Is Your Gut Causing Sleepless Nights?

gut health sleep connection

Story at-a-glance -

  • It’s already known that sleep influences your gut health, in part because lack of it makes it harder for you to control your impulses and manipulates hormones linked to food intake, causing you to eat more and crave unhealthy foods
  • Now researchers are asking whether the opposite also holds true and perhaps your microbiome influences your ability to sleep as well
  • There could be a link between sleep quality, composition of gut microbiome and cognitive flexibility in older adults
  • Prebiotics, which act as food for beneficial bacteria, or probiotics, in your gut, have been found to influence sleep in animal studies
  • When men slept for just four hours a night for two nights in a row, the balance of bacteria in their gut shifted in ways linked to metabolic disturbances

By Dr. Mercola

You share your body with trillions of microorganisms, the bulk of which reside in your gut, including your stomach and small and large intestines. There, however, they are not restricted to influencing only the goings-on of your digestive process.

Far from it, these microorganisms, collectively known as your microbiome, influence your body's homeostasis daily and are intricately tied to other body systems via a number of complex pathways, including the gut-brain axis and a recently revealed gut-brain-bone marrow axis, the latter of which may influence your blood pressure, mood and more.

One of the most compelling avenues of study relating to your microbiome is how it relates to your sleep. It's already known that sleep influences your gut health, in part because lack of it makes it harder for you to control your impulses and manipulates hormones linked to food intake, causing you to eat more and crave unhealthy foods.

So skimping on sleep is a remarkably good bellwether of a poor diet, the latter of which can quickly take a toll on your gut health. Now researchers are asking whether the opposite also holds true and perhaps your microbiome influences your ability to sleep as well.

Can Your Microbiome Keep You Up at Night?

Although the science is in its early stages, researchers are looking into whether improving gut health could act as a new form of sleep therapy. Michael Breus, Ph.D., a clinical psychologist and fellow of the American Academy of Sleep Medicine, told The Guardian:1

"There is no question in my mind that gut health is linked to sleep health, although we do not have the studies to prove it yet. Scientists investigating the relationship between sleep and the microbiome are finding that the microbial ecosystem may affect sleep and sleep-related physiological functions in a number of different ways: shifting circadian rhythms, altering the body's sleep-wake cycle, affecting hormones that regulate sleep and wakefulness."

For instance, writing in the journal Chest, researchers pointed out that changes in gut microbiota have long been linked to lifestyle behaviors such as diet, travel, exercise and disturbances to circadian rhythm.2 Meanwhile, diseases once primarily attributed to lifestyle, such as obesity, heart disease and depression, are turning out to have increasing links to microbiota. In this case, they believe that "microbial-immune cross-talk" may be playing a role in obstructive sleep apnea (OSA), particularly in fatal cases.

"[W]e posit that altered patterns of sleep and oxygenation, as seen in OSA, will promote specific alterations in gut microbiota which in turn will elicit the immunological alterations that lead to OSA-induced end-organ morbidities," they stated. Likewise, in the Journal of Clinical Gastroenterology, researchers evaluated the interplay between sleep dysfunction, gastrointestinal health and disease, with particular focus on how the effects of sleep and circadian rhythm disruption could affect the microbiota.3

Yet another study pointed out that partial sleep deprivation is known to alter gut microbiome, and its composition is linked to cognitive flexibility. Their study found that there could be a link between sleep quality, composition of gut microbiome and cognitive flexibility in older adults, such that "improving microbiome health may buffer against sleep-related cognitive decline in older adults."4

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Prebiotics Affect REM and Non-REM Sleep

Prebiotics, which act as food for the beneficial bacteria, or probiotics, in your gut, have already been found to influence sleep in animal studies. When young rats were fed a diet containing prebiotic fiber or a control diet for four weeks, the prebiotic group spent more time in restful and restorative non-rapid eye movement (NREM) sleep cycles.5

In addition, rats eating prebiotics had an increase in beneficial gut bacteria as compared to the control group and spent more time in REM sleep after being stressed, which is important for promoting recovery. The researchers noted:6

"The results of the current study demonstrate that a … diet rich in prebiotics … started in early life increases the growth of Lactobacillus rhamnosus and alleviates the stress-induced disruption of REM sleep, diurnal physiology and gut microbial alpha diversity.

Rats on the test diet exhibited decreased impact of the stressor, including increased REM sleep rebound following stress, attenuated disruption of the diurnal rhythm of CBT [core body temperature], and prevention of dysbiosis in all three measures of alpha diversity …

Given that sufficient NREM sleep and proper nutrition can impact brain development and function and that sleep problems are common in early-life, it is possible that a diet rich in prebiotics started in early-life could help improve sleep, support the gut microbiota and promote optimal brain/psychological health."

Dr. Michael Mosley, a doctor-journalist with BBC News, conducted a similar trial on himself, taking prebiotics for five days, and noticed a remarkable improvement in his sleep. Prior to the prebiotics, he spent 21 percent of his time in bed awake but this dropped to 8 percent after the prebiotics.7

This isn't definitive proof that prebiotics improve sleep, but considering the many other benefits they add to your health, there's little harm, and potentially great gain, in adding them to your diet. If you're interested in adding more prebiotic fiber to your diet to improve the health of your microbiome, and possibly your sleep, the following foods are good sources:8





Breast milk

Burdock root


Chicory root


Fennel bulb



Green peas

Jerusalem artichokes


Konjac root







Savoy cabbage



Snow peas


Too Little Sleep Alters the Bacteria in Your Gut

The many ties between your microbiota, your sleep and your overall health only continue to grow. For instance, melatonin, the sleep hormone, is made from serotonin, and is normally found in abundance in your gut — even more so than in your brain. Gut bacteria affect both serotonin and melatonin production.

Further, the composition and functions of your gut microbiome is affected by circadian rhythm disruptions, including jet lag. Researchers believe circadian rhythms play a key role in regulating the gut microbiome as well as its responses to gastrointestinal pathogens.9

If you skimp on sleep, you also prompt changes in your body's microbial community. When men slept for just four hours a night for two nights in a row, the balance of bacteria in their gut shifted.10 Specifically, they had increased firmicutes to bacteroidetes ratio, higher abundances of the families Coriobacteriaceae and Erysipelotrichaceae and lower abundance of Tenericutes, changes that have previously been linked to metabolic disturbances. The researchers concluded:11

"Our findings demonstrate that short-term sleep loss induces subtle effects on human microbiota. To what extent the observed changes to the microbial community contribute to metabolic consequences of sleep loss warrants further investigations in larger and more prolonged sleep studies."

The Link Between Sleep, Depression and Your Gut

Your gut microbiome plays an intricate role in your mood, and sleep plays a role in depression, raising intriguing questions about how all three — microbiome, sleep and depression — are related. Tim Spector, professor of genetic epidemiology at King's College London, told The Guardian:12

"We know that people who live with depression and people who sleep poorly both have abnormal microbes in the gut, which would suggest there is a very real connection here between all three … I've always found that if you help someone sleep, it improves their depression, and vice versa. If we can also look after the gut, this may have an impact on both sleep disturbances and mood disorders."

Also intriguing, a small study involving adults diagnosed with irritable bowel syndrome (IBS) and depression found the probiotic Bifidobacterium longum provided depression relief. At six weeks, 64 percent of the treatment group had reduced depression scores compared to 32 percent of the control group that received a placebo.13

Those receiving the probiotic also reported fewer symptoms of IBS and improved overall quality of life. At the end of 10 weeks, approximately twice as many in the treatment group were still reporting lower levels of depression.

Interestingly, functional MRI scans revealed a link between reductions in depression score and actual changes in brain activity, specifically in areas involved in mood regulation, such as the amygdala. As noted by Dr. Roger McIntyre, professor of psychiatry and pharmacology at the University of Toronto, who was not involved in the study:14

"We know that one part of the brain, the amygdala, tends to be red-hot in people with depression, and it seemed to cool down with this intervention. It provides more scientific believability that something in the brain, at a very biological level, seems to be affected by this probiotic."

Could Your Diet Improve Both Your Sleep and Your Gut Health?

Another common thread affecting both your sleep and your gut is your diet. One study evaluating the diets and sleep patterns of more than 4,500 people found distinct patterns:15

  • Very short sleepers (less than five hours a night): Had the least food variety, drank less water and consumed fewer total carbohydrates and lycopene (an antioxidant found in fruits and vegetables).
  • Short sleepers (five to six hours): Consumed the most calories but ate less vitamin C and selenium, and drank less water. Short sleepers tended to eat more lutein and zeaxanthin than other groups.
  • Normal sleepers (seven to eight hours): Had the most food variety in their diet, which is generally associated with a healthier way of eating.
  • Long sleepers (nine or more hours): Consumed the least calories as well as less theobromine (found in chocolate and tea), choline and total carbs. Long sleepers tended to drink more alcohol.

Further, Spector told The Guardian, "[I]f we eat badly, we sleep badly … If you wanted to improve sleep, you could try a gut-friendly regime by eating a broad and inclusive diet with real food, not processed."16 Indeed, it's likely that eating a varied, whole food diet is one key to normal, healthy sleep and gut health alike. If you need some help in this area, check out my nutrition plan for a step-by-step guide to optimizing your eating habits.

As for how to support a healthy microbiota, which could do more to improve your sleep than is currently appreciated, it isn't very complicated, but you do need to take proactive steps to encourage its health while avoiding factors known to cause harm. This includes:

Do Avoid

Eat plenty of fermented foods. Healthy choices include lassi, fermented grass fed kefir, natto (fermented soy) and fermented vegetables.

Antibiotics, unless absolutely necessary, and when you do, make sure to reseed your gut with fermented foods and/or a high-quality probiotic supplement.

Take a probiotic supplement. Although I'm not a major proponent of taking many supplements (as I believe the majority of your nutrients need to come from food), probiotics are an exception if you don't eat fermented foods on a regular basis

Conventionally raised meats and other animal products, as CAFO animals are routinely fed low-dose antibiotics, plus GE grains loaded with glyphosate, which is widely known to kill many bacteria.

Boost your soluble and insoluble fiber intake, focusing on vegetables, nuts and seeds, including sprouted seeds.

Chlorinated and/or fluoridated water. Especially in your bathing such as showers, which are worse than drinking it.

Get your hands dirty in the garden. Exposure to bacteria and viruses can help to strengthen your immune system and provide long-lasting immunity against disease.

Getting your hands dirty in the garden can help reacquaint your immune system with beneficial microorganisms on the plants and in the soil.

Processed foods. Excessive sugars, along with otherwise "dead" nutrients, feed pathogenic bacteria.

Food emulsifiers such as polysorbate 80, lecithin, carrageenan, polyglycerols and xanthan gum also appear to have an adverse effect on your gut flora.

Unless 100 percent organic, they may also contain GMOs that tend to be heavily contaminated with pesticides such as glyphosate. Artificial sweeteners have also been found to alter gut bacteria in adverse ways.17

Open your windows. For the vast majority of human history, the outside was always part of the inside, and at no moment during our day were we ever really separated from nature.

Today, we spend 90 percent of our lives indoors. And, although keeping the outside out does have its advantages it has also changed the microbiome of your home.

Research shows that opening a window and increasing natural airflow can improve the diversity and health of the microbes in your home, which in turn benefit you.18

Agricultural chemicals, glyphosate (Roundup) in particular is a known antibiotic and will actively kill many of your beneficial gut microbes if you eat foods contaminated with it.

Wash your dishes by hand instead of in the dishwasher.

Research has shown that washing your dishes by hand leaves more bacteria on the dishes than dishwashers do, and eating off these less-than-sterile dishes may actually decrease your risk of allergies by stimulating your immune system.

Antibacterial soap, as it too kills off both good and bad bacteria and contributes to the development of antibiotic resistance.