10 ways optimizing circadian rhythms can help fix the gut

The gut is under heavy circadian regulation, and circadian disruption can cause a number of problems when it comes to gut function.  Fortunately, many of these issues can be corrected through modifying your behavior.

Whether you’re talking about SIBO, IBS, IBD, gastroparesis, or any of the number of functional gut disorders out there, all can be improved by doing things that optimize your circadian rhythms.  For people with mild issues, one can tinker with modifying light exposure and time-restricted eating.  But for those with bigger problems and a number of food sensitivities, more effort is needed.

Just how does optimizing circadian rhythms help with the gut?  Well, here are 10 ways that optimizing circadian rhythms can improve gut function.

1)Increasing salivary enzyme and IgA secretion

The first step in the digestive process begins with chewing in the mouth.  In addition to mechanically breaking food down, chewing seems to set the stage for digestion throughout the gut.  Chewing enhances blood flow and oxygen consumption in the gut, and also stimulates the production of saliva.

Saliva contains some important substances that digest food and kill bacteria that may be in our food.  This is done by salivary enzymes and IgA, respectively.  Both are under circadian control and are altered under circadian disruption.  How so?

Salivary enzyme secretion is altered under constant light in mice, and this causes a decrease in enzyme secretion during their subjective day, when they eat most of their food.  In humans, salivary IgA peaks overnight as a way to kill any remaining bacteria in the mouth and prevent overgrowth that could lead to periodontitis.

This is pretty interesting given that the oral commensal/pathogen Candida albicans is the most common fungal infection in humans,.  A recent study showed that good oral care can reduce a person’s exposure to it.

2)Coordinating gastric acid and mucus secretion

Gastric acid secretion and the replenishment of the gastric mucus layer are both under circadian control.  This regulation is under control of the circadian hormones gastrin and ghrelin.  Interestingly, ghrelin is secreted during periods of fasting to stimulate motivation and arousal to find food.

In the stomach, ghrelin seems to stimulate acid secretion and helps build up the mucus layer during fasting.  This is important because gastric acid can damage the cells in the stomach and cause ulcers, and a thick mucus layer can prevent this from happening.  It also helps prevent pathogens from making it past the stomach intact, and from damaging the stomach lining.

3)Replenishing the intestinal mucus layer

The mucus layer in the gut plays many roles including lubricant, shield from bacteria and enzymes, and as the site for enzymatic breakdown of your food.  Many people are aware of the first 2, but not the second 2.  The digestive enzymes that we make can actually destroy our gut wall.

Fat and protein digesting enzymes from the saliva, stomach, and pancreas could tear our gut to shreds.  So having a barrier between the cells lining the gut and these enzymes is crucial to maintaining a healthy gut.  However, the mucus layer also helps our digestive enzymes by giving them longer contact time with the food we eat.  This helps optimize digestion while at the same time saving the cells of the intestinal wall from damage due to friction, bacteria, or immune activation.

The mucus layer is regulated not only by our circadian rhythms, but also the circadian rhythm of our microbiome, which is also important for gut health.

4)Modifying the microbiome

The microbiome has become a hot topic in health over the last 10 years.  This led to the belief that, in short order, we’d be able to figure out what an ideal microbiome is and recapitulate it with probiotics or fecal microbiota transplants.  Then came the last couple of years and that all went up in smoke.

It turns out that the microbiome has its own circadian rhythm, with different bacterial species increasing/decreasing in number and closeness to the gut wall throughout the day.  Not only does this have an effect on our circadian rhythm, but the circadian rhythm of the microbiome appears to be regulated by…wait for it…our circadian rhythms.

This makes sense, the nutrients that the microbiome has access to are directly affected by when and what we eat.  When we eat we see an increase in the abundance of bacteria that snack on carbohydrates, and when we fast we see an increase in bacteria that snack on our mucus layer.  This allows us to replace the mucus layer daily to prevent bacterial overgrowth, particularly in the small intestine.

But it turns out it’s not simply just when and what we eat.  Aberrant light/dark cycles change both the types of bacteria in our gut as well as their functions, leading to “leaky gut”.  In fact, most of our behaviors that alter circadian rhythms have an effect on the microbiome and vice versa  Successfully using probiotics or FMT will require addressing circadian rhythms to be even remotely useful, save for addressing acute problems such as C. diff infection.

5)Repairing and replacing damaged cells

At the cellular level, circadian rhythms help separate functions that can’t go on at the same time due to conflicting metabolic processes.  Nothing illustrates this concept more than the separation of use and repair.  In the most basic sense, you can’t repair or replace something while it’s in use.

Anabolic(Building up) and catabolic(breaking down) processes need to be separated because they often use the same substrates.  They also need to be separated because some of the byproducts of catabolic processes, such as free radicals, damage cellular components including DNA, which if altered during replication, can lead to cancer.

Think of it like getting an oil change in your car.  You can’t run the engine while changing your oil because removing the oil would cause the engine to seize.  Therefore, you must take your car off the road to change the oil.  In the same way, sending the proper signals to your cells via the correct environmental exposures will allow your cells to separate use from repair, keeping your gut healthy all day every day.

6)Preventing leaky gut

“Leaky gut” has become quite a frequently searched term on google.  But, every one of us experiences it every day.  The permeability of our gut waxes and wanes throughout the day due to circadian rhythms and there’s no way around it.  Eating is an inherently inflammatory event, and the gut needs some downtime every day to replace damaged cells.  Thus, if you put food down there at the wrong time, you’re going to cause some real damage.

But it’s not as simple as, “Don’t eat at night”.  Replacing damaged cells isn’t the only circadian factor that plays a role in “leaky gut”.  Hyperglycemia can cause it, as can the overgrowth of pathogens and commensal bacteria from the microbiome.  Additionally, secreted factors from basically every tissue throughout the body can play a role in making sure your gut stays sealed and bacteria stay out of your bloodstream.  The specifics of these factors will be discussed briefly below.

7)Improving bile output

When we think of bile output, most people only think of the emulsification and absorption of fat and fat soluble vitamins.  But bile also plays a role in mucosal defense through its direct antimicrobial action and secretion of antimicrobial peptides, promotion of the housekeeping phase of the gut known as the migrating motor complex(MMC), and increased expression of tight junction proteins to seal up the gut.

But bile can also cause injury to the gut, and circadian disruption can change the composition of bile making it more damaging.  This is due to changes in both the types of bile acids synthesized in the liver as well as the bacterial species in the gut that convert primary bile acids in to toxic secondary bile acids.

8)Strengthening mucosal defense

The gut is constantly exposed to bacteria and other microorganisms that can cause damage.  Lucky for us there’s a system in place inside the gut to prevent that from happening called the mucosal defense system, which is under circadian regulation.  Mucosal defense is an umbrella term used to describe the various ways the gut prevents damage to it and us.

I’ve already mentioned a few of the ways the gut protects us such as mucus secretion, enzyme secretion, barrier integrity, and bile output.  But another important mechanism of mucosal defense is the secretion of antimicrobial peptides. Secreted by Paneth cells, antimicrobial peptides kill bacteria, particularly in the ileum where components from bile trigger their release.

This location is key as it’s at the border of the small and large intestine, where bacterial numbers move from very low to their highest.  If even healthy bacteria overgrow in to the ileum, we get increased inflammation and increased movement of bacteria in to the blood.

9)Correcting dysregulated motility

Proper motility throughout all areas of the gut is crucial to proper digestion and preventing bacteria from overgrowing in areas they shouldn’t grow.  It’s also important for the consistency of our stool.  Motility in all areas of the gut is under circadian regulation.

In the small intestine, motility is greatest during the day and lowest at night.  It’s not surprising, then, that people who eat at night are at an increased risk for functional gut disorders such as SIBO, IBS, and IBD.  For most people, their greatest period of fasting is during the night.  The problem is that the migrating motor complex(MMC), which cleans house to prevent bacterial overgrowth, functions poorly at night, particularly during sleep.

Motility in the colon is also lower at night, and affected by meal timing.  Generally, colonic motility is greatest during the morning and after meals.  When disrupted, this can cause low colonic motility which leads to constipation or rapid colonic motility which leads to diarrhea.  Meal size and substances such as coffee also affect colonic motility, so timing these things incorrectly can lead to problems in stool consistency.

10)Quelling inflammation

What goes on in the gut isn’t solely dictated by things in the gut.  Just like the microbiome communicates with us, other organs and tissues throughout our body communicate with each other to optimize function.  In my opinion, ignoring this fact is probably one of the biggest factors preventing people from overcoming functional gut disorders.

When we zoom away from the hyperfocus on the avoidance of foods most people have in curing gut problems, we can get a pretty good picture of how expansive the interaction is between our gut and the rest of the body.

  1. Cortisol, secreted from the adrenal glands in a circadian manner, promotes the recycling of bile acids, increased motility,  and functions as a systemic anti-inflammatory.
  2. Irisin, a myokine secreted from exercising muscles, also functions as a systemic anti-inflammatory and promotes the healthy remodeling of the lymphatic system in the gut.
  3. Insulin, secreted by the pancreas to prevent hyperglycemia, also plays a role in preventing hyperglycemia-induced leaky gut and inflammation.
  4. Many different adipokines, signaling molecules secreted from fat cells, can increase inflammation in the gut.  Particularly when secreted from a fatty liver or the creeping fat surrounding the intestine in people with Crohn’s disease.

These are just a few of the different local signaling molecules released from distant tissues that can have an impact on inflammation in the gut.


As I’ve mentioned numerous times, the gut is under heavy circadian regulation.  To ignore this critical aspect of gut health is probably one of the biggest factors leading to a gradual increase in the number of foods people with gut disorders become sensitive to.  As a result, pulling more and more foods out of our diet and ignoring circadian rhythms leads to a very short list of foods people can eat that lead to nutritional deficiencies.

In my experience, addressing circadian rhythms is the most bang-for-your-buck therapeutic approach to fixing sensitivities to foods and optimizing gut function.  When we look at the many functions in the gut regulated by circadian rhythms and how they impact food sensitivities, a pretty clear picture emerges.

Without adequate enzyme secretion and a thick mucus layer, we get undigested food that can interact with our gut lining or feed a bacterial overgrowth.  With poor motility and inadequate antimicrobial peptide secretion we promote an environment conducive to bacterial overgrowth.  Finally, with poor cell turnover and tight junction expression, we end up with a damaged leaky gut that leads to system-wide inflammation, metabolic dysfunction, and an even leakier gut.

Do you need help addressing the circadian component of gut health?  Addressing circadian rhythms is the first step one should take when addressing gut problems. And you’re in luck, you can still get a lifetime membership to my Circadian Retraining Program.

 Never heard of the Circadian Retraining Program? Check out the details below:


3 thoughts on “10 ways optimizing circadian rhythms can help fix the gut

  1. Rosa says:

    Please can you give specific as to what one must do to get those circadian rhythms to be in harmony. I mean what are the practical things that can fix the rest of the issues?

    • cincodm says:

      Hey Rosa,

      Most people start with controlling their light exposure, getting more sunlight exposure to the eye and blocking blue light at night 2 hours before bed by either avoiding TV and shutting off their lights, using lights that don’t put out blue light, or blocking blue light with blue blocking glassess.

      From there, time-restricted eating is an absolute necessity for many reason particularly if you have gut issues. This requires you to sequester your daily eating period to a 10-12 hr period every day.

      Most people see some significant improvement doing those 2 things. To really sync everything up requires attending to a lot of things and there is quite a bit of individual variation that goes in to it based off of your health, lifestyle, age, etc. You also want to measure things like sleep, heart rate, physical activity, and heart rate variability to see how you respond. I can’t really give you a short blurb on that, but I have developed a program that shows people how to take care of that. You can find the details of that program here:


      Thanks for reading and let me know if you have any other questions.


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