Updated at: 25-02-2022 - By: Jane

For Mother’s Day last year, I received a feces test. If that sounds weird, I’ve wanted one for years. Please allow me to back up a bit and explain.

My stomach has always been a problem for me, ever since I can remember. It seems that my mother’s claim that I was born with digestive issues is correct, based on my childhood memories of frequent stomach pains and visits to the doctor.

Lactose intolerance, food allergies, and even Irritable Bowel Syndrome were all diagnoses I received throughout the years. My symptoms worsened as I got older, and I began to notice issues in other areas, such as my temperament, sleep, and hormones. My leaky gut wasn’t diagnosed until I started doing research on my own and found out what was really wrong with me.

The health of your gut is not only linked to your sleep, but it can also influence the health of your gut. Curious? To begin, let’s explore the interesting world of sleep and the microbiome.

What is the Microbiome?

What would you think if I told you that you’re only 10% human and 90% bacteria? Yes, that’s exactly right. Cells and DNA govern only 10% of your body’s activity; the other 90% is controlled by the trillions of microorganisms that live in and on you. As a matter of fact, your body contains 150 times more microbial DNA than that of a human being.


Microbiomes are made up of various kinds of living organisms, including viruses, bacteria, protozoa, and other microorganisms. Each and every microbial organism that lives in or on a host is included in the microbiome.

We are made up of countless micro-ecosystems, all of which must work in harmony to ensure the long-term well-being of the entire. Humans are like living, breathing rainforests if you think about it!

To learn more about the human microbiome and how it affects our health and disease, the Human Microbiome Project was started in 2008. In the previous five years alone, there have been more than 50,000 scholarly papers published. And yet, we’re only scraping the surface of what we might learn from this, the most significant scientific revolution in history.

Scientists, for example, once believed that the womb and blood were sterile parts of the body. In addition to the blood, our brain, cerebrospinal fluid, and eyes (among other places), we have 1,000 bacterial cells per milliliter of blood now, thanks to new research. However, the gut has the most microorganisms of any part of the body.

Why is the Gut Called the “Second Brain?”

As a child, you may have been taught that the brain is the body’s primary control 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.

In some ways, the brain and the gut may be described as close friends because they work together every day to keep this system running well. The “gut-brain axis” is one of the ways in which they communicate back and forth. A nerve that goes from your brainstem to your intestines is called the vagus nerve, and it connects the gut and the brain.

The enteric nervous system, which includes all of the nerves in the digestive tract, is connected to the vagus nerve. After the brain, this system has the highest density of neural activity. That’s why the word “gut feeling” holds more weight than you might believe.

The vagus nerve provides entry to the enteric nervous system for all gut bacteria. As a result, they have direct access to the brain, and the brain can impact gut microorganisms. They communicate with one another constantly throughout the day.

To assist you to know when you’ve had enough food when you need a rest, and when it’s time for bed, your gut bacteria must be in good health. You may want sugar, feel anxious and melancholy, or be awake at night counting sheep if they’re not healthy.

The Relationship Between the Microbiome and Sleep

The microbiome is influenced by sleep, and sleep is influenced by the microbiome. One can’t function correctly without affecting the other in a reciprocal relationship. 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. Besides the microbiome, your body has a slew of additional clockwork processes. 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. After two nights of sleep deprivation, a 2016 study examined the microbiota of healthy young adults with regular sleeping and eating habits. The results were astounding:

  • Insufficiency of insulin
  • Predominantly unhealthy gut microbiota
  • Type 2 diabetes and altered microbiota

More and more research suggests that a variety of health issues like metabolic syndrome, obesity, diabetes, and inflammatory disease can be caused by sleep disorders such as circadian rhythm abnormalities, insomnia, and others.

In recent years, a great deal of focus has been placed on the relationship between sleep deprivation and the later onset of Alzheimer’s disease. These cognitive alterations may be caused by bacteria in the microbiome, according to recent research. Researchers showed that enhanced sleep quality was associated with improved cognitive performance and a more healthy microbiota in healthy older persons in 2017.

How the Microbiome Influences Sleep

Leaky Gut

Think of the digestive tract as a long tube that’s open at both ends, and you get the idea. An organism can only enter its body through its digestive tract, which is lined by mucus membranes. Chronic illness has a critical intersection at the management of what is allowed to pass through that lining: you want healthy nutrients to enter and harmful garbage to stay out.

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. “All sickness begins in the intestines,” Hippocrates wrote in his Hippocratic Oath hundreds of years ago.

An imbalance of good and bad bacteria in your digestive system can lead to “leaky gut,” which is a typical term for this disease. Endotoxins and other inflammatory substances escape into your bloodstream when you have a leaky gut. The “fight-or-flight” response is activated by these substances on a constant basis.

You need your parasympathetic nervous system to engage at night so that you can “relax and digest,” which is especially difficult when you’re trying to get some shut-eye. People who are continually in a state of “fight-or-flight” struggle to get to sleep and stay asleep.

When is a leaky stomach more common? It’s more prevalent than you might imagine! Scientific research suggests that chronic disease is mostly caused by a buildup of toxins in the gut. Many Americans have several chronic conditions, according to data from the Centers for Disease Control (CDC).

And what’s worse is that leaky guts don’t simply affect the sick. 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

Bacteria in your gut may be to blame if you can’t sleep at night. GABA, dopamine, and serotonin—the precursor to the well-known sleep-inducing hormone, melatonin—are all neurotransmitters produced and released by the microbiota.


These neurotransmitters are created in the brain, but a large portion of serotonin is produced by specific bacteria in the stomach. In the absence of these bacteria, your body is less likely to make enough melatonin to assist you in falling asleep at night, resulting in sleep deprivation.

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. 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. According to a circadian function, these identical markers appear to release more of them as the sunsets. You get drowsy because your gut microbes enhance the production of cytokines that cause you to feel drowsy.

When your immune system is activated by inflammatory signals like these, it can go into repair and patrolling mode while you sleep. Infectious viruses, dangerous bacteria, and any other foreign substance are alerted to your body’s immune system by this. Taking a good night’s sleep is essential to preventing illness and maintaining good health.

During sleep, this circadian-controlled inflammation is expected to reduce. You’ll see an increase in the body’s inflammatory response when you’re weary, but you won’t have the necessary bacteria to bring it down as the night develops if your microbiome is malfunctioning. Chronic inflammation builds up over time, resulting in a net accumulation of inflammation.

Additionally, you may wake up too early since the bacteria haven’t had time to communicate with your body and reduce these inflammation signals. The rise and fall of inflammation can only occur if adults get at least seven to eight hours of sleep each night.


Evening cleaning chores don’t stop with the dishes and floors. During the night, the microbiome activates particular microorganisms that carry out household chores. One such example is the removal of damaged mitochondria.

In order to determine how healthy your cells are, it is important to understand the role of mitochondria. The health of your mitochondria is a key determinant of your aging process. 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.

After a long day of creating toxic waste, cells need to be cleaned out at night, which is when the microbiome generates something called autophagy. This is a process of cleaning out damaged cells and DNA as well as proteins that are no longer needed. The accumulation of toxic waste can lead to inflammatory conditions, such as cancer.

Being in a fasting condition is a factor in some bacteria’s ability to do these housekeeping tasks. Your cells and mitochondria will not be able to go through the necessary purification procedure if you consume large meals before bed or wake up in the middle of the night and eat.

Your body should be in a fasting condition at night if you can stop eating three or four hours before to 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.


Kiran Krishnan, a microbiologist, believes that diversity 1 is the most critical element of the microbiome that influences sleep. There are two ways to assess diversity: richness (the number of distinct creatures you have) and uniformity (the number of organisms that are the same) (amount of each individual species). When your gut has 300 distinct bacteria, but only 290 of them contribute to your health, that’s a problem.

Having a diverse microbiome is linked to a variety of factors, including your lifespan. Those who live into their 90s and beyond have the same microbial variety as those in their 30s, according to research. The longer you live and the healthier you are, the more your diversity reduces with age (as it does in the majority of people).

Chronic illness is significantly more likely when there is less diversity in your environment. The less diverse you are, the less likely you are to have a good night’s sleep. 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

Probiotic-rich foods like yogurt, kefir, sauerkraut, kimchi, and my personal favorite, kombucha, can be found in almost any grocery store’s fresh food section. Commercial probiotic pills have also grown highly popular and are even advised by doctors for relieving conditions like colic in babies, diarrhea and constipation, immunological health, and IBS.

Poor sleep is a common complaint, but it’s one that most people don’t consider treating with probiotics. Medic students preparing for a key exam were compared to those taking a placebo in one study. They found that the probiotic group had less anxiety and a better night’s sleep before and after the exam than the placebo group.

A steady supply of prebiotics, the indigestible dietary components found in nonfibrous foods, is essential to the survival of 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

If you think about it, you have a living ecosystem inside of you that influences everything from your immune health to the quality of your sleep, the risk of chronic illness, and even your lifespan. However, if you want your microbial garden to thrive, you’ll need to give it some love and attention. You can improve the variety of your gut microbiota by following these eight steps:

Increase Diversity in Your Diet

Your stomach will be more diversified if you eat a wide variety of foods. This does not imply that you may enhance your gut health by consuming a wide variety of potato chips; rather, you must consume entire meals such as fruits, vegetables, dairy products, and grains. Try one new cuisine a week from an ethnic market in your neighborhood, focusing on roots, tubers, and fruits that you can’t find anywhere else.

Get Fresh Air

A fantastic method to get a wide diversity of microorganisms is to spend time in nature. Take a walk in the woods, go hiking, go camping, anything to get you outside. Open your windows and doors to let the breeze into your home as another approach to receive more fresh air.

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? Owning an indoor/outdoor pet like a dog increases your home’s microbial diversity and exposes you to a wide range of outside bacteria, according to research.


Exercise is a great method to sleep better and feel better in general. People who are physically active have a more diverse gut microbiome than those who are not. Choosing activities that you enjoy is the best approach to staying motivated. If you’re not sure where to begin, try running, dancing, paddleboarding, rollerskating, or even yoga!!

Intermittent Fasting

Intermittent fasting, which is the practice of restricting food consumption to a specific period of time each day, is also a popular health fad. 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 beginning an intermittent fasting regimen.

Use the Right Prebiotic and Probiotic

Many foods, such as yogurt, asparagus, artichokes, and onions, contain prebiotics and probiotics, but some people prefer to take a supplement. Sadly, many commercial probiotic pills won’t last in your body because of the hostile circumstances there. Choose live strains, double-encapsulated choices, or spore-based organisms that don’t need to be refrigerated to ensure that your probiotics work.

Manage Stress

Stress is one of the worst things you can do for your gut health. Leaky gut, increased opportunistic and pathogenic microbial growth, inflammation, and a shrinking microbiome are all symptoms of chronic stress. Practicing mindfulness techniques like deep breathing, meditation, prayer, or yoga can help you manage stress.


In the course of your sleep, some microorganisms multiply rapidly, but this does not occur in the course of your waking hours. Those microorganisms suffer and are unable to multiply and improve the diversity of your microbiome if you reduce the amount of time you spend sleeping. 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 and other internal and external stimuli Sleep is considerably affected by eating from a trusted source. Circadian rhythms are 24-hour cycles based on the body’s internal clock that govern important biological processes and functions.


The sleep-wake cycle is one of the most significant circadian rhythms. Sleep disruptions can be caused by factors that disrupt the sleep-wake cycle.

The Brain-gut axis or “microbiota-gut-brain axis” is a term used to describe the relationship between gastrointestinal metabolism and brain function via the circulatory system and the vagus nerve.

Many aspects of mental health and cognitive performance can be affected by the gut microbiome (the bacteria, viruses, and fungi that dwell in the gut), according to research by Trusted Source.

Microbiota composition, size, and day-to-day rhythms vary depending on when and what people eat. There are a number of gut metabolites that are produced by microorganisms that belong to the microbiota. These molecules originate from chemical reactions that take place during digestion.

A person’s sleep may be improved or less problematic if they alter their diet. 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 available to the experimental animals. Antibiotics were used to decrease the intestinal microbiota of the mice. Meanwhile, the control mice drank water that was devoid of antibiotics.

The mice who drank the antibiotic water had much fewer intestinal metabolites than the control animals after 4 weeks, according to the researchers.

Prof. Yanagisawa states, “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 researchers discovered that antibiotic therapy had a significant impact on the production of neurotransmitters, the substances that neurons use to communicate.

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.

Vitamin B6 metabolites, which speed up the production of serotonin and dopamine, were also decreased in the microbiota-depleted mice.

EEG/EMG data, which measure electrical brain activity, were then gathered by implanting electrodes in their scalps.

At night, when mice should be active, the microbiota-depleted mice had more rapid eye movement (REM) and non-REM sleep than the control mice. Additionally, the microbiota-depleted mice saw a decrease in daytime non-REM sleep.

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.

Microbiota-deficient animals were shown to be more often transitioning between sleep and waking states than control mice. Serotonin levels may have a role in these sleep disruptions, but further study is needed to understand the mechanism.


Study limitations and future research

The study’s shortcomings include the fact that the researchers were unable to ignore the direct effects of antibiotics on the brain’s functioning. To avoid this problem, the researchers recommend using germ-free mice in future investigations.

Studies in the future could also use controlled eating and microbe delivery to evaluate the gut microbiota, allowing the researchers to examine each microorganism’s specific impact on the sleep-wake cycle.

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.

Human volunteers will have to be used in future studies to see if these findings remain true.


Sleep and intestinal health are intertwined. Sleep deprivation affects your microbiome. A weakened immune system, leaky gut, decreased serotonin production, and a weakened microbiome are all symptoms of a weakened microbiome, which in turn exacerbates the difficulty of falling asleep.

Improving your gut health has been shown to improve sleep quality and vice versa. Many of our suggestions for increasing microbial diversity are simple and cost nothing. Taking a stroll, eating new food, or adopting a dog are all simple ways to improve your sleep and intestinal health.

Questions for Your Doctor

How do I know if I have a leaky gut?

As a “subclinical” disorder, leaky gut often goes unnoticed until it has progressed to the point of chronic disease. The health of your gut microbiome may be measured, but these tests are expensive and only a few are available. Make gut health a priority in your life by following the guidelines outlined above if you’re concerned about leaky gut.

Should I take probiotics before bed?

Consistency is more crucial than timing when it comes to taking probiotics. If you’re most likely to remember to take your supplement at bedtime, you’re good to go. If you’re thinking about taking a probiotic supplement, make sure you talk to your doctor first.

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