How Your Gut Health Affects Your Sleep

Most people think of the gut and the brain as separate systems. One deals with food and digestion, the other with thoughts and feelings. But science tells a very different story. Your gut and your brain are constantly talking, and what happens in your digestive tract may be one of the most important (and overlooked) factors affecting how well you sleep.

In this comprehensive guide, we explore the emerging science of how gut health influences sleep. We’ll look at the gut-brain axis, neurotransmitters like serotonin and GABA, the role of circadian rhythms, and how things like diet, inflammation, and short-chain fatty acids all play a part. Importantly, everything here is based on real, peer-reviewed research — no pseudoscience, no guesswork.

Whether you’re struggling with insomnia, waking up at night, or simply want to understand your body better, this article will show how gut health can be the missing piece of your sleep puzzle.

What is the Gut-Brain Axis?

The gut-brain axis refers to the bidirectional communication system between the gastrointestinal tract and the brain. This isn’t metaphorical: it’s a physical, chemical, and biological feedback loop.

The vagus nerve is the key pathway connecting your gut to your brain. It relays information in both directions: from your intestines to your brainstem and vice versa. But the conversation doesn’t stop there. Hormones, cytokines (inflammatory signals), neurotransmitters, and bacterial metabolites all help mediate this dialogue.

Studies show that gut bacteria can influence everything from mood to cognition to pain perception. And now, there’s growing evidence they can directly affect your ability to fall asleep, stay asleep, and feel rested the next day.

One paper from King’s College London emphasised the link between the microbiome, emotion regulation, and stress resilience — all of which are tightly linked to sleep (source).

Neurotransmitters Made in the Gut

Your brain needs a number of neurotransmitters to sleep properly. Three of the most important are serotonin, GABA, and melatonin. All three are influenced — and in some cases directly produced — by gut microbes.

Serotonin

Most of your body’s serotonin is produced in the gut. Though serotonin itself cannot cross the blood-brain barrier, it helps regulate circadian rhythms, pain perception, and emotional balance. It’s also the chemical precursor to melatonin: your body’s key sleep hormone.

According to Sam Tejada, author of “How to Win in Modern Wellness,

“About 90% of serotonin, which converts into melatonin, is produced in the gut. If your gut is unhealthy, it’s difficult to absorb the nutrients from foods or supplements, and it can disrupt serotonin levels and, in turn, melatonin production"

A 2015 study in Cell found that certain strains of gut bacteria stimulate the production of serotonin in the gut’s enterochromaffin cells. This suggests that microbiome composition can directly impact sleep by modulating serotonin availability.

GABA

GABA (gamma-aminobutyric acid) is the brain’s main inhibitory neurotransmitter. It plays a calming role in the nervous system, reducing neuronal excitability and allowing the body to wind down. Some strains of Lactobacillus and Bifidobacterium produce GABA.

A review published in Frontiers in Neuroscience in 2020 identified multiple pathways by which gut bacteria influence GABA levels and proposed that microbiota-targeted interventions could one day serve as treatments for sleep disorders.

Melatonin

Melatonin is the hormone most directly responsible for controlling your sleep-wake cycle. Although it’s commonly associated with the pineal gland, far more melatonin is produced in the gastrointestinal tract — up to 400 times more.

A 2013 article in the World Journal of Gastroenterology argued that gut-derived melatonin plays a central role in not only gastrointestinal function, but sleep regulation more broadly.

Gut Microbes and the Circadian Clock

Circadian rhythms are 24-hour biological cycles that govern everything from hormone secretion to temperature regulation to alertness. These rhythms are influenced by environmental cues like light, but also by internal signals, including gut bacteria.

The human microbiome itself follows a circadian rhythm. The relative abundance of different bacterial species shifts throughout the day. When this rhythm becomes misaligned, as it can during jet lag, shift work, or sleep deprivation, it may contribute to insomnia and metabolic dysfunction.

A 2019 review in Sleep Medicine Reviews found that microbiota rhythms and host circadian rhythms are closely linked, with each influencing the other. Disruption in one can disturb the other, leading to chronic sleep problems.

Short-Chain Fatty Acids and Sleep

Short-chain fatty acids (SCFAs) — including butyrate, acetate, and propionate — are produced when gut bacteria ferment dietary fibre in the colon. SCFAs are involved in a wide range of biological functions, including inflammation reduction, blood sugar regulation, and, crucially, brain function.

Animal studies have shown that SCFAs can influence brain activity and promote restorative sleep. In a 2020 study published in Scientific Reports, mice fed a diet that increased SCFA production experienced deeper and longer sleep.

Butyrate in particular has neuroprotective properties. It supports the blood-brain barrier, reduces systemic inflammation, and appears to enhance slow-wave sleep — the deepest, most restorative stage.

Diet Patterns That Improve Gut Health and Sleep

Studies have linked diets rich in polyphenols with better sleep

Diet is one of the most important levers you can pull to improve gut health. And by doing so, you may significantly improve sleep quality.

Fibre-Rich Diets

Fibre is the number one nutrient for nurturing healthy gut bacteria. The NHS recommends 30g of fibre per day for adults. High-fibre diets increase microbial diversity and promote SCFA production, both of which are tied to better sleep.

A 2016 study in the Journal of Clinical Sleep Medicine found that higher fibre intake was associated with more time spent in slow-wave sleep.

Fermented Foods

Fermented foods like kefir, sauerkraut, yoghurt, and kimchi introduce live probiotic strains into the gut. These strains can enhance microbial diversity and help rebalance an unhealthy microbiome.

A 2019 paper in Frontiers in Psychiatry reported that probiotics may improve sleep quality, particularly in individuals with mild to moderate anxiety or stress (source).

Polyphenol-Rich Foods

Polyphenols, plant compounds found in berries, tea, cocoa, and olive oil, act as prebiotics and promote the growth of beneficial gut bacteria. A 2020 review in Nutrients linked polyphenol intake with improved gut health and sleep outcomes, particularly via reduced inflammation.

Poor Sleep Worsens Gut Health: A Two-Way Street

It’s important to understand that the relationship between gut health and sleep goes both ways. Poor sleep doesn’t just result from gut issues — it can also cause them.

Sleep deprivation has been shown to reduce microbial diversity, increase intestinal permeability ("leaky gut"), and promote inflammation. A 2019 study in Molecular Metabolism showed that partial sleep restriction caused significant changes in the gut microbiome within just two nights.

These changes may then feed back into mood, appetite, and immune function, creating a vicious cycle of poor sleep and worse gut health.

Special Populations: Gut-Sleep Links in Real Life

Menopause

Hormonal fluctuations during perimenopause and menopause are associated with both gut dysbiosis and sleep disturbances. Oestrogen plays a regulatory role in maintaining gut barrier function and microbial balance, while its decline contributes to insomnia and hot flashes.

Improving gut health during this period may help buffer some of the hormonal impacts on sleep. For more, see our guide on menopause and sleep problems.

Irritable Bowel Syndrome (IBS)

People with IBS frequently report poor sleep quality. In fact, there’s growing evidence that insomnia can worsen IBS symptoms, and vice versa. The use of probiotics and gut-directed hypnotherapy has shown promise in improving both gut symptoms and sleep.

Athletes and High Performers

People undergoing intense physical training often experience disruptions in both gut health and sleep. Heavy exercise increases gut permeability and inflammation. Combined with early training sessions, caffeine use, or travel, this can lead to disturbed sleep.

Nutrition strategies that support the gut (e.g. adequate fibre, resistant starches, probiotics) may improve sleep recovery in this population.

Do Gut Supplements Really Help You Sleep?

With the growing awareness of the gut-sleep connection, many people are turning to supplements. These include:

• Probiotics (live bacteria)

• Prebiotics (fibres that feed good bacteria)

• Synbiotics (a mix of both)

Some studies have found that probiotics can reduce cortisol, improve mood, and shorten sleep onset latency — the time it takes to fall asleep.

That said, supplements should never replace whole food strategies. They can be a helpful addition, especially if chosen based on specific strains. For example, Lactobacillus rhamnosus and Bifidobacterium longum are two strains studied in the context of stress and sleep improvement.

Conclusion: Feed Your Gut, Rest Your Brain

The connection between gut health and sleep is complex, but increasingly clear. Your microbiome affects how you feel, think, and sleep, and in turn, your sleep patterns influence your gut.

Improving your sleep doesn’t always mean taking a sleeping pill or adjusting your pillow. It might mean adjusting your diet, boosting your fibre intake, and adding more fermented foods to your plate.

When in doubt, support your gut. It just might help you sleep better tonight.