Insomnia: Circadian Rhythms & The Gut Microbiome

 In Insomnia/Sleep Medicine

Yasaman Tasalloti, ND


With about 60 million Americans affected each year by insomnia and an estimated 8.5 million taking sleep medications, there is clearly a need for a slightly different therapeutic approach to this health concern. As the incidence of chronic conditions increases, the gut microbiome is becoming the center stage in terms of its contributions to the onset and/or progression of these disorders. As for sleep, we have learned much over time about circadian rhythms and our sleep/wake cycle. Newer research has focused on the rhythm of the microbiome, the patterns of the estimated 100-trillion microbes that reside within our bodies, and how they affect our circadian rhythms, including sleep.

The Microbiome & Circadian Rhythms

The human body is an extremely intelligent, intricately designed organism. From the microscopic cell to the organ systems, there is a distinct organization, consistent communication, and continual feedback occurring to maintain the body’s homeostasis. The gut microbiota contribute to this homeostasis by performing a wide variety of physiological functions, ranging from energy production and immune modulation to production of nutrients, hormones, and neurotransmitters.

Researchers have demonstrated a bidirectional relationship between circadian rhythms and the microbiome; for example, disturbance of circadian rhythms, such as with jet lag, has been found to disrupt the gut microbiota including their diversity.1 Circadian rhythms have been hypothesized to impact gut motility, liver detoxification, and nutrient transport. When either the circadian rhythm or microbiome rhythm is disrupted, glucose intolerance, weight gain, and metabolic changes can occur.

Fascinating research has shown that gut microbes do not remain in the same position all day long; rather, they migrate throughout the day.2 The microbiome rhythm can be influenced in a few ways: by the time of day we eat, by the types of foods that we eat, and by our circadian rhythm itself.3 Being consistent in our daily habits and engaging in healthy choices help to maintain a well-regulated circadian rhythm.

The Microbiome & Neurotransmitters

A neurotransmitter that significantly contributes to healthy sleep patterns is serotonin. We have learned that at least 80% of serotonin is actually produced by the gut bacteria (specifically Streptococcus, Escherichia, and Enterococcus strains4). Serotonin influences the sleep/wake cycle in 2 ways: First, it contributes to optimal sleep patterns via its conversion to melatonin. Secondly, it regulates mood by alleviating anxiety or depression, either of which can prevent an individual from falling or staying asleep. High stress levels can lower serotonin levels and produce sleep disruption. Another neurotransmitter produced by the gut bacteria is gamma-aminobutyric acid (GABA). Its anxiolytic and relaxant effects promote optimal sleep by decreasing beta brain waves and increasing alpha brain waves.5

The Microbiome & Cytokines

As we have learned, much of our immune system resides in our digestive tract. Gut bacteria can influence sleep by inducing immune signaling molecules, called cytokines, by T-cells and macrophages. In his review article, Krueger cites research in which the injection of tumor necrosis factor (TNF) or interleukin (IL)-1 in animals and humans was shown to increase non-REM sleep.6 In his book, Brain Maker, Dr David Perlmutter elaborates on these effects of cytokines such as TNFα, IL-1β, and IL-187:

Cytokines essentially have circadian cycles dictated by gut bacteria. When cortisol levels go up in the morning, the gut bacteria inhibit production of cytokines, and this shift defines the transition between non-REM and REM sleep. Hence, disruption of the gut bacteria can have significant negative effects on sleep and circadian rhythms. Balance the gut, break through the insomnia. (Perlmutter, 2015)

Activation of inflammatory cytokines such as IL-6 can disrupt sleep patterns; in turn, sleep disruption can increase these cytokines, leading to fatigue and further sleep disruption. Sleep deprivation increases risk of infections and promotes the development of chronic diseases, such as inflammatory bowel disease and colon cancer.8 An important neurohormone, melatonin, has been found to increase levels of IL-10 (anti-inflammatory) and decrease levels of pro-inflammatory cytokines.8

Clinical Application

To conclude, our circadian rhythm and the microbiome’s rhythm have a bi-directional relationship. Maintaining healthy gut microbiota is necessary for regulating cortisol levels, producing key neurotransmitters for sleep, and regulating the circadian rhythm itself. Disrupting the circadian rhythm can, in turn, contribute to intestinal dysbiosis. To ensure successful treatment of insomnia, a well-rounded approach, including nutrient and mineral repletion and lifestyle modifications, is essential. Herbal and homeopathic medicines have also been shown to effectively modulate the nervous system response.

Strategies for Optimal Sleep

  • Address abnormal intestinal permeability and dysbiosis
    • Eat foods rich in probiotics and prebiotics
    • Take a prebiotic and probiotic supplement
    • Employ strategic supplementation to address both digestive and nervous systems
  • Sleep hygiene
    • Sleep in a completely dark room
    • Set the bedroom temperature to 60-68°F
      • I cannot tell you how many patients of mine have noticed a significant impact by this single lifestyle modification
    • Eliminate Wi-Fi in the bedroom (put cell phones in airplane mode, or turn off the Wi-Fi before sleep)
    • Dim the lights at home in the evening
  • Movement
    • Exercise increases serotonin levels9
    • Exercise can increase the diversity of gut microbes10
  • Create daily routines
    • Having an erratic schedule can create both mental and physical disturbances. Start the day with a morning ritual of self-care, and end the day on a peaceful note with meditation, prayer, and/or relaxing music.
  • Daily mindset practice
    • Resolve any past emotional traumas
    • Manage counterproductive thoughts throughout the day with effective strategies
    • Practice positivity and gratitude in every moment


  1. Rosselot AE, Hong CI, Moore SR. Rhythm and bugs: circadian clocks, gut microbiota, and enteric infections. Curr Opin Gastroenterol. 2016;32(1):7-11. 
  2. Thaiss CA, Levy M, Korem T, et al. Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations. Cell. 2016;167(6):1495-1510.e12.
  3. Asher G, Sassone-Corsi P. Time for food: the intimate interplay between nutrition, metabolism, and the circadian clock. Cell. 2015;161(1):84-92.
  4. Galland L. The gut microbiome and the brain. J Med Food. 2014;17(12):1261-1272.
  5. Abdou AM, Higashiguchi S, Horie K, et al. Relaxation and immunity enhancement effects of gamma-aminobutyric acid (GABA) administration in humans. Biofactors. 2006;26(3):201-208.
  6. Krueger JM. The role of cytokines in sleep regulation. Curr Pharm Des. 2008;14(32): 3408-3416.
  7. Perlmutter D, Loberg K. Brain Maker. New York, NY: iBooks; 2015.
  8. Ali T, Choe J, Awab A, et al. Sleep, immunity and inflammation in gastrointestinal disorders. World J Gastroenterol. 2013;19(48):9231-9239.
  9. Young SN. How to increase serotonin in the human brain without drugs. J Psychiatry Neurosci. 2007;32(6):394-399.
  10. Monda V, Villano I, Messina A, et al. Exercise Modifies the Gut Microbiota with Positive Health Effects. Oxid Med Cell Longev. 2017;2017:3831972.
Image Copyright: <a href=’′>tab1962 / 123RF Stock Photo</a>

Yasaman Tasalloti, ND, graduated in 2015 from SCNM in Tempe, AZ. Dr Tasalloti’s background is working with patients experiencing mental health disorders, such as panic attacks, depression, and ADHD. She knows firsthand how quickly the brain can become impacted by lifestyle and environmental factors. By providing individualized care and addressing the underlying cause of disease, she achieves great results with her patients. She firmly believes it is possible for every patient to achieve his or her greatest level of health, given the appropriate treatment options and the patient’s willingness to fully take part in their health journey. Website:

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