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Sleep and the Gut Microbiome

Our brain and gut are deeply intertwined; from hunger and fullness to mood and concentration, our intestinal metabolism is highly connected to our brain function by the vagus nerve, creating the “gut-brain axis”. Within these two organ systems are complex systems and structures that dictate everything we do, all day long. 

Research is now showing that what we eat has a major impact on our body as a whole, including feeding the microorganisms that live in our gut. One of the most important bodily functions, sleep, is highly correlated with healthy digestive health. 

During sleep, our body repairs and regenerates itself, the brain stores information, and toxic waste is filtered and sent to our digestive system to be excreted. Hence, when we don’t sleep enough or when our quality of sleep is poor, our digestive system feels it, too. Keep reading to learn the how and why of sleep and digestion, aka rest and digest, and what we can do to make sure we’re optimizing both systems, even when we’re dreaming. 

Sleep and Digestion, an Overview

Though we can’t feel a rumbling stomach or bloating when we’re fast asleep, our bodies are working extremely hard to process, absorb, and separate the nutrients and waste from the food we consumed during the day. Digestion is a process done by the parasympathetic nervous system, deemed the ‘rest and digest’ system because it functions optimally when our bodies are in a low stress state. 

New data strongly suggests that there are very specific consequences for digestive functioning and several gastrointestinal disorders that accompany lack of, poor quality, or short duration of sleep. Sleep affects our gut-brain axis, hormone regulation, and immune system, which all together have a large impact on how we digest and absorb the nutrients from our food. Scientists have now determined that sleep can affect how well the digestive system functions, and that digestive health plays a role in how well someone sleeps. The correlation between sleep and digestion is a two way street; furthermore, our gut microbiome are also affected. 

How Does Sleep Affect Our Gut? 

Inadequate sleep is known as sleep debt, or the amount of sleep needed to restore the body and its processes to baseline. Poor sleep, aka high sleep debt, is strongly correlated to poorer overall gut health, especially bloating and abdominal pain.  

Increased Cortisol: Hormone imbalance is a common consequence of not catching enough Z’s. When the stress hormone, cortisol, is out of balance, our intestinal permeability increases, letting out food and toxins from the intestine into the bloodstream and causing leaky gut. This leads to various health issues, including bloating, inflammation, stomach pains, and even changes in the gut microbiome. 

Poor Nutrition: Just like with a cortisol imbalance, hormones known as leptin and ghrelin, which are responsible for our hunger and fullness, can get a little out of whack. This leads to an increased appetite, particularly for sugary and high-fat foods, that our bodies crave for quick energy, satisfying taste, and fullness. These food choices directly correlate to poorer digestion, affecting our gut health in numerous ways. 

Lack of Melatonin: Many of us are familiar with melatonin and its use for helping us to fall asleep and stay asleep. Our bodies naturally make melatonin at bedtime, but its use is more than for just dozing off. Melatonin regulates gastrointestinal motility, or the smooth muscle contractions of our intestines that help to move food through our system. Without enough melatonin, our chances of bloating and abdominal discomfort drastically increase as food becomes stuck in our colons. 

Late-Night Snacking: While we’ve covered that overall nutrition is important for maintaining high sleep quality and a healthy digestive tract, the time at which we eat is significant, too. Research shows a negative correlation between late-night eating and sleep; simply put, the more full our stomachs are before sleep, the worse our sleep actually is. When our bodies are focused on digesting our food, the energy given to the natural sleep wind-down processes decreases; our sleep and our digestive system are both negatively affected. We should aim to eat our last meal two to three hours before bedtime to ensure a peaceful sleep and optimized digestion.

The Gut Microbiome 

The word “microbiome” refers to all microorganisms in or on our bodies as well as the genetic material they’re made up of. While the gut microbiome is tucked away deep in our digestive system, it impacts our entire body, and therefore, our sleep. New emerging research shows that the balance of these microbes may be the single most important factor in understanding gut health and its impact on the rest of our body. In fact, the Human Genome Project led scientists to discover that the genetic information in our microbiome may have a stronger influence on our health than the genes we inherited from our parents. These bacteria help us to digest food, control our immune system, and help us to control brain health, along with significantly impacting our sleep. 

Cortisol, mentioned above, also plays a role in dictating the balance of our gut bacteria. The most crucial measure of our gut health is how diverse these microbes are. The more kinds of ‘good’ bacteria we have, the more beneficial they will be to our digestion, and, therefore, overall health. Overall, a diverse gut flora helps us to better absorb nutrients and aids in improving bloating, cramping, diarrhea, and constipation. 

Melatonin, also touched on prior, aids in improving the good bacteria in the digestive tract. Melatonin is released through our Circadian Rhythm (read more on that here), and demonstrates the importance of a regular sleep pattern. When our sleep routine is altered, our hormones are unable to optimize digestion, leading to a negative impact on our gut bacteria. 

Sleep and Microbiome Diversity 

The gut microbiota and its metabolites regulate the bidirectional signaling of the gut-brain microbiome axis, which influences both sleep and circadian rhythm. A2019 study aimed to address the relationship between sleep physiology and the diversity of the gut microbiome. Researchers used a sleep analysis program to quantify sleep measures along with gut microbiome sampling to determine how these bacteria directly affect various measures of sleep physiology. The study found that total microbiome diversity was positively associated with increased sleep efficiency and total sleep time, and was negatively correlated with wake after sleep onset. This study shows that gut microbiome is involved in promoting better sleep, overall. 

Improving Sleep by Improving our Gut Health

So, now we know how important sleep is for our body, but also how affected it is by our gut, specifically the diversity of the bacteria in our digestive tract. While some of us may feel rested and refreshed every day, many of us struggle to consistently wake up without any morning grogginess. Using new research, we’re able to discern that what we eat can affect our gut in numerous ways, including our ever-so-important sleep. 

Diversify the Diet: Diet diversity is paramount to diversifying our gut and important for sustainable, healthy eating. Eating a diet rich in whole foods, like vegetables, fruits, whole grains and lean sources or protein, is a great way to promote long-term digestive wellness. 

Focus on Fiber: Fiber is great for keeping us regular, but it has major benefits when it comes to feeding the good bacteria and starving the bad. While the body itself can’t digest fiber, certain gut bacteria can; this promotes their growth and improves the ratio of good bacteria to bad. High fiber foods include berries, artichokes, leafy greens, lentils, and beans. 

Fermented Foods: Fermented foods are rich inlactobacilli, a beneficial type of gut bacteria. Yogurt, specifically Greek yogurt, has been found to enhance the function and composition of the microbiome. Other fermented foods include kimchi, sauerkraut, kefir, kombucha, and tempeh. 

Incorporate Whole Grains: Whole grains contain fiber and nondigestible carbohydrates, which make their way to the large intestine to promote the growth of good bacteria. Try adding in a serving of brown rice, quinoa, barley, or whole wheat pasta to your lunch and dinner meals to do your gut a big favor. 

There you have it! Our complex, highly interconnected body systems affect everything, especially sleep. Eating a diet rich in variety and whole foods benefits the balance and diversity of our gut microbiome, promoting better quality and longer duration of sleep, while promoting great digestive health, too. 


“How Lack of Sleep Can Affect Gut Health.”Henry Ford LiveWell, 

Robertson, Ruairi. “9 Ways to Improve Your Gut Bacteria, Based on Science.”Healthline, Healthline Media, 4 Aug. 2021, 

Smith RP, Easson C, Lyle SM, Kapoor R, Donnelly CP, Davidson EJ, et al. (2019) Gut microbiome diversity is associated with sleep physiology in humans. PLoS ONE 14(10): e0222394.

“The Surprising Link between Sleep and Digestion.”Reverie, Reverie - US, 

Serena Pratt

Serena Pratt

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