/wake cycles, hormone balance, and metabolism (1).

Could the bacteria in your gut be throwing off your circadian rhythms? #microbiome

To keep our bodies running “on schedule,” our body clocks need to be synchronized with each other. Cues from our external environment such as light, temperature, and food intake sync our body clocks, initiating circadian rhythms. Depending on what cues we provide our bodies, and when we provide the cues over the course of a 24-hour circadian cycle, we either keep our body clocks ticking in synchrony or throw a wrench into their cyclical processes, creating circadian rhythm disruption. Circadian rhythm disruption has been linked to many disease processes, including metabolic syndrome, obesity, cardiovascular disease, intestinal dysbiosis, inflammatory bowel disease, neurodegenerative disease, and cancer (2, 3) (4).

Intestinal Cells Undergo Circadian Rhythms

The “master” body clock in the SCN and the peripheral clocks in the liver and pancreas have long been considered the primary regulators of circadian rhythms. However, it was recently discovered that cells in the intestine also undergo circadian rhythms (5). Intestinal cell circadian rhythms influence gut motility, nutrient absorption and metabolism, and cell proliferation (6, 7, 8). Perturbation of the circadian rhythm caused by abnormal sleep/wake cycles renders intestinal cells more vulnerable to injury. Considering this information, it is not surprising that research has found circadian rhythm disruption to be linked to gastrointestinal diseases such as irritable bowel syndrome and colorectal cancer.

Gut Microbes Have Their Own Circadian Rhythms

The circadian rhythms in the gut are not limited to intestinal cells; it turns out that gut microbes also play a key role in the regulation of circadian rhythms. The collection of microbes that resides in your gut undergoes its own circadian rhythms every 24 hours. These circadian rhythms involve changes in the location of gut microbes within the intestine, fluctuations in their adherence to the intestinal wall, and variations in their production of metabolites such as short-chain fatty acids, which modulate gene expression and biochemical pathways both locally in the gut and systemically throughout the body. Through these cyclical mechanisms, the circadian rhythms of gut microbes ultimately affect our own circadian rhythms, which regulate our sleep/wake cycles, hormone release, and metabolism (9). In addition, our circadian rhythms provide feedback to our gut microbes.

The Gut and Circadian Rhythms Are Tightly Linked

Our circadian rhythms are therefore linked to the rhythms of our intestinal cells and gut microbes in a multi-directional feedback loop. Factors that influence the integrity of the gut and the microbiome therefore affect our circadian rhythms, and vice versa. Taking steps to “synchronize” the rhythms of our gut microbiome with our other circadian rhythms, such as sleep/wake cycles and food intake patterns, appears to be crucial for preventing diseases associated with circadian disruption, such as metabolic syndrome, obesity, cardiovascular disease, and cancer.

Diet and Meal Timing Affect Circadian Rhythms

While light exposure and temperature are the primary cues that affect the master body clock in the brain, intestinal and gut microbe circadian rhythms are primarily influenced by the timing of food intake and composition of the diet. Diet-induced dysbiosis and erratic meal consumption disturb both intestinal cell and gut microbe circadian rhythms and have systemic effects on the body (10).

A study in which mice were fed a high-fat, high-carb diet loaded with polyunsaturated fats and processed sugars (designed to mimic the Standard American Diet) experienced profound disruptions in their intestinal and gut microbe circadian rhythms. These disrupted rhythms altered microbial metabolite production, which led to disorganized gene expression in the mice’s body clocks. The disordered gene expression down-regulated the mice’s metabolism, causing them to develop dysfunctional glucose homeostasis, hypercholesterolemia, and obesity (11). This research suggests that a high-fat, high-carb SAD blunts gut circadian rhythms and has systemic effects on body clocks that control metabolism. Conversely, a diet that is low in processed sugars and polyunsaturated fats and rich in EPA, DHA, and antioxidants has been shown to normalize gut circadian rhythms (12, 13, 14).

Erratic eating patterns, such as skipping meals and eating late at night, can also disrupt intestinal cell and gut microbe circadian rhythms. However, temporal modification of eating behaviors has been shown to normalize gut microbe rhythms. Time-restricted feeding, a practice in which eating is only allowed during a certain window of time each day, has been found to normalize aberrant gut microbe rhythms and reverse some of the negative effects associated with circadian disruption, such as insulin resistance (15).

This research suggests that shifting away from the Standard American Diet and instead consuming a whole-foods-based diet low in polyunsaturated fats and sugars and high in antioxidants may be key for normalizing circadian rhythms and preventing diseases associated with circadian disruption, such as metabolic syndrome and obesity.

Antibiotics Disrupt Gut Circadian Rhythms

Antibiotic use has been found to disrupt circadian rhythms in animals by impairing the circadian activity of their gut microbes. Ultimately, this leads to an uncoupling of overall circadian rhythms in the host (16). However, restoration of gut microbes via prebiotics and probiotics may help restore normal circadian rhythms.

Sleep Affects Gut Circadian Rhythms

Chronic sleep disruption—which can include waking multiple times per night, shift work, or chronic jet lag from frequent travel—alters the rhythms of gut microbes and has been linked to detrimental changes in metabolism such as insulin resistance and obesity (17). This suggests that practicing “sleep hygiene” may help us normalize both our own circadian rhythms and the rhythms of our gut microbes.

Examples of sleep hygiene practices include avoidance of blue light and excessive artificial light at night, powering down electronic devices a couple hours before bed, sleeping in a cool room, and ceasing to eat several hours before bed. These practices sync the body clock in the suprachiasmatic nucleus and send signals to the brain to produce melatonin, the hormone that helps us fall asleep. Melatonin, in turn, helps regulate the rhythms of our gut bacteria (18).

Disrupted Circadian Rhythms and Gut Disorders

Disrupted circadian rhythms, both those originating in the gut and those produced by the SCN, can increase the risk of developing gut disorders.

Circadian disorganization induced by abnormal sleep/wake cycles combined with a “Westernized diet” high in processed carbs and damaged fats has been linked to the development of inflammatory bowel disease (IBD) (19). Disruption of gut microbe circadian rhythms by the high-fat, high-sugar diet alters the production of metabolites that keep the gut healthy, such as short-chain fatty acids. This promotes an abnormal immune response in the gut, resulting in IBD.

Circadian rhythm disruption initiated by abnormal sleep habits, such as those seen in shift workers, promotes intestinal hyperpermeability, also referred to as leaky gut (20). Leaky gut enables the movement of proinflammatory bacterial endotoxins across the intestinal wall and into the systemic circulation, a process linked to metabolic, cardiovascular, and neurodegenerative diseases.

Finally, circadian rhythm disorganization caused by disrupted sleep/wake cycles may increase one’s risk of acquiring gastrointestinal infections. Alterations in the sleep/wake cycle produced by the SCN affect the host immune defense, lowering human resistance to enteric pathogens. Disordered sleep/wake cycles also affect gut microbe circadian rhythms, impairing their ability to defend your gastrointestinal tract against infection (21). This research indicates that improving sleep habits may help protect the body against gut infections.

Genetics Impact Gut–Circadian Rhythm Connection

Genetic variability in CLOCK genes, which are involved in regulation of body clocks and circadian rhythms, affects circadian rhythms. Variations in this gene may make some people more susceptible to circadian rhythm disruption and gut health issues such as dysbiosis. People with these genetic variations may need to be especially conscious of their sleep habits and gut health in order to keep their bodies functioning optimally (22, 23).

Intestinal cells and gut microbes are key regulators of our circadian rhythms. Disruptions to either our gut health or our other circadian rhythms, such as sleep/wake cycles and feeding/fasting cycles, can have significant, widespread implications for our health. Appropriate maintenance of our gut health and circadian rhythms is crucial for finely tuning our physiology from the cellular and microbial level to the whole body. By taking care of your gut and body clocks, you may very well be able to prevent or reverse chronic diseases associated with circadian rhythm disruption and thus attain optimal health.

Key Takeaways

Since this was a pretty complex article, I thought I’d end by summarizing the key takeaways:

  • It’s not just our own human cells that have circadian rhythms; the microbes that live in our gut have them too
  • Things that affect our gut health—like diet, antibiotics, probiotics, and prebiotics—may also affect our sleep, hormones, immune system, and metabolism via circadian rhythms
  • On the other hand, things that affect our circadian rhythms—like abnormal sleep patterns, artificial light, shift work, etc.—may affect our gut health
  • Taking care of your gut will help your circadian rhythms, and vice versa


  1. I have noticed at sometimes I would sleep too heavy. Over the last 2 years I have noticed issues with constipation, brain fog, acne and a white tongue/yellow tongue. In addition, I had noticed intolerances to plain yogurt, Fage is the one I ate, and breads. Since last year I have reduced wheat breads and ones with chemicals and dough conditioners. I have been taking DE on and oil of oregano in and off along with bouts of drinking pau de arco tea. I have added the prescript assist to this. Just to name a few things. I am curious what I had, which I believe was possibly parasites, from poor washed leafy greens, leaky gut (due to these foods mentioned, stress and too much coffee). What do you think? What more can I do that is not a shot in the dark?

  2. This a great article with lots of good information. Keep up the good work.

    All the best

  3. My digestion slows to 0 at night. If I eat at night a disturbed sleep results from the food remaining in my stomach. My morning and early afternoon meals digest fairly normal (as long as I don’t eat a huge amount at one sitting). This is regardless if I do enzymes, HCL, or any other supplement (with minor improvement from triphala).

    I mentioned this phenomenon to my GI doc and she have me that ‘look’ like I was crazy. However, after reading this article perhaps I’m not the crazy one after all.

  4. I definately find a correlation here, I am currently being treated for SIBO, I am also using probiotics as I find them useful in regulating my immune system. I use probiotics every second or third day and I find the first night after taking probiotics that I have a restless sleep. I never manage to get into a deep sleep level and I definately believe the bugs are keeping me awake. Not sure the mechanism maybe the probiotics due to its anti microbial effect are killing off the bad bacteria but one thing is for sure is that my circadian rythem gets interrupted.

    • Hello Oktay,

      I have the same problems, sleeping troubles etc. due to dysbiosis. Which probiotics supplement do you take?

      Best regards

  5. Such a great article! I am strugglig with under eating and restricting during day and then over eating at night and can’t sleep. I am 80lbs and 5’4″ and anxious that these patterns are further contriving to ill health and will further slow and disrupt metabolism despite people telling me I can eat whenever and it’s okay. How do I stop this? Thanks

  6. My husband is totally blind and suffers from Non-24-Hour Sleep-Wake Disorder. The first drug of its kind was approved in 2015 for this condition. We wonder if there is an approach that does not require the use of pharmaceutical drugs for the rest of my husband’s life. Here is information about the disorder along with information about the current prescription.

    Non-24 is a circadian rhythm disorder. Your circadian rhythms are controlled by your master body clock and tell you when to sleep, when to wake, when to eat, among other things.

    In most people, the master body clock runs slightly longer than 24 hours. What this means is that rather than cycle on a 24-hour day, most people’s natural rhythms actually cycle a bit longer. Whether the cycle runs two minutes or 30 minutes longer, if you have Non-24 these minutes add up day after day, a few one day adding to a few more the next, eventually causing a noticeable change in the times during the day when your body expects to sleep and expects to be awake.

    Though Non-24 may appear to be a sleep disorder, it isn’t. It’s actually a serious, chronic circadian rhythm disorder very common in people who are totally blind, and it can arise at any age. Currently, there are 1.3 million people who are legally blind in the United States. Of the legally blind, 130,000 have no light perception (i.e., totally blind), and as many as 70% suffer from Non-24.

    Non-24 brings about two significant symptoms.
    First is a profound inability to sleep or to stay asleep at night, and the second is an overwhelming urge to sleep during the day. Both changes are caused by the timing of the release of the hormones, melatonin and cortisol. Melatonin controls sleep, and cortisol controls when to wake up and when to eat.
    Cortisol also controls your metabolism, cardiovascular function, immune system, and appetite. Because the release of melatonin and cortisol shifts continually, not all nights are the same. Some are sleepless, others are normal, and poor sleep happens only when the master body clock is out of sync with the typical day-night cycle. And when poor sleep happens, sleep deprivation may make it difficult to focus on the task at hand.

    Non-24 comes about when the master body clock runs on its own natural rhythm. Hence the name, Non-24, which indicates a master body clock that is not 24 hours long. For unknown reasons, most people’s body clock runs a little longer than 24 hours, which means most people could have Non-24 to some degree.
    The difference is that for sighted people, environmental light cues signal the brain to reset the master body clock every day to 24 hours.

    For people who are totally blind, the master body clock runs its natural course. This means that if your body clock runs on a 24.5-hour schedule, today you’re 30 minutes behind and tomorrow your body clock will be an hour behind. The next day will be 90 minutes, and so on. Day by day, this time adds up until you’re many hours behind, creating a rhythm that’s out of sync with the typical day-night cycle. Eventually, your body operates as if night is day and day is night. While you could try to maintain your usual schedule, more often than not you have a hard time sleeping at night and then feel an overwhelming urge to sleep during the day. In time, you once again reach the point when your body clock is in sync with the typical day-night cycle. But then, just as quickly, it moves out of sync again.

    You can find more information about the disorder at:

    You can find more information about the only drug available for this condition at:

    He began taking cod liver and skate liver oil. Because skate liver oil is said to cleanse the pineal gland, which helps with melatonin production, we think that skate is helping.

    The following article got me thinking that Skate Liver Oil might be a good option for my husband. And you know something? It has helped. He has a higher quality of sleep and does not suffer the extreme level of tiredness he did throughout his life before taking skate liver oil.

    I worry a lot about my husband’s inability to significantly reduce his weight. We have drastically moved to a Primal diet and eliminated processed foods, and this has helped, but I wonder what else we should be doing for my husband’s unique situation

    We do not want to resort to life-long use of medication. I welcome any suggestions, and I appreciate your thoughtfulness in reading my note.