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Are You Having Trouble Sleeping?: Learn About The Surprising Link Between Your Gut Microbiome and Sleep Disorders

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Are You Having Trouble Sleeping?: Learn About The Surprising Link Between Your Gut Microbiome and Sleep Disorders

An estimated 50-70 million people are affected by sleep disorders, most commonly including insomnia, sleep apnea, and narcolepsy. Science has begun to uncover a connection between sleep disorders and the microbiome, opening a new avenue to explore the comprehensive management of disordered sleeping patterns. What role does dysbiosis have in promoting poorer sleep quality? Read on to find out.


What Are Sleep Disorders?

Sleep disorders encompass a diverse range of conditions that disrupt the normal sleep pattern, affecting the quality and duration of restorative sleep. There are more than 80 types of sleep disorders, the most prevalent type being insomnia, characterized by difficulty falling asleep or staying asleep. Sleep apnea, another common condition, involves interruptions in breathing during sleep, resulting in recurrent awakenings and decreased oxygen levels. Circadian rhythm disorders disrupt the body's internal clock, causing misalignment between sleep-wake cycles and external time cues. Symptoms of sleep disorders can manifest as excessive daytime sleepiness, irritability, difficulty concentrating, and mood disturbances. Furthermore, the long-term health consequences of poor sleep are irrefutable and include an increased risk for cardiometabolic dysfunction, cognitive decline, and death. (28

Traditional approaches to diagnosing these disorders involve thorough medical histories, sleep assessments, and polysomnography (sleep study), which records physiological data during sleep to aid diagnosis. Management strategies often include lifestyle modifications, such as improved sleep hygiene and behavioral therapy, alongside medical interventions like prescription medications or continuous positive airway pressure (CPAP) therapy for sleep apnea. Addressing sleep disorders requires a comprehensive and individualized approach to improve overall sleep quality and mitigate associated health risks. (28

The Gut Microbiome Explained

The gut microbiome refers to the ecosystem of microorganisms, including bacteria, viruses, fungi, and archaea, that reside within the gastrointestinal tract. A diverse and balanced community of microorganisms characterizes a healthy gut microbiome. Key elements of a healthy gut microbiome include microbial diversity, balanced proportions of different species, the presence of beneficial microbes like Bifidobacterium and Lactobacillus, and the absence of pathogenic microbes. (27)

Microbiome research developments have continued expanding our understanding of the benefits of a healthy gut microbiome for the host. Beyond its primary function in aiding digestion and nutrient absorption, the microbiome synthesizes essential compounds, such as short-chain fatty acids and neurotransmitters, influencing both gut and brain function. This microbial community actively regulates the immune system, helping distinguish between harmful pathogens and beneficial microbes. Moreover, the gut microbiome contributes to the maintenance of the intestinal barrier, preventing the entry of harmful substances into the bloodstream and thereby supporting overall gut integrity. Studies indicate that a diverse and balanced gut microbiome is associated with improved metabolic processes, including the regulation of hormones involved in appetite control. Additionally, emerging research suggests that the gut microbiome may play a role in modulating inflammation, impacting various aspects of human health. (9, 17

Dysbiosis refers to a change in the composition of the microbiota, whether it be a loss of beneficial bacteria, an overgrowth in opportunistic organisms, or a loss of overall microbial diversity. Factors influencing the gut microbiome to perpetuate dysbiosis include diet and other lifestyle habits, stress, and medication usage. Understanding the multiple hats the gut microbiota wears to enhance human health, it should be no surprise that gut dysbiosis has been associated with gastrointestinal, dermatologic, cardiovascular, renal, and other chronic diseases. (12, 27

Linking the Microbiome to Sleep Disorders

The gut microbiome plays a crucial role in sleep physiology through its intricate interaction with the gut-brain axis, a bidirectional communication pathway linking the central nervous system and the gastrointestinal tract. This dynamic relationship involves the exchange of signals, neurotransmitters, and immune system modulators, collectively influencing various physiological processes, including sleep. The gut microbiome produces many neuroactive and immunomodulatory molecules, such as short-chain fatty acids and neurotransmitters, which can influence brain function. For instance, the gut microbiota synthesizes 95% of the body's serotonin, which affects mood and sleep. 

Reduced microbial diversity and marked changes in the gut microbiota composition have been associated with conditions such as obstructive sleep apnea (OSA) and insomnia. Studies have reported alterations in the gut microbiome in individuals with OSA, including changes in the abundance of specific bacterial taxa. For instance, a 2023 study found that the severity of OSA correlated with differences in the structure and composition of the fecal microbiome, with distinct bacterial taxa associated with intestinal barrier damage and other metabolic markers.

Similarly, insomnia has been linked to changes in gut microbiota composition. Studies have observed decreased microbial diversity in individuals with chronic insomnia, with specific shifts in the abundance of bacterial phyla, including an increase in Bacteroidetes. Additionally, a 2022 analysis identified significant differences in the composition and structure of gut microbiota and metabolism in insomnia patients compared to healthy controls, revealing potential microbial and metabolic markers associated with insomnia. (29

These findings underscore the intricate connections between the gut microbiome, neurotransmitter synthesis, and sleep regulation. Maintaining a balanced and diverse gut microbiome may promote healthy sleep patterns and offer avenues for potential interventions in addressing sleep disorders.

Functional Medicine Labs for Sleep Disorders

Functional medicine labs can facilitate diagnosing microbiome-related sleep issues. Along with the patient's medical history, these lab results help to customize treatment plans that address microbiome-related sleep issues.

Sleep Study

A sleep study is the gold standard evaluation method for sleep disorders. Performed in a medical center or at home, a patient's brain waves, oxygen levels, heart rate, respiratory rate, and eye and leg movements are monitored overnight while they sleep. This test helps to detect why and the extent to which sleep is disrupted. (26


Cortisol and melatonin are hormones produced by the adrenal glands and the pineal gland, respectively, and their secretion patterns are tightly regulated in response to the circadian rhythm, the body's internal 24-hour clock. Cortisol is often referred to as the body's "stress hormone." Its secretion follows a diurnal pattern, peaking in the early morning, shortly after waking, and gradually declining throughout the day. This cortisol awakening response is a natural part of the circadian rhythm and helps prepare the body for the day's activities. In contrast, melatonin is often called the "sleep hormone." Melatonin production is influenced by the absence of light, typically increasing in the evening as it gets dark and reaching its peak during the night to promote sleep.

Cortisol and melatonin have an inverse relationship, meaning one is suppressed when the other is elevated. Cortisol levels decrease in the evening as melatonin levels rise, preparing the body for sleep. This intricate dance between cortisol and melatonin helps synchronize the body's internal clock with the external light-dark cycle, ensuring optimal functioning and appropriate responses to the environment. Disruptions in this cortisol-melatonin relationship can occur with irregular sleep patterns, shift work, or exposure to artificial light at night, potentially leading to sleep disturbances and circadian rhythm disorders. Understanding and maintaining the balance between cortisol and melatonin secretion is crucial for promoting healthy sleep. The Sleep and Stress Panel by Ayumetrix provides a thorough assessment of cortisol and melatonin levels throughout the day.

Stool Testing

A comprehensive stool test, like the GI-MAP + Zonulin test by Diagnostic Solutions and the GI Effects® Comprehensive Profile from Genova Diagnostics, evaluates the functional health of the gastrointestinal system to assess the extent to which digestion, absorption, inflammation, immune function, and gut microbiome disturbances may contribute to disordered sleep patterns.

Diet, Probiotics, and Sleep Quality

Maintaining a healthy gut microbiome through dietary choices and incorporating probiotics can positively impact sleep quality. Dietary recommendations to support a healthy gut microbiome and, by extension, improve sleep quality include consuming a variety of fruits, vegetables, whole grains, and legumes. These fiber-rich foods serve as prebiotics, nourishing the beneficial microbes in the gut. Additionally, fermented foods like yogurt, kefir, sauerkraut, and kimchi introduce live beneficial bacteria (probiotics) to the digestive system. Studies indicate that adherence to the Mediterranean diet may be linked to better sleep (29). (21

Understanding the nuances of how the gut microbiome influences sleep opens new avenues for potential interventions in managing sleep disorders. Researchers are exploring the use of probiotics to modulate the gut microbiota in ways that could positively impact sleep quality. While the mechanisms are still being elucidated, some studies have indicated that regular consumption of probiotics may contribute to improvements in sleep latency, quality, and duration by shifting the balance of the microbiome. The majority of these studies have used various species of Lactobacillus and Bifidobacterium. (5, 16, 24, 34)

Lifestyle Modifications for Microbiome Health

Making lifestyle changes can positively influence the gut microbiome and, in turn, promote better sleep health. In addition to adopting healthy dietary patterns to support the gut microbiome, as discussed above, here are some tips for optimizing sleep:


Regular exercise has been consistently associated with improved sleep quality and positively impacting the gut microbiome. Exercise has been shown to regulate circadian rhythms, enhance mood, and reduce stress and anxiety—factors that contribute to a more conducive sleep environment. Moreover, studies suggest that regular physical activity can positively influence the composition and diversity of the gut microbiome. (13, 22

Stress Management

Chronic stress can disrupt the balance of the gut microbiota and interfere with deep sleep. Incorporate stress-reduction techniques such as meditation, deep breathing exercises, yoga, or mindfulness practices into your daily routine. (32)

Sleep Hygiene

Maintain a regular sleep routine by going to bed and waking up at the same time each day, even on weekends. Consistency helps regulate circadian rhythms and supports a healthy sleep-wake cycle. Wind down before bedtime with calming activities such as reading, gentle stretching, or a warm bath; this signals your body that it's time to prepare for sleep. Make your bedroom conducive to sleep by keeping it dark, quiet, and cool. Invest in a comfortable mattress and pillows to enhance sleep quality. Reduce consumption of caffeine and alcohol, especially in the hours leading up to bedtime; these substances can interfere with sleep patterns and the gut microbiome. (1, 14, 25)

Integrative Treatment Approaches

Integrative and holistic approaches for addressing sleep disorders often consider the interconnectedness of various factors, including microbiome health. Here are several additional complementary and integrative approaches to supporting sleep:

Botanical Medicine

Valerian has been traditionally used to promote relaxation and alleviate insomnia. It may influence the GABA receptors in the brain, contributing to a calming effect.

Chamomile tea is known for its mild sedative properties, promoting relaxation and aiding sleep.

Lavender aromatherapy or essential oil may have calming effects, potentially reducing anxiety and improving sleep quality.


Acupuncture, a key component of traditional Chinese medicine (TCM), involves the insertion of thin needles into specific points on the body. Some studies suggest that acupuncture may help regulate the circadian rhythm, modulate stress, and improve sleep quality by influencing the release of neurotransmitters. (2, 3


Your Gut Microbiome and Sleep Disorders: Key Takeaways

Understanding the intricate link between the gut microbiome and sleep disorders is important for fostering a comprehensive approach to managing sleep-related issues. The bidirectional communication of the microbiota-gut-brain axis underscores the influence of gut microbes on sleep physiology and vice versa. The gut microbiome actively synthesizes neurotransmitters, hormones, and bioactive compounds that regulate sleep. Research indicates that dysbiosis in the gut, characterized by imbalances in microbial diversity and composition, is associated with sleep disorders. By recognizing and addressing the impact of the gut microbiome on sleep, individuals and healthcare professionals can explore holistic interventions, including dietary modifications, probiotics, and lifestyle changes, to complement traditional approaches to sleep disorder management.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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