Your Gut Microbiome + Circadian Rhythms: The Surprising Connection
You probably know that your circadian rhythm is key for maintaining your sleep-wake cycle. But this internal clock does a lot more than tell your body when it’s time to start your day in the morning or climb into bed at night.
Circadian rhythms help regulate the function of cells, organs, and systems, including your immune system, appetite, digestion, metabolism, hormones, and much more. They’re also a major player in gene expression and, ultimately, they determine whether you stay healthy or feel lousy.
Now experts have uncovered a new piece of the circadian rhythm puzzle: Gut bacteria. Recent research shows that the trillions of intestinal bacteria you play host to (aka, your microbiome) actually have their own circadian rhythms. And those rhythms impact the balance and type of microbes that reside in your GI tract, as well as their activity.
“Everything on earth has some rhythm,” says Dr. Bill Rawls, M.D., Medical Director of Vital Plan. “So it makes sense that even microbes would have resting and active phases.” And, as it turns out, those oscillations in your microbiome’s circadian rhythm affect your main body clock, and vice versa — your rhythms as the host can also impact those of your gut bacteria.
This two-way street means that if you mess with one, the other can get thrown out of whack, too. That could have far-reaching implications. After all, your microbiome is responsible for roughly 70 percent of immune function, and it’s integral in so many other processes, Dr. Rawls says.
What Happens When Your Microbiome Body Clock is Thrown Off
Unlike your body’s circadian rhythm, which relies on light/dark cues to maintain a roughly 24-hour cycle, gut microbes aren’t exposed to light. Instead, new research suggests they rely on three main factors to regulate their rhythms:
- What you eat
- When you eat
- Your circadian rhythm, particularly your sleep-wake cycle
When any of these factors are off enough to disturb your gut bacteria’s circadian rhythms, it can have significant ramifications on your well-being. Take diet, for instance. Researchers found that eating a high-fat diet akin to a modern Western-type one interfered with the circadian rhythms of gut bacteria in mice, causing a decrease in the number of a key type of bacteria and a drop in the production of short-chain fatty acids in the intestines.
That’s bad news, considering the fatty acids are known for their anti-inflammatory activity, plus they help bolster intestinal barrier function, keeping pathogens and toxins from leaking across the gut-blood barrier (known as leaky gut). Unsurprisingly, the mice on a high-fat diet showed signs of an overly permeable gut and toxins in their blood, both of which have been linked to inflammation.
A compromised gut barrier, toxins in the blood, and resulting inflammation have also been linked to metabolic syndrome and obesity. The same goes for low fatty acid production in the gut. Normally, these fatty acids help gut bacteria communicate with your brain and liver in ways that may help regulate appetite and metabolism.
But when mice ate fatty, late-night meals—which again, threw off their gut’s rhythms—they became obese and showed other signs of metabolic syndrome. The good news is that restricting when the mice ate their fatty food (normal waking times versus, say, midnight) seemed to moderate the effects.
Even more compelling evidence of the role of microbes’ circadian rhythms in our health comes from a team of researchers in Israel and their findings, published in the journal Cell. When they transplanted intestinal microbes from people with jet lag — which is known to disrupt the body’s and the gut’s internal clocks — into mice raised without any gut bacteria, the mice became glucose intolerant and obese. On the other hand, mice given microbes from non-travelers with a normal sleep-wake cycle stayed healthy.
This is only a small sampling of the growing body of research, and more is needed to paint the full picture. But it’s clear that respecting the circadian rhythms of both your body and your microbes may be a key component to health.
7 Ways to Reset Your Microbes’ Circadian Rhythms
In good news, the same methods you’d take to help restore balance to your gut microbiome are the ones that help keep your gut microbes’ rhythms on an even keel, too, says Dr. Rawls. Here are the seven steps he recommends:
1. Stick to a mostly plant-based diet
“When it comes to eating habits, the advice is almost always the same,” Dr. Rawls says: Move away from the typical high-fat Western diet — which was shown to interfere with gut bacteria’s circadian rhythms — and aim for one that’s composed of mainly vegetables, fruit and other plants, plus some lean protein, fewer grains, and less animal fat. “This is more like the diet humans have been eating for about 200,000 years, minus the last 100 years, and it’s the diet that best cultivates a healthy microbiome.”
2. Avoid eating late at night or irregular eating patterns
The research is mixed on just how bad late-night eating may be and why, but evidence does seem to suggest it’s best to close your kitchen at least two hours before bedtime. Along with the science on jet-lagged transplanted microbes, a recent study found that eating close to bedtime or when your body wants you to be sleeping can indeed alter your circadian rhythms, which can in turn influence your microbes’ circadian rhythms.
3. Support your gut’s lining and microbiome with herbs
“Normalizing herbs help balance your whole system,” Dr. Rawls says. Slippery elm bark in particular helps maintain the lining of the GI tract, while berberine and andrographis promote healthy gut flora and support your immune system. Dandelion root also helps soothe the digestive system. Adaptogens like ashwaganda are another way to support a healthy balance of bacteria in your gut, he says. Supporting a balanced and healthy microbiome helps maintain the microbes’ normal rhythms, while a strong gut barrier helps protect your system.
4. Maintain a consistent 8-hour sleep schedule — even on Saturday
You can’t always avoid jet lag, but you can sidestep another, more common disruptor of the body’s circadian rhythms: What scientists sometimes refer to as “social jet lag” — shifting your sleep schedule on certain days for lifestyle reasons.
Regularly having days each week when you stay up later or sleep in longer (weekends, anyone?), and/or days when you wake up much earlier than usual can make it hard for your body and gut to maintain a normal balance of rhythms. So try to go to bed and wake up around the same time every day. And be sure to give yourself enough time to sleep: “There’s good evidence we all need eight hours of sleep a night to be healthy,” Dr. Rawls says.
5. Unplug at night
Avoid your computer, cell phone, and TV in the hours leading up to bed — their blue light can trick your body into thinking it’s daytime, which interferes with the cascade of hormones and chemicals needed to fall asleep and have a good night’s rest, Dr. Rawls says.
6. Move more
Staying active helps support healthy sleep and, in turn, maintain your circadian rhythms and that of your gut microbiome. But it’s about more than simply going to the gym for an hour or hitting the running trail for a weekly 5K. “We all need to be more active throughout the day, every day,” Dr. Rawls says.
Why? “When you don’t move for eight straight hours during the workday, your body doesn’t make as much nitric oxide,” Dr. Rawls explains. That then disrupts the normal production of adenosine, a neurotransmitter that’s key for what’s called “sleep pressure” — an unconscious biological response that makes you feel sleepy and drift off at bedtime. So, along with bouts of more intense and intentional exercise, be sure to also take regular movement breaks if you have a desk job or tend to sit for long periods.
7. Limit alcohol intake
Alcohol consumption on its own can disrupt your body’s circadian rhythms, but it may make the effects of a high-fat diet or unpredictable sleep habits on your microbiome even worse. Studies link alcohol to an increase in inflammatory bacteria and a decrease in bacteria that produce anti-inflammatory chemicals.
More and more, experts are pointing to the microbiome’s key role in overall physical and mental health. Take simple steps to balance yours, and not only will you help maintain its circadian rhythm, but you’ll also help support healthy immune, digestive, and cardiovascular function, and so much more.
Discover more in Dr. Bill Rawls' new #1 Bestselling book: The Cellular Wellness Solution: Tap Into Your Full Health Potential with the Science-Backed Power of Herbs.
"An eye-opening and empowering book that the world needs right now: The Cellular Wellness Solution will fundamentally change how you think about herbs and the powerful role they play in cultivating wellness at the cellular level."
1. R.M. Voigt, C.B. Forsyth, et. al. Circadian Rhythm and the Gut Microbiome. International Review of Neurobiology, Volume 131, Chapter 9, pp 193-205
2. Leone, V., Gibbons, S. M., et al. (2015). Effects of diurnal variation of gut microbes and highfat feeding on host circadian clock function and metabolism. Cell Host & Microbe, 17(5),
3. Thaiss, C. A., Zeevi, D., et al. (2014). Transkingdom control of microbiota diurnal oscillations
promotes metabolic homeostasis. Cell, 159(3), 514–529.
4. Deaver, J.A., et. al. Circadian Disruption Changes Gut Microbiome Taxa and Functional Gene Composition. Frontiers in Microbiology April 2018, volume 9.
5. Summa, K. C., Voigt, R. M., et al. (2013). Disruption of the circadian clock in mice increases
intestinal permeability and promotes alcohol-induced hepatic pathology and inflammation.
PLoS One, 8(6), e67102.
6. Forsyth, C. B., Voigt, R. M., et al. (2015). Circadian rhythms, alcohol and gut interactions.
Alcohol, 49(4), 389–398.
7. Swanson, G. R., Gorenz, A., et al. (2015). Decreased melatonin secretion is associated with
increased intestinal permeability and marker of endotoxemia in alcoholics. American Journal
of Physiology. Gastrointestinal and Liver Physiology, 308(12), G1004–G1011.
8. Acosta-Rodríguez, V.A., de Groot, M.H.M. et. al. “Mice under Caloric Restriction Self-Impose a Temporal Restriction of Food Intake as Revealed by an Automated Feeder System.” Cell Metabolism, 2017; 26 (1): 267