How The Microbiome Influences Sleep? Tips for Sleeping Better Update 05/2024

For Mother’s Day last year, my daughter gave me a feces test. As absurd as it may sound, I’d had my eye on one for quite some time. To better understand, let me go back in time.

I’ve had stomach problems for as long as I can remember. According to my mother, I was born with stomach issues, and based on my recollections of numerous trips to the ER as a child, I would agree.

From lactose intolerance to different food allergies and even IBS, I’ve received numerous diagnoses throughout the years. As I grew older, my symptoms worsened, and I began to have issues with my hormones, mood, and sleep as well. It wasn’t until I started investigating gut health for myself that I discovered what I had been suffering with was a leaky gut.

The health of your gut is not only linked to your sleep, but it can also influence the health of your gut. Curious? Explore the interesting realm of sleep and the microbiome in this article.

What is the Microbiome?

What would you think if I told you that you’re only 10% human and 90% bacteria? It is true. Only 10% of your body is controlled by your cells and DNA, while the other 90% is controlled by the billions of bacteria that live in you and on you. As a matter of fact, your body contains 150 times more microbial DNA than that of a human being.

Scientists call this microbial ecosystem the “microbiome,” and it consists of viruses, bacteria, protozoa, and a wide variety of other living species. Microbiome includes all microorganisms and their genetic components that reside in or on their host—which is us!!

Each of us is a tiny ecosystem that must work together to keep total health. People are like walking, talking jungles if you think of them that way!

In 2008, the Human Microbiome Project was established with the goal of learning more about the microbiome and how it affects health and disease in humans. In the previous five years alone, there have been more than 50,000 scholarly papers published. It’s the biggest scientific revolution ever, and yet we’ve only begun to scratch the surface of what we can learn from it.

As an example, until recently, experts believed that the womb and blood were sterile. Our blood contains 1,000 bacteria per milliliter, as well as cerebrospinal fluid (CSF), eyes, and all other parts of our bodies. The stomach, on the other hand, contains the greatest number of microorganisms of any organ in the body.

Why is the Gut Called the “Second Brain?”

You were undoubtedly told as a child that the brain is the body’s supreme command center. This is somewhat accurate, but you also have a command center in your belly that is equally vital. Many processes, including hormone synthesis, metabolic activity, appetite, and mood—and—sleep are controlled by microbes.

When it comes to keeping this sophisticated system running well on a daily basis, you could say that the brain and the stomach are good friends. The “gut-brain axis” is one of the ways in which they communicate back and forth. The vagus nerve, which extends from the brainstem to the intestines, connects the gut and the brain.

Energetic communication between your digestive tract and your brain is facilitated by the vagus nerve. This is the second most active area of the brain, behind the hippocampus. That’s why the word “gut feeling” holds more weight than you might believe.

The vagus nerve allows all of the bacteria in the gut to communicate with the enteric nervous system. As a result of this nerve, gut microorganisms are able to directly influence the brain and vice versa. They communicate with one another constantly throughout the day.

For example, if you’ve had a good night’s sleep, your gut bacteria can assist tell you that it’s time to stop eating and take a break. Some foods can cause you to crave sugar, feel nervous and unhappy or keep you up at night while you need sleep since they’re not healthy.

The Relationship Between the Microbiome and Sleep

There is a direct link between the microbiome and sleep. Their relationship is cyclical, and if one isn’t working well, the other will be affected as well. Healthy gut microbiota can help you sleep better, and a good night’s sleep can help you maintain a healthy gut microbiome.

How Sleep Influences the Microbiome

When it comes to your sleep-wake cycles, the circadian rhythm plays an important role. The microbiome is just one of several bodily systems that rely on an internal clock. What you eat, when you eat, and how you sleep all affect the microbiome’s circadian cycle.

Even a small amount of sleep deprivation might have a harmful effect on gut health, according to studies. Healthy young people with regular sleeping and eating habits were studied in a 2016 study to see how their microbiota changed following two nights of sleep of just 4.24 hours. The mind-blowing findings were as follows:

  • Insulin sensitivity decreases.
  • Bacterial imbalance in the intestines.
  • Type 2 diabetes is connected to changes in the microbiome.

Sleep disorders, such as circadian rhythm abnormalities, insomnia, and others, have been connected to a wide range of health issues, including metabolic syndrome, obesity, diabetes, and inflammatory disease, according to new research.

In recent years, a lot of attention has been paid to the link between Alzheimer’s disease and sleep deprivation. A recent study suggests that these cognitive alterations may be caused by bacteria in the microbiome. A better microbiota and better cognitive function were found to be associated with greater sleep quality in a 2017 research of healthy older individuals.

How the Microbiome Influences Sleep

Leaky Gut

Think of the digestive tract as a long tube with both ends open. The intestinal lining in the gut is the only entry point for foreign substances into the body. Toxic substances should not be permitted to enter your body through this lining, which is a critical juncture for chronic sickness.

If your body is unable to handle the transition between waking and sleeping, you’re more likely to suffer from a wide range of health problems, including those related to sleep. Hippocrates, who supposedly coined the phrase “All disease begins in the gut,” may have been on to something hundreds of years ago.

The lining of your intestines may become permeable if there is an imbalance between good and harmful bacteria, leading to the condition known as “leaky gut.” Endotoxins and other inflammatory substances flow into the bloodstream as a result of a leaky gut. The “fight-or-flight” response is activated by these substances on a constant basis.

Because you require your parasympathetic nervous system to “rest and digest” while you sleep, this is extremely problematic. A continual “fight or flight” state will keep you awake and unable to fall and stay asleep.

How frequent is the condition known as leaky intestine? It’s a lot more common than you’d imagine! Chronic disease may have its genesis in the gut, according to a growing body of research. 60% of adults in the United States have at least one chronic condition, and 40% have many chronic illnesses, as reported by the CDC.

It’s even more worrisome to learn that a leaky gut isn’t limited to those who are unwell. A 2017 study of 80 healthy college students discovered that 40% of them had leaky stomachs, even though they had no symptoms or underlying disease.

Low Levels of Serotonin-producing Bacteria

It’s possible that the bacteria in your gut are to fault if you’re constantly tossing and turning when you’re sleeping. In addition to GABA, dopamine, and serotonin, which are precursors to the well-known sleep-inducing hormone melatonin, the microbiota produces and releases several other neurotransmitters that have a role in sleep.

These neurotransmitters are created in the brain, but a large portion of serotonin is produced by specific bacteria in the stomach. Your body will be unable to make enough melatonin at night if you have a deficiency in the bacteria that produce serotonin.

Accumulation of Inflammation

Sleep and the microbiota have a lot in common because 70% of your immune system resides in your gut. The inflammatory reaction in your gut and throughout your body is under the direction of this immunological tissue. It’s important to remember that not all inflammation is harmful. Inflammatory indicators are critical to getting you to sleep!

It’s common to feel exhausted and desire to take a nap when you’re unwell because of an increase in inflammatory markers (also known as cytokines) including interleukin 1 beta and interleukin 6. During the night, when the sun sets, these same markers are released in larger concentrations, suggesting that they have a circadian function. These cytokines are increased by microbes in your intestines to induce drowsiness.

Inflammatory indicators also activate your immune system while you sleep, allowing it to repair and patrol your body. Infectious viruses, dangerous bacteria, and any other foreign substance are alerted to your immune system by this. That’s why getting enough sleep is so critical to preventing illness and maintaining good health.

After a good night’s sleep, this circadian-controlled inflammation should subside. A dysfunctional microbiome causes an increase in the inflammatory response in the body as you get fatigued, but you lack the bacteria to bring it down as the evening wears on. This is a serious problem. Chronic inflammation builds up over time, resulting in a net accumulation of inflammation.

In addition, you may experience this if you wake up too early before your body’s microorganisms have had a chance to tell inflammatory markers to drop. The rise and fall of inflammation can only occur if adults get seven to eight hours of sleep.


Evening cleaning chores don’t stop with the dishes and floors. During the night, the microbiome activates particular microorganisms that carry out household chores. An illustration of this is the removal of toxic byproducts of damaged mitochondria.

Mitochondria are your cell’s powerhouses, and the health of your mitochondria is what makes your cells healthy.

Mitochondrial dysfunction is the primary factor in determining how old you are. Mitophagy is activated at night by bacteria, which may find and destroy malfunctioning mitochondria, as well as make new ones, to keep your cells healthy and powerful.

An additional method of clearing damaged cells, broken DNA, unnecessary proteins, and “junk” is generated by the microbiome during the night. It is called “autophagy.” Throughout the day, cells produce a lot of waste that needs to be eliminated, which can contribute to inflammatory illnesses, such as cancer.

Being in a fasting state is part of the trigger for some bacteria to perform these housekeeping duties. Eat a substantial meal shortly before bedtime or in the middle of the night and your diurnal microbiome system will be entirely disrupted, which will prevent the necessary cleaning of your cells and mitochondria.

Your body should be in a fasting condition at night if you can stop eating three or four hours before bedtime. This will provide your body time to complete the digestion process, allowing the housekeeping bacteria to wake up at some point during your resting period.


Diversity is the most essential element of the microbiome that affects sleep, according to Kiran Krishnan. Richness (the number of creatures you have) and uniformity (the number of organisms you have) are two ways to quantify diversity (amount of each individual species). Many bacteria in your gut aren’t doing much for you because they’re at such low concentrations.

In addition to everything else, the diversity of your microbiome has a direct impact on your lifespan. The microbial diversity of persons in their 30s has been found in people who live to be at least 90 years old with excellent health. The longer you live, the more likely you are to suffer from poor health outcomes as a result of a lack of variety in your social circle.

You have a considerably greater chance of developing a chronic illness if your diet lacks variety. The worse your sleep becomes, the lesser your diversity is. It is widely accepted that sleep efficiency, sleep length, and all of the metabolic activities that take place during sleep are all influenced by the variety of the microbiome.

Probiotics and Sleep

Several probiotic-rich foods are readily available in the fresh food section of most supermarkets. These include yogurt, kefir, sauerkraut, kimchi, and my personal favorite, kombucha. Commercial probiotic pills have also grown highly popular and are even advised by doctors for relieving problems like colic in babies, diarrhea and constipation, immunological health, and IBS, among others.

Probiotics can help with a variety of health issues, but poor sleep is one that most people overlook when looking for a solution. Medic students preparing for a key test were compared to those taking a placebo in a trial of probiotic supplementation. Compared to the placebo group, the probiotic group reported less anxiety and better sleep quality in the days leading up to and following the exam.

Prebiotics, the indigestible dietary components found in nonfibrous foods, is the bacteria’s preferred food source because they ensure a constant supply of food for the probiotic bacteria. Prebiotic chow improved microbial diversity and sleep quality in stressed rats, according to a new study that fed rodents either conventional chow or prebiotic chow.

8 Ways to Improve Diversity in the Gut Microbiome

Think about it: you have a living ecosystem inside of you that affects everything from your immune system to how well you sleep and how likely you are to develop chronic illnesses. It’s important to maintain the health of your microbial garden, though, if you want it to thrive. Gut microbiome diversity can be improved by following these eight suggestions:

Increase Diversity in Your Diet

Your stomach will be more diversified if you eat a wide variety of foods. Whole foods including fruits, vegetables, dairy, and grains must be consumed in order to have a positive effect on your digestive system. Try one new food a week from an ethnic market in your neighborhood, focusing on roots, tubers, and fruits that you don’t often find at your local grocery shop.

Get Fresh Air

When you’re out in nature, you’re more likely to come into contact with a wide range of bacteria. Take a walk in the woods, go hiking, or go camping. Additionally, you can open your windows and doors and let some fresh air into your home.

Get a Dog

Research shows that dogs can help you live longer and reduce allergies in children, but did you know that Fido may also be healthy for your digestive system? You can boost your home’s microbial diversity by keeping an indoor/outdoor companion like a dog, which also exposes its owners to a wide range of outside bacteria.


In addition to helping you sleep better, exercise can also help you lose weight. People who engage in regular physical activity are more likely to have a diverse digestive system than those who do not. Choosing activities that you enjoy is the best approach to staying motivated. If you’re not sure where to begin, consider running, dancing, paddleboarding, rollerskating, or practicing yoga.s:

Intermittent Fasting

Among the latest health trends is intermittent fasting, which is the practice of restricting food consumption to a specific period of time each day. Several studies have shown that intermittent fasting can help with aging, metabolic and cardiovascular illness, as well as the microbiota. Make an appointment with your doctor before embarking on an intermittent fasting regimen.

Use the Right Prebiotic and Probiotic

For those who choose to supplement, prebiotics and probiotics can be found in a wide range of foods such as yogurt and asparagus. The harsh circumstances in your digestive tract make it impossible for many commercial probiotic supplements to live. The most effective probiotics are those that do not require refrigeration, are double-encapsulated or are spore-based.

Manage Stress

Stress is one of the most detrimental factors in intestinal health. Inflammation, the expansion of opportunistic organisms, and the loss of variety in your microbiome are all exacerbated by stress. Take time each day to practice mindfulness exercises like deep breathing, meditation, or prayer.


There are bacteria that flourish in great numbers while you sleep, but they don’t do so well when you’re awake. If you shorten the amount of time you spend in bed, your bacteria suffer and don’t have the chance to grow and diversify your microbiome. Getting the recommended seven to eight hours of sleep each night is critical to the well-being of your body, brain, and digestive system.

The microbiota-gut-brain axis

Circadian rhythms, for example, are both internal and external stimuli. Eating and getting a good night’s sleep are directly linked. Essential bodily processes or functions that follow a 24-hour cycle are known as circadian rhythms, and are determined by the body’s internal clock.

The sleep-wake cycle is an essential circadian rhythm. Sleep disruptions can be caused by factors that disrupt the sleep-wake cycle.

The “brain-gut axis” or “microbiota-gut-brain axis” is a network formed by the circulatory system and the vagus nerve that links intestinal metabolism to brain function.

Many aspects of mental and physical well-being are affected by one’s microbiome, according to research conducted by a reputable source. This microbiome is made up of trillions of trillions of microorganisms that live in one’s gut.

The gut microbiota’s makeup, size, and daily rhythms are all influenced by when and what people eat. Intestinal metabolism can be altered by changes in the gut microbiota, which produces several gut metabolites — the chemicals formed as a result of chemical reactions occurring during digestion.

As a result, altering one’s eating habits may help one’s sleep or lessen one’s insomnia. There are a number of undesirable side effects associated with sleep drugs, such as daytime tiredness and digestive issues, that might be avoided if this is the case.

Conducting the study

Two groups of 25 genetically identical 8-week-old male mice were created in the study by researchers.

There were four commonly used broad spectrum antibiotics given to the mice in the experimental group to drink water with. Antibiotics were used to decrease the intestinal microbiota of the mice. The mice in the control group, on the other hand, drank water that was devoid of antibiotics.

Compared to the control mice, those that drank antibiotic water had significantly fewer digestive enzymes in their bodies after four weeks.

Prof. Yanagisawa explains, “We identified more than 200 metabolite variations across mice groups. Microbiota-depleted animals had about 60 typical metabolites missing, and those that were present had varying levels of abundance compared to those in the control group.

The team discovered that antibiotic therapy had the greatest impact on the biochemical processes involved in the production of neurotransmitters, the substances neurons use to interact with one another.

There were no signs of a tryptophan-serotonin pathway remaining after antibiotic therapy. Serotonin levels were nearly nonexistent in the microbiota-depleted mice. Thus, it appears that the role of gut microorganisms in the production of serotonin from tryptophan in meals is crucial.

When their microbiome was stripped away, mice lacked the vitamin B6 metabolites necessary to increase the creation of serotonin and dopamine.

The researchers next used electrodes implanted in the mice’s scalps to record electroencephalogram (EEG)/electromyogram (EMG) data, which measure the electrical activity of the brain, to investigate the mice’s brain activity.

This phase revealed that the microbiota-depleted mice had more rapid eye movement (REM) and non-REM sleep at night, a time when mice should be active, than the control mice. Non-REM sleep, which mice spend the majority of their waking hours in, was also reduced in the mice whose microbiome had been removed.

This study’s researchers found that the microbiota-depleted mice had more REM sleep events during the day and more non-REM sleep episodes during the night than the control mice.

According to these findings, mice that had their microbiota removed slept and woke up more frequently than mice that had their microbiota intact. Sleep difficulties may be linked to decreased levels of serotonin, although further study is needed to determine the process.

Study limitations and future research

As a result of this, the researchers were forced to account for antibiotics’ potential impact on brain function. Using germ-free mice may be an option for future investigations, according to the researchers.

The gut microbiota could be studied in the future using controlled eating and the delivery of specific microorganisms, allowing the scientists to analyze the impact of each bacterium on the sleep-wake cycle individually.

Some research It has been found that prebiotics, which supports a healthy microbiome, improve sleep quality in individuals, as reported by Trusted Source. Stress-related sleep disruptions in rats may also be reduced by supplementation with prebiotics.

Future studies will need to see if these findings hold up when applied to real participants.


The two are intertwined, and it’s impossible to have one without the other. Your microbiome suffers when you don’t get enough sleep. Your immune system declines, you create less serotonin, and the cycle continues since it becomes more difficult to get to sleep when you have a damaged microbiota.

You can improve your sleep quality by improving your gut health, and vice versa. You don’t have to spend a lot of money to improve microbial diversity—many of the tips we provided are simple and free! It’s easy to enhance your sleep and intestinal health by taking walks, eating a different diet, or adopting a puppy.

Questions for Your Doctor

How do I know if I have a leaky gut?

Due to the term “subclinical,” many persons with leaky gut do not show any symptoms until the ailment is so severe that it becomes a long-term health issue. A microbiome test can reveal the health of your gut, but it is expensive and there are few alternatives. Make gut health a priority in your life by following the suggestions stated above if you’re worried about leaky gut.

Should I take probiotics before bed?

Time of day doesn’t matter as much when it comes to taking probiotics as the constancy of the dose. If you’re most likely to remember to take your supplement at bedtime, you’re good to go. If you’re considering taking a probiotic supplement, be sure to talk to your doctor first.

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