Your Microbiome Has Its Own Circadian Clock

Written by Emma Loewe: Writer, author, and editor of Cultured. Her writing explores the intersection of nature, climate, and human health. Emma is the author of “Return to Nature” and “The Spirit Almanac.”
Reviewed by Jennie O’Grady: Senior SciComms Specialist at Seed Health

The sun always rises. And when it does, it kickstarts a cascade of activity across life on Earth. Plants transform light into nutrients, honey bees start foraging for food, and certain types of algae and bacteria begin the process of photosynthesis. We, too, operate in tight synchronicity with sunlight thanks to our bodies’ circadian rhythms. 

These internal clocks play a foundational role in our sleep-wake cycle and when we feel energized vs. tired. But their influence doesn’t stop there. Chronobiology research shows that there is also a strong circadian component to our gut health, meaning that our intestinal microbes shift alongside external cues like sunlight and temperature. 

Here’s an overview of your gut’s circadian rhythm—and how it might help explain why you always feel constipated while traveling to new time zones, why your stomach is a mess after a night of poor sleep, and why you have trouble digesting food late at night. 

The Circadian Clock(s) of Your Gut Microbiome 

The suprachiasmatic nucleus (SCN) of the brain is home to the human body’s “master clock,” which sends hormonal and neuronal signals that keep peripheral organ systems running on a roughly 24-hour cycle. Without this central pacemaker, our ability to sleep, regulate mood, and fight illness would all go haywire.^1,2 

External cues like sunlight, temperature, and food intake are zeitgebers (German for “time givers”) that help this master clock stay ticking on schedule in a process known as entrainment.³

The SCN also indirectly communicates essential cues to your gut microbiome, and having a regular circadian rhythm helps promote eubiosis (a state of balance between a host and its microbiota) in the gut.⁴ 

At the same time, your gut microbes have a rhythmicity of their own.⁵ Even without the influence of the central SCN, these bacteria can still undergo processes like nutrient absorption, detoxification, and bowel formation according to day-night cues. You can think of the gut microbiome like a young child: It follows orders from its caretakers (the SCN), but it also forges its own path and follows its own intuition at times. 

Across various points of the day, the location, activity, and metabolism of your gut bacteria will shift depending on a unique and multifaceted cellular schedule.⁵ This is one reason why it’s important to consider timing when collecting samples of the microbiome for things like gut testing.

Why Your Gut Loves a Schedule

When your circadian clock is properly entrained with its environment through cues like the light-dark cycle, the ecosystem of bacteria in your gut can maintain a steady rhythm. This allows your microbiome to do more of what it does best: maintain a strong gut barrier, defend you from pathogens, break down your food, and stay on top of waste excretion.^6,7,8,9

However, when your circadian rhythm faces disruptions (like sleep deprivation or time zone changes), your gut likely suffers too. Early research (mostly on animals like mice and rats) shows that circadian disruption may be associated with gastrointestinal issues like reduced gut barrier integrity and a suppressed immune response, potentially predisposing us to chronic diseases.^4,10

Within the last 10 years, researchers have also discovered a bidirectional relationship between the gut microbiome and the central circadian clock. This suggests that an imbalance of bacteria in the gut may disrupt the body’s master rhythms. Scientists realized this after finding that germ-free mice (lacking an intestinal microbiome) have altered circadian clock gene expression in the brain and peripheral tissues, even when exposed to normal light-dark signals.¹¹ 

Tips for Staying on Track

Your circadian clock allows for synchronization and coordination between you and your microbial residents. This means that supporting it through regular sleep, diet, and light exposure can also pay off for your gut health and comfort. Here are a few habits to adopt for a steadier internal clock:

• Eat meals around the same time each day: Research has demonstrated that when you eat (in addition to what you eat) can affect the bacterial abundance and function of your gut.¹² For example, if you usually eat dinner at 6 p.m., your gut microbes will start preparing to utilize additional nutrients around this time. If you then switch to eating dinner at 9 p.m., your microbes might not be as “prepared” to digest food, leading to problems like bloating or upset stomach. Microbes are incredibly adaptive and they can adjust quickly. Still, keeping your meal times as consistent as possible can be beneficial.
• Try not to eat too close to bedtime: Eating later in the evening than usual and eating high-fat meals have both been shown to dysregulate gut microbial communities in studies on rats.^13,14 While we need more research on humans to be sure, this suggests that following an early time-restricted feeding schedule (fasting later in the day) and eating a lower-fat, higher-fiber diet may help prevent microbial disruptions caused by late or irregular eating schedules.^15,16
• Get consistent sleep: Sleep deprivation doesn’t just leave you feeling out of sorts; it disrupts your microbes too.⁴ Insomnia and irregular sleep schedules (and the stress and anxiety they cause) can negatively impact microbial community structure in the gut, likely due in part to the gut-brain axis. One study on nine men showed that after two nights of getting less than five hours of sleep, participants’ gut flora tends to have a higher ratio of Firmicutes: Bacteroidetes bacteria, which is associated with weight gain, obesity, and type 2 diabetes.¹⁷ Piling another stressor onto sleep disruption seems to put the microbiome at additional risk. So, if you do have a sleepless night (hey, it happens to all of us!), just do your best to keep other gut disruptors like alcohol and highly processed food to a minimum the next day.¹⁸ 
• Be mindful of clock changes: The U.S. is currently preparing to turn the clocks backward an hour on Sunday, November 3 to end daylight saving time. This change theoretically gives us an extra hour of sleep, but any clock shift (even if it’s in the “right” direction) can disrupt the circadian rhythm and gut microbiome. (Hence why some sleep experts are calling for an end to stop the transition from standard time to daylight saving time altogether.¹⁹) To combat this, do your best to keep other factors (like meal timing and sleep schedule) consistent over the next few weeks as your body adjusts. Try to maintain gut-supportive habits as the season progresses, too—as it could help brighten your mood when the days get darker. Emerging evidence shows that some types of gut microbes, like Lactobacillus, have been shown to reduce depression behaviors in mice, suggesting that the gut microbiome could play a role in easing the symptoms of SAD.²⁰

The Key Insight

Humans are inseparable from our environments. The external cycles of day and night help conduct vital internal processes, including the microscopic ones that occur in our guts. Keeping up with regular eating and sleeping times can help ensure that your gut microbiome stays on schedule.