The connection between gut health and sleep quality
The brain-gut axis
There is growing evidence that your digestive tract is directly connected to your brain. The health of your gut can influence sleep, emotions, behavior, and physical performance. That’s why it’s becoming more and more known as 'the body’s second brain.' It also works the other way around: the health of your brain, including your sleep patterns, directly affects your gut health.
The gut microbiome
You can think of your digestive tract as a long tube running from your mouth to your anus. It has a surface area nearly the size of two tennis courts. Because it’s in contact with the outside world at both ends, your gut is home to a complex and dynamic population of trillions of bacteria, viruses, and fungi. This is called the gut microbiome.
A healthy and balanced gut microbiome consists of both beneficial and harmful bacterial species that influence overall health. The goal is to maintain a balance with more 'beneficial' than 'harmful' bacteria.
We humans share about one-third of the composition of our gut microbiome with one another, while the remaining two-thirds are unique to each individual. The composition of the microbiome changes constantly throughout your life; at birth, your gut is sterile, but is colonized by microorganisms immediately afterward.
Factors affecting the composition
The environment in which you live and your diet have a major influence on the composition of your gut microbiome. A vegan living in the Veluwe region does not have the same gut microbiome composition as someone who lives in a big city and enjoys red meat. In addition to your daily environment, numerous lifestyle factors can disrupt the normal balance of the gut microbiome. Processed foods, excessive sugar, a lack of fiber, insufficient hydration, lack of exercise, emotional or mental stress, excessive use of antibiotics, and many other factors can influence your microbiome.
Some stressors can lead to an increase in pathogenic bacteria ('bad bacteria') in your gut and ultimately result in health issues such as inflammatory bowel disease, leaky gut, diabetes, obesity, and sleep disorders. Other factors, however, can have a positive effect on this balance.
We all need a well-balanced gut microbiome for the body’s daily functioning (metabolism, digestion, and immune function). In addition, we are beginning to understand that the gut microbiome is also important for optimal sleep.
The Gut and sleep
Research has shown that adults who report poor sleep quality also have a less-than-ideal gut microbiome, as well as reduced cognitive flexibility. Yet the relationship between the gut and sleep works both ways: sleep disorders also have a negative impact on the gut microbiome.
The relationship between the gut and sleep is complex. Does poor sleep cause a disrupted gut microbiome, or does an unhealthy gut microbiome actually disrupt sleep?
We know that insufficient, irregular, or poor-quality sleep is linked to an increased risk of chronic conditions such as diabetes, heart disease, obesity, and depression. These conditions, in turn, are associated with an imbalance in gut bacteria, also known as dysbiosis.
What happens exactly?
The brain contains millions of neurons that transmit signals to the body, including the nervous system of the intestines (the 'second brain'), which controls the gastrointestinal tract. The vagus nerve connects a network of nerves in the intestine to various parts of the brain. In fact, there is constant communication between the gastrointestinal tract and the brain via this nerve. This is called the gut-brain axis.
There are still many things that researchers do not fully understand, but we do know that bacteria in the gut can produce certain neurotransmitters, such as GABA, dopamine, and serotonin.
Interestingly, 90 percent of serotonin is found in the gut. These neurotransmitters can stimulate the neurons of the gut’s nervous system to send signals back to the brain.
What does this have to do with sleep?
Here’s how it works: melatonin, a sleep hormone produced primarily by the pineal gland (a small gland deep within the center of the brain), regulates the body’s biological clock. If the pineal gland isn’t functioning optimally, the body can rely on the gut as a sort of backup.
In the gut, tryptophan can be converted into melatonin to regulate the sleep-wake cycle. This occurs through a series of chemical reactions: tryptophan is first converted into serotonin and then into melatonin.
However, this 'backup' only works if the gut is functioning properly, which means that the condition of your gut affects how well you sleep.
What can you do to support your gut health and sleep?
1. Get more out of your diet.
You are what you eat (and what your body absorbs). Choose nutritious, high-quality foods in the right portions.
2. Don’t sweat the small stuff.
Less stress has a positive effect on your gut health. Learn how stress affects you and how you can reduce it.
3. Use probiotics or fermented foods.
Daily intake of probiotics or products such as yogurt, kefir, and fermented vegetables supports healthy gut flora.
4. Exercise every day.
Regular physical activity improves both the quality and diversity of your gut microbiota.
5. Reduce your sugar intake.
Too much sugar promotes the growth of harmful bacteria. Opt instead for high-fiber carbohydrates and aim for 25–30 grams of fiber per day.
6. Avoid excessive use of antibiotics.
Antibiotics kill both good and bad bacteria. Use them only when absolutely necessary. Follow up by feeding gut with foods or supplements that replenish the healthy microbiome.
This blog article is a translation and adaptation of a Take 5 Daily article on Thorne.com
Thorne Author: Laura Kunces, PhD, RD, CSSD
Dutch Editor: Marcella van der Wel
Published on: April 6, 2026