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Sleep and the Microbiome listening to your gut may help improve your sleep

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Last year, I got a poop test for Mother’s Day. As crazy as that sounds, I’d wanted one for years. Let me backup a bit and explain.

For as long as I can remember, I’ve struggled with stomach issues. My mother says I was born with digestive woes, and based on my memories of frequent tummy aches and trips to the doctor growing up—I’d say she was right.

Over the years, I received countless diagnoses from lactose intolerance to multiple food allergies and even IBS. The older I got, the worse my symptoms became, and I started noticing problems in other areas, like my hormones, mood, and sleep. But it wasn’t until I started researching gut health for myself that I finally realized that what I had been dealing with all along was a leaky gut.

Not only does the health of your gut play a role in your sleep, but sleep (or lack thereof) can also influence your gut. Curious? Let’s dive deep into the fascinating world of sleep and the microbiome.

What is the Microbiome?

What if I told you that you’re really only 10% human and 90% microbes? It’s true. Only 10% of your body is controlled by your cells and DNA, and the other 90% of your functioning comes from the trillions of microbes living in you and on you. In fact, you have 150 times more microbial DNA in your system than human DNA.

This microbial ecosystem is what scientists call the “microbiome,” and it includes viruses, bacteria, protozoa, and all kinds of living organisms. The microbiome encompasses all of the microorganisms and their genetic elements that are in and on their host—which is us! 

We are made up of thousands of little ecologies that have to work together to perpetuate the health of the whole. When you think about it, humans are like walking, talking rainforests!

The Human Microbiome Project was launched in 2008 to study the microbiome and its role in human health and disease. This has led to an explosion of scientific research, including more than 50,000 research papers in the last 5 years alone. It’s the biggest scientific revolution—ever—yet we are still just scratching the surface of all there is to know.

For example, not long ago, scientists thought that certain areas of the body like the womb and blood were sterile. Now, they’ve discovered that we have 1,000 bacterial cells per milliliter of blood, and we also have them in our brain, cerebrospinal fluid, eyes, and everywhere else too. But by far, the gut has the highest concentration of microbes in the entire body.

Why is the Gut Called the “Second Brain?”

Growing up, you were probably taught that the brain is the master command center of the body. While that’s partly true, you have another command center that’s equally important, and it’s in your gut. Microbes have genetic elements that regulate all sorts of functions, including hormone production, metabolic activity, appetite, mood, and—sleep.

In some ways, you could say that the brain and gut are close friends because they work as intricate partners to run this complex system day in and day out. One of the ways they do this is by communicating back and forth through something called the “gut-brain axis.” The gut and the brain are directly connected through the vagus nerve which runs from your brainstem to your intestines.

The vagus nerve connects to the enteric nervous system, which encompasses all the nerves in your digestive tract. This system is the second most dense area of neuronal activity next to the brain. That’s why there’s a lot more truth to the phrase “gut feeling” than you may think.

All of the microbes in the gut have access to that enteric nervous system via the vagus nerve. This nerve also gives them direct access to the brain and vice versa—the brain can influence the gut microbes too. All day long, they talk to each other and relay messages back and forth. 

If the bacteria in your gut are healthy, they can help to relay messages about when you’re full, when you need a little R&R, and when it’s time for bed. If they’re not healthy, they can make you crave sugar, feel anxious and depressed, or keep you counting sheep at night when you’re desperate for some rest.

The Relationship Between the Microbiome and Sleep

Sleep affects the microbiome and the microbiome affects sleep. They have a cyclical relationship, and if one isn’t functioning properly, the other will be impacted too. Likewise, improving the health of the gut microbiome can have a direct impact on your sleep, and getting adequate rest can promote a healthy gut.

How Sleep Influences the Microbiome

You may be familiar with the circadian rhythm’s role in regulating your sleep-wake cycles. Many other functions in your body run on an internal clock too, including the microbiome. The microbiome’s circadian rhythm is affected by what you eat, when you eat, and how you sleep.

According to research, even just mild sleep deprivation can have a negative impact on gut health. A 2016 study looked at healthy young adults who had regular sleeping and eating patterns and looked at what happened to their microbiome after two nights of only 4.24 hours of sleep. The staggering results showed:

How Sleep Influences the Microbiome

Growing evidence shows that sleep disorders, like circadian rhythm disorders, insomnia, and others, can upset the balance of healthy bacteria in the gut, and this damage is linked to a range of health problems, including metabolic syndrome, obesity, diabetes, and inflammatory disease. 

Lately, a lot of attention has been focused on the role of sleep in the development of Alzheimer’s disease later in life. Some new research suggests that the bacteria in the microbiome may be behind these cognitive changes. A 2017 study of healthy older adults found that better sleep quality was linked to better cognitive functioning and a healthier microbiome.

How the Microbiome Influences Sleep

Leaky Gut

If you think about the digestive tract, it’s really one long tube that’s open on both ends. The only way that things can enter into the body is through the intestinal lining in the gut. The regulation of what is allowed to pass in through that lining is a highly important junction for chronic illness—you want healthy nutrients to enter in and toxic junk to stay out.

It’s considered the “ground zero” of most health disorders because how your body manages that juncture will dictate your risk for virtually every chronic illness, including all of the sleep-associated disorders. Hundreds of years ago, when Hippocrates said that “All disease begins in the gut,” he may have been right.

If you have an imbalance of beneficial and problematic bacteria in your intestines, the lining can become permeable, and you develop what’s commonly known as a “leaky gut.” Leaky gut causes endotoxins and lots of other inflammatory compounds to leak into your circulation. These compounds continuously stimulate your sympathetic nervous system, also known as your “fight-or-flight” response.

This is especially problematic when it comes to sleep because you need your parasympathetic nervous system to activate at night so you can “rest and digest.” If you’re constantly in “fight-or-flight” mode, you’ll have difficulty falling and staying asleep.

How common is leaky gut? More common than you might think! A lot of scientific evidence points to chronic disease originating in the gut. According to CDC data, 60% of American adults have at least one chronic illness, and 40% have multiple chronic illnesses. 

Even more alarming, it’s not just people who are sick that have a leaky gut. A 2017 study looked at 80 healthy college students with no symptoms or underlying disease and found that 40% had leaky guts.

Read More: Digestion and Sleep

Low Levels of Serotonin-producing Bacteria

If you’re tossing and turning at night, the bacteria in your gut could be to blame. Many of the neurotransmitters that influence sleep are made and released by the microbiome, including GABA, dopamine, and serotonin—the precursor to the well-known sleep-inducing hormone, melatonin. 

While the brain also makes some of these neurotransmitters, 90% of the serotonin in the body is made in the gut by certain types of bacteria. If you have low levels of those bacteria, you are likely also low in serotonin, and your body won’t be able to produce enough melatonin to help you fall asleep at night.

Accumulation of Inflammation

An interesting factor about sleep and the microbiome is that 70% of your immune system is in your gut. This immune tissue controls the inflammatory response in your gut and in the rest of the body as well. Keep in mind that not all inflammation is bad. Certain types of inflammatory markers are important to get you to sleep!

Interleukin 1 beta and interleukin 6 are two examples of inflammatory markers (also known as cytokines) that increase when you are sick so you feel tired and want to rest. These same markers appear to have a circadian function and are released in higher concentrations when the sun goes down at night. Microbes in your gut increase these cytokines to make you sleepy.

These inflammatory markers also have the benefit of activating your immune system so that it goes into the repair and patrolling mode while you’re asleep. This tells your immune system to look for infectious viruses, harmful bacteria, and anything foreign. That’s why rest is so important for controlling infections and keeping your body healthy. 

This circadian-controlled inflammation is supposed to decrease after sleep. The problem is when the microbiome is dysfunctional, you’ll get an increase in the inflammatory response in the body when you start getting tired, but then you don’t have the right microbes to bring that back down as the evening progresses. What you end up with is a net accumulation of chronic inflammation over time.

Another way this can occur is if you wake up too soon because the microbes haven’t had time to signal those inflammatory markers to decrease yet. Adults need seven to eight hours of sleep to allow this entire rise and fall of inflammation to occur.


Your dishes and floors aren’t the only things that need cleaning up at night. Overnight, the microbiome turns on certain microbes that do housekeeping functions while you sleep. One example is the clean-up of dysfunctional mitochondria.

Mitochondria are the powerhouses of your cell and are the determining factor in how healthy your cells are. Aging is determined by how dysfunctional your mitochondria are. At night, microbes have the ability to turn on mitophagy to discover dysfunctional mitochondria, remove them, and generate new mitochondria so your cells are healthy and strong.

The microbiome also generates something called autophagy at night, which is another process of cleaning up damaged cells, damaged DNA, proteins that aren’t needed, and removing the “junk.” Throughout the day, cells create a lot of waste that needs to be removed, otherwise the accumulation of toxic waste can lead to inflammatory conditions, including cancer.

Part of what triggers certain groups of bacteria to conduct these housekeeping functions is being a fasting state. If you eat a big meal right before bed or wake up in the middle of the night and eat, you completely disrupt the diurnal system within the microbiome and your cells and mitochondria don’t undergo the clean-up process that they need.

Ideally, if you can stop eating three to four hours before bed, you should give your body enough time to finish the digestive process so you can be in a fasted state at bedtime and allow the housekeeping bacteria to wake up at some point during your resting phase.

Read more about why it is bad to eat just before going to bed here.


According to microbiologist, Kiran Krishnan, the most important feature of the microbiome that dictates sleep is diversity 1. Diversity is measured by two factors: richness (how many different organisms you have) and uniformity (amount of each individual species). For example, you could have 300 different microorganisms in your gut, but 290 aren’t helping you out because they’re at such low levels.

Diversity in the microbiome is connected to all sorts of things, including how long you live. Studies show that people who live into their 90’s and above with really good health outcomes have the microbial diversity of people in their 30’s. If your diversity decreases over time (as it does with most people), it dramatically influences your longevity and your health outcomes as well.

The lower the diversity, the much higher the risk you have for chronic illness. The lower your diversity, the worse your sleep patterns are. According to research, diversity in the microbiome dictates sleep efficiency, sleep duration, and all of the metabolic processes that occur during sleep as well.

Live in interview with Kiran Krishnan on July 21, 2020

Probiotics and Sleep

Walking down the fresh food aisle in just about any grocery store, you’re likely to spot several probiotic-rich foods, like yogurt, kefir, sauerkraut, kimchi, and my personal favorite—kombucha. Commercial probiotic supplements have also become very trendy and are even recommended by doctors for improving things like colic in babies, diarrhea and constipation, immune health, and IBS.

But one problem most people don’t think about using probiotics for is poor sleep. One study looked at a group of med students undergoing a major exam and compared a probiotic supplement to a placebo. They found that the group receiving the probiotic had less anxiety and better quality of sleep during the period of time leading up to and after the exam than the placebo group. 

Probiotic bacteria can only survive if they have an abundant supply of food, and their food of choice is prebiotics, the indigestible dietary compounds found in fibrous foods. A recent study fed rats a diet of standard chow or prebiotic chow, and the group eating the prebiotic diet had better microbial diversity and sleep quality when facing stress.

8 Ways to Improve Diversity in the Gut Microbiome

Isn’t it amazing to think that you have a living ecosystem inside of you that plays a role in everything from immune health to the quality of sleep, your risk for chronic illness, and even how long you live? But if you want your microbial garden to flourish, you have to take care of it. Here are eight tips for improving diversity in your gut microbiome:

Increase Diversity in Your Diet

The more diverse your diet is, the more diverse your gut will be. This doesn’t mean you can eat 100 different types of potato chips and improve your gut—it needs to whole foods, like fruits, veggies, dairy, and grains. A simple tip is to try to go to an ethnic store in your area and try one new food a week—aim for roots, tubers, and fruits that you don’t typically find elsewhere.

Get Fresh Air

Being in nature is a great way to expose yourself to a variety of microbes. Go for a walk in the forest, take a hike, go camping, just get outside. Another way to get more fresh air is to open your windows and doors and allow the breeze to flow through your home.

Get a Dog

We know from research that dogs are great for increasing longevity and decreasing allergies in kids, but did you know that Fido may be good for your gut health too? Research shows that owning an indoor/outdoor pet like a dog can improve the microbial diversity of your home and exposes owners to a wide variety of outdoor microbes.


Exercise is a wonderful way to improve your sleep—and your gut! Studies show that people who stay active have more diversity in their guts than people who don’t exercise. The best way to stick with it is to choose activities that you love. If you’re not sure where to start, try running, dancing, paddleboarding, roller skating, or yoga!

Intermittent Fasting

Another health aspect that’s trending is intermittent fasting, which is the practice of limiting food intake to a set amount of time each day. Studies have discovered many health benefits of intermittent fasting on aging, metabolism, obesity, cardiovascular disease—and the microbiome. If you do decide to try intermittent fasting, make sure to speak to your doctor first.

Use the Right Prebiotic and Probiotic

While prebiotics and probiotics can be found in many foods, like yogurt, asparagus, artichokes, and onions, some people prefer to take a supplement. Unfortunately, many commercial probiotic supplements won’t survive the harsh conditions in your digestive tract. To ensure your probiotics are effective, look for live strains that don’t have to be refrigerated, double encapsulated options, or spore-based organisms.

Manage Stress

One of the worst things for gut health is stress. Stress increases leaky gut, encourages the proliferation of opportunistic and pathogenic organisms, increases inflammation, and reduces the diversity of your microbiome. To combat stress, try to incorporate mindfulness activities into your day such as breathing exercises, meditation, prayer, or yoga.


Certain microbes proliferate really abundantly while you’re sleeping, and they don’t proliferate well during the day. If you cut the duration of sleep, those microbes suffer and don’t get the opportunity to proliferate and improve the diversity of your microbiome. Getting the optimal seven to eight hours of sleep is extremely important for a healthy body, mind, and gut!

Questions for Your Doctor

How do I know if I have a leaky gut?

Unfortunately, leaky gut is considered a “subclinical” condition, meaning many people don’t have any symptoms until it’s gotten so bad that a chronic disease sets in. While there are microbiome tests that can show you the health of your gut, they can be costly, and options are limited. If you’re concerned about leaky gut, the best thing you can do is to make gut health a priority in your life by following the tips listed above.

Should I take probiotics before bed?

When it comes to taking probiotics, time of day isn’t as important as consistency. If you find that bedtime is when you’re most likely to remember to take your supplement, that should be fine. Just remember, if you’re considering a probiotic dietary supplement, it’s important to consult your health care provider first.


Sleep and gut health go hand-in-hand. When you don’t get enough sleep, your microbiome suffers. Likewise, when your microbiome is compromised, you become more susceptible to leaky gut, you produce less serotonin, your immune system suffers, and the cycle perpetuates because it becomes harder to get to sleep.

The good news is that improving your gut health can have a positive effect on your sleep and vice versa. Improving microbial diversity doesn’t have to be hard or expensive—many of the tips we recommended are easy and free! If you’re looking to improve your sleep and gut health, what could be easier than taking a walk, trying a new food, or getting a dog?

Raina Cordell

Raina Cordell

RN, RHN, Certified Health Coach

About Author

Raina Cordell is a Registered Nurse, Registered Holistic Nutritionist, and Certified Health Coach, but her true passion in life is helping others live well through her website, Her holistic approach focuses on the whole person, honing the physical body and spiritual and emotional well-being.

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