sync up your biological clock

Gut Circadian Rhythm: How to Restore Your Biological Clock

Our circadian rhythm is our biological clock. It’s an autonomous system dependent on cells that guard vital organs. These cells are dependent on their hosts (us) to maintain a regular schedule. That’s because there are many smaller biological clocks in our bodies that need to sync up. One of these is our gut circadian rhythm. Therefore, our stomach bacteria play a critical role in regulating our system’s biological clock. Let’s learn why.

What is Circadian Rhythm?

Our circadian rhythm is more than just our sleep cycle. It’s essentially your body’s 24-hour itinerary of biological functions.

This complex system is affected by many outlying factors. So, it’s best we just start at the top. The easiest way to describe our circadian rhythm is that it’s set up sort of like a pyramid scheme.

At the top, we have the suprachiasmatic nucleus (SCN) within the hypothalamus region of the brain 1. The SCN has over 20,000 neurons. These communicators are in touch with peripheral biological clocks throughout the system 2.

Peripheral clocks are present in every cell and tissue in our body. So, the SCN is the regulator of our circadian rhythm.

What Controls Our Circadian Rhythm?

There are several factors at play that may impact our circadian rhythm. Many of them are parts of our environment. Others are lifestyle choices. Let’s take a look at what may affect our biological clock and gut circadian rhythm.


Light is the primary regulator of our circadian rhythm 3. Our body knows that when the sun is out, we must be productive and expend the most energy. It’s also aware that the nighttime is when you go to bed.

As sunlight enters the bedroom in wee morning hours, the ultraviolet rays permeate our eyelids and activate our pineal gland. This reaction causes the body to stop producing so much melatonin. When the sun goes down, that charge drops, and melatonin production commences.

Sleep Cycles

One of the best ways to foster new habits is to do these activities at the same time every day. Our bodies are built to thrive in repetitive sequences. So, when your sleep cycles are thrown off, it messes up the whole shebang.

Perhaps the most significant assault on our sleep patterns is the blue LED lights in our smart devices and TV screens. Too much screen time sends false signals to the brain.

Your pineal gland records these blue wavelengths as the sun rising, causing you to feel less tired. Inevitably, erratic sleep will throw off your gut circadian rhythm.


Our body temperature fluctuates throughout the day. Your cells have thermoreceptors on them 4. These are gauges that measure the temperatures outside the body. It figures out the average temperature for the time of the day so our SCN can prepare us for nighttime.

When our temperatures get thrown off, so does circadian rhythms. Colder days may make us feel lethargic earlier, while hotter ones might cause a sleepless night. Therefore, exceedingly cold or warm days can disrupt your sleep cycle, hormone production, and stomach bacteria.

Food Intake

Biological processes need a full 24 hours to get their work done. However, we’re always throwing wrenches into their plans by causing more work for them. The most timely process our body must contend with is the digestion of food.

According to the Medical Research Council in Science Daily,

“Experiments in cultured cells, and replicated in mice, show that insulin, a hormone released when we eat, adjusts circadian rhythms in many different cells and tissues individually, by stimulating production of a protein called PERIOD, an essential cog within every cell’s circadian clock 5. “

Medical Research Council

If you eat before bed, your body is going to be busy breaking down food particles and absorbing nutrients. It won’t get all the other necessary functions done, such as producing hormones and immune cells.

Gut Bacteria

There’s nothing worse than trying to sleep next to a horrible neighbor. Our body is teeming with trillions of microbes. When most of these stomach bacteria are beneficial, the surrounding cells that report back to the SCN leave good Yelp! reviews.

However, pathogenic bacteria can be disruptive. They promote inflammation that destroys healthy cells. Many peripheral clocks in the neighboring area will report back to the system, inevitably shocking our circadian rhythm.

What is the Gut Circadian Rhythm?

In our microbiome, all of our cells are working in unison to achieve betterment for the whole. Different cells have their own set of strengths and weaknesses that are determined by where they are in the body. So, each “department” needs 24 hours to accomplish these tasks. Let’s go to another analogy.

The SCN is the CEO of the company. It has many key peripheral clocks that are in vital organs and regions, such as our pancreas, liver, and gut. Each of the cells distinct to these areas has its own 24-hour process to undergo.

Not meeting their deadline will cause a negative report turned into the SCN. Anyone ever feel the wrath of an unhappy CEO? Not pretty. Let’s take a look at components of the gut circadian rhythm.


Research with mice suggests that the SCN sets a rhythm with benchmarks that microbes must follow to ensure the 24 hours’ worth of tasks is completed. At specified times, stomach bacteria will induce the expression of histone deacetylase 3 (HDAC3) 6.

HDAC3 is an enzyme that acts as a catalyst for the oscillation of gut cells. Activated gut cells cause many metabolic processes, such as nutrient transports to the bloodstream and fat absorption.

Even more remarkable is that the microbes only activate HDAC3 in epithelial cells of the small intestine but not the colon. This realization further exemplifies that stomach bacteria know how to manipulate the gut circadian rhythm.

Gut Motility

Gut motility is the stretching and contracting of muscles in the GI tract.

Your GI tract covers:

  • Mouth
  • Esophagus (or food tube)
  • Stomach
  • Small Intestine
  • Large Intestine
  • Colon/Bowels

When you begin eating, the aroma of your food trigger saliva production, kicking off the digestion process. All systems get moving, and your GI tract gets in sync through a process known as peristalsis 7. That’s just a fancy way to explain a smaller-scale gut circadian rhythm!

Harmful stomach bacteria and opportunistic stomach flora destroy tight junctions that regulate our gut barrier and villi that help us absorb nutrients. Therefore, we’re more susceptible to toxins and solid food particles from our intestines that cause GI problems, such as Irritable Bowel Syndrome (IBS).

Cell Proliferation

The average gut cell lives up to five days. So, that means they must divide and boost up other cells adequately during their short lifespan. That means their 24-hour processes have very little room for error.

When cell proliferation gets behind, it leaves the body susceptible to pathogenic attack. In turn, this can throw off our gut circadian rhythm, as well as functions throughout the rest of the body.

Diet and Gut Circadian Rhythm

The toughest obstacle facing our gut circadian rhythm is the food we eat. A Standard American Diet (SAD) is rich in omega-6 fatty acids and nutrient-deficient carbohydrates. Research confirms an influx of these dietary choices can severely alter your gut circadian rhythm.

One study fed a high-fat, high-carb diet rich in polyunsaturated fatty acids and refined sugars to mice 8. Notably, the gut bacteria changed the production times and yield of metabolites. Without gut bacteria producing useful gut healers like butyrate, our lining gets compromised, as does our gut circadian rhythm.

Inevitably, the mice developed:

  • Dysfunctional Glucose Homeostasis
  • Hypercholesterolemia
  • Obesity

These disorders are all common for people who follow a typical Western Diet. One of the most prominent, obesity, is heavily linked to insomnia 9. Insomnia is a clear indicator your circadian rhythm is out of whack.

Therefore, having an out-of-sync gut circadian rhythm can mess up all the biological processes going on in the body. Ultimately, this can cause a person to develop a litany of diseases.

Intermittent Fasting and Gut Circadian Rhythm

We wouldn’t recommend skipping out on meals. This practice can actually throw off your circadian rhythm. It doesn’t know when to expect food if you’re randomly opting out of meals. An effective way to regulate your gut circadian rhythm is through intermittent fasting.
The easiest fast is known as Leangains. Leangains is where you go 16 hours without food. During an eight-hour window, you can eat again.
Research shows that these fasts are long enough for your gut circadian rhythm to get back into rhythm 10.
Furthermore, intermittent fasting promotes autophagy. This process helps with cell proliferation. If you remember, cell proliferation is one of the functions of good gut circadian rhythm.

Regulating Gut Circadian Rhythm

Our microbes play a significant role in not just our gut circadian rhythm, but the system as a whole. Unfavorable stomach bacteria and sneaky intestinal flora can spur inflammation throughout the body. In turn, many cells won’t be able to meet their 24-hour deadline…or five-day lifespan.

The first step in getting your metabolism and sleep cycle back on track is to get your gut bacteria in check. An easy way to accomplish this task is by finding out which stomach bacteria are holding your gut biome hostage. Do this with an Ombre Gut Health Test.

Once we know which stomach bacteria are disputing your gut circadian rhythm, we can recommend probiotic bacteria to help promote the balance back in favor. From there, Ombre will offer you food recommendations to keep that biological clock ticking!

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  • 1 Herzog1, Erik D., et al. “Regulating the Suprachiasmatic Nucleus (SCN) Circadian Clockwork: Interplay between Cell-Autonomous and Circuit-Level Mechanisms.” Cold Spring Harbor Perspectives in Biology, Cold Spring Harbor Lab, 1 Jan. 1970, cshperspectives.cshlp.org/content/9/1/a027706.full.
  • 2 Richards, J., & Gumz, M. L. (2012). Advances in understanding the peripheral circadian clocks. FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 26(9), 3602–3613. doi:10.1096/fj.12-203554
  • 3 Mead M. N. (2008). Benefits of sunlight: a bright spot for human health. Environmental health perspectives, 116(4), A160–A167. doi:10.1289/ehp.116-a160
  • 4 Sherburne-Michigan, Morgan. “Even Tiny Temp Changes Affect These ‘Clock Neurons’.” Futurity, 26 Feb. 2018, www.futurity.org/sleep-timing-neurons-temperature-1688092/.
  • 5 “How Eating Feeds into the Body Clock.” ScienceDaily, ScienceDaily, 25 Apr. 2019, www.sciencedaily.com/releases/2019/04/190425143607.htm.
  • 6 Kuang, Zheng, et al. “The Intestinal Microbiota Programs Diurnal Rhythms in Host Metabolism through Histone Deacetylase 3.” Science, American Association for the Advancement of Science, 27 Sept. 2019, science.sciencemag.org/content/365/6460/1428.
  • 7 Sanders, K. M., Koh, S. D., Ro, S., & Ward, S. M. (2012). Regulation of gastrointestinal motility–insights from smooth muscle biology. Nature reviews. Gastroenterology & hepatology, 9(11), 633–645. doi:10.1038/nrgastro.2012.168
  • 8 Leone, Vanessa, and Sean M. Gibbons. “Effects of Diurnal Variation of Gut Microbes and High-Fat Feeding on Host Circadian Clock Function and Metabolism.” Cell Host & Microbe, Cell, Vol. 17(5), 13 May 2005, doi.org/10.1016/j.chom.2015.03.006.
  • 9 Hargens, T. A., Kaleth, A. S., Edwards, E. S., & Butner, K. L. (2013). Association between sleep disorders, obesity, and exercise: a review. Nature and science of sleep, 5, 27–35. doi:10.2147/NSS.S34838
  • 10 Parkar, S. G., Kalsbeek, A., & Cheeseman, J. F. (2019). Potential Role for the Gut Microbiota in Modulating Host Circadian Rhythms and Metabolic Health. Microorganisms, 7(2), 41. doi:10.3390/microorganisms7020041

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