Gut health affects sleep, but you can improve yours

Getting the right amount of good quality sleep is important because it doesn’t just affect whether you feel tired. Lack of sleep and poor quality sleep are both associated with increased risk of certain diseases and cardiovascular issues.

Research suggests that your gut health can affect your sleep, and vice versa.

This is in part due to the connection between your brain and what’s known as your gut microbiome — the trillions of bacteria and other microscopic organisms that live in your gut. 

The range of “good” and “bad” microbes in your gut has been linked to how well you sleep, and some researchers believe that changing your microbiome can improve your sleep. 

Meanwhile, lack of sleep can impact your digestive health by increasing the risk of obesity, type 2 diabetes, and gastrointestinal diseases, as well as by influencing the foods you choose to eat. 

Researchers have even found that poor sleep quality is linked to heart problems.

Changes to your diet can help improve your gut health, which may also lead to better sleep. ZOE’s PREDICT program — the largest nutritional study of its kind — has found associations between certain foods and some of the “good” and “bad” gut bugs we’ve identified.

How are the gut and the brain linked?

Your gut and your brain are connected, and they can communicate with each other in a number of ways. These different mechanisms all involve your gut bacteria and can influence things like your mood, appetite, sleep, and stress levels.

The gut-brain connection works in both directions. Your gut can send signals to your brain, and your brain can in turn influence the makeup of your gut microbiome.

There are three main ways that your microbiome and your brain can affect each other:

  • One way is through interacting with the immune system. 

  • Another is by regulating the production of essential neurotransmitters, like serotonin, which signal your brain cells to take certain actions. 

  • A final way is through the vagus nerve, which connects your gut directly to your brain. Through this route, substances produced by your gut microbiome can affect brain functions including sleep. 

How gut health can affect sleep

There’s an increasing amount of evidence that the makeup of your gut microbiome is linked to how well you sleep.

In one study, researchers analyzed samples of the participants’ gut bacteria and then used activity watches to record their sleep behavior over a 30-day period. 

The study found that increased microbiome diversity correlated with longer sleep times and better sleep efficiency, which is how much of the time the participants spent actually sleeping while they were in bed.

The results also showed that specific types of bacteria were associated with increased sleep efficiency, while other types of bacteria were linked to measures of poorer sleep quality. 

Other research has looked at the relationship between gut bacteria, sleep, and levels of the neurotransmitter serotonin.

Serotonin is involved in regulating our sleep cycle, and our gut microbiome is a part of the process that controls the amount of serotonin in our body.

A study involving mice whose gut bacteria had been severely reduced by antibiotics showed that they had lower serotonin levels and that their sleep cycles were disrupted.

Researchers suggested that gut microbes had affected the mice’s sleep cycles by altering their serotonin levels. 

It’s important to remember that the results of animal studies may not be replicated in humans. However, this provides one possible avenue for further research into the links seen between gut bacteria and sleep in studies that involve human volunteers. 

How lack of sleep can affect gut health

We’ve already seen that poor sleep is associated with serious health conditions including type 2 diabetes and heart disease. 

But studies also suggest there is a link between disturbed sleep and increased risk of gastrointestinal diseases such as gastroesophageal reflux disease (GERD), which can cause heartburn or acid indigestion.   

Lack of sleep can also affect your food choices and, in turn, the microbes in your gut. 

Fresh research by ZOE published in Diabetologica showed that people who go to bed earlier and sleep longer have better blood sugar control after eating their first meal the next morning.

That means they’re less likely to experience significant dips in their blood sugar several hours later. 

The study also showed that sleeping for longer than usual on a single night can improve blood sugar control after breakfast, while going to bed later is associated with a worse blood sugar response after eating the next morning. 

Blood sugar dips like this can lead to increased appetite and eating more processed foods, which can have negative effects on your gut health.

ZOE's PREDICT program — which has collected nutritional data from over 10,000 people — found that eating processed foods is linked with more of the “bad” gut bacteria associated with markers of worse health. 

How to improve gut health with food   

As well as the 15 “bad” gut bacteria associated with eating more processed foods, ZOE has also identified 15 “good” gut microbes linked to a diet rich in minimally processed plant-based foods.  

Having more of the “good” gut bugs and less of the “bad” ones is favorable for your gut and your health.

To feed these “good” bugs and reduce the amount of “bad” bugs in your gut, you should eat a wide range of plants.

Aim for 30 different plant foods each week and try to “eat the rainbow” by including a variety of different colored plants in each meal.

These foods are high in both fiber and antioxidants called polyphenols, which your “good” gut bugs thrive on.

Good foods for gut health include: 

  • fruits and vegetables 

  • nuts and seeds

  • prebiotic foods

  • legumes

  • wholegrains

  • probiotic fermented foods

  • coffee

  • unprocessed or minimally processed foods 

Probiotic foods are fermented foods that contain live microbes, such as unsweetened natural yogurt, kefir, kimchi, sauerkraut, and certain cheeses, like parmesan, aged cheddar, and Swiss cheeses. 

When you eat probiotic foods, these bacteria may take up residence in your gut, increasing the diversity of your microbiome.

Prebiotic foods contain fiber that feeds the bacteria in your gut and encourages a diverse microbiome, rich in beneficial microbes. 

Foods that contain prebiotics include asparagus, onions, leeks, garlic, bananas, Jerusalem artichokes, beans like chickpeas and lentils, and certain whole grains, including barley, oats, and rye.

At ZOE, we know that everyone’s gut microbiome and their responses to food are different. ZOE’s advanced personalized testing tells you which foods are your personal “gut boosters” and which are your “gut suppressors.” 

The ZOE program can help you to eat more of the right foods for you, which may increase the diversity of your “good” gut bugs.


Poor sleep is associated with an increased risk of a number of serious health conditions. 

Research suggests that the quality of your sleep can be affected by the health of your gut and the diversity of your gut microbiome — the bacteria that live there.

Greater microbiome diversity and beneficial types of bacteria correlate with measures of better sleep, while other types of bacteria are linked with poor quality sleep. 

There is also some evidence that the gut microbiome may influence the production of serotonin, which is involved in regulating sleep. However, this is based on animal studies, and further research is needed.

Problems sleeping may also have an impact on your gut health — including on gastrointestinal diseases like GERD — and on the foods you choose to eat. 

A recent study by ZOE showed that people who go to sleep earlier have better blood sugar control after eating the next morning, while those who go to bed later have worse control. Blood sugar dips can increase appetite and may lead you to eat more processed foods.

Eating processed foods is linked with increased amounts of the 15 “bad” gut bacteria in the gut microbiome.

You can improve your gut health with changes to your diet. The best way to do this is to take ZOE’s at-home test to get a better understanding of your individual responses to foods, and then follow the ZOE program, which will show you how to eat more of the right foods for you.

Take a free quiz to learn more about how you can start eating gut-friendly foods for your unique microbiome.


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Gut microbiome diversity is associated with sleep physiology in humans. PLOS One. (2019).

Gut microbiota depletion by chronic antibiotic treatment alters the sleep/wake architecture and sleep EEG power spectra in mice. Scientific Reports. (2020).

Inadequate Sleep as a Contributor to Obesity and Type 2 Diabetes. Canadian Journal of Diabetes. (2013).

Sleep Duration and Sleep Quality in Relation to 12-Year Cardiovascular Disease Incidence: The MORGEN Study. Sleep. (2011).

Sleep Dysfunction and Gastrointestinal Diseases. Gastroenterology & Hepatology. (2015).

The Role of Microbiome in Insomnia, Circadian Disturbance and Depression. Frontiers in Psychiatry. (2018).