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Insomnia: Is the cause in the gut?

August 12th, 2021  

Your gut may determine the quality of your sleep

We spend about a third of our lives asleep. Sleep is vital – it is as important to our bodies as eating, drinking and breathing. Getting enough sleep is essential for maintaining good mental and physical health. Sleep and relaxation is the body’s way of recharging and re-energising. We all probably know the feeling when we haven’t had enough sleep, we are tired, sluggish and somehow not fully present. The gut microbiome – the collection of trillions of microorganisms that live in your gut – not only has a huge impact on your overall health, but may also help determine how well you sleep. Let’s take a closer look at the link between the gut microbiome and sleep, as well as current research.

The gut microbiome influences the sleep-wake cycle

The microbial ecosystem can influence sleep and sleep-related physiological functions in a number of ways, including altering the body’s sleep-wake cycle and affecting the hormones that regulate sleep and wakefulness. In turn, the quality of our sleep can influence the health and diversity of our microbiome. (1)

There is a constant interaction between the gut and the brain, which means that a disturbance in either can affect sleep. The microbiome actually promotes the release of many of the neurotransmitters – including dopamine, serotonin and GABA – that help regulate mood and promote sleep. Studies show a strong link between microbiome imbalance and stress, anxiety and depression, which in turn can trigger or exacerbate sleep disorders. (2, 3)

Research also links gut health to pain perception. An unhealthy microbiome appears to increase sensitivity to visceral pain, which can then make it much more difficult to fall asleep and stay asleep. (4)

Sleep disturbances can be detrimental to gut health

Just as dysbiosis (imbalance of gut bacteria) can affect sleep, unhealthy sleep patterns can disrupt the gut microbiome. This is the case, for example, with the common sleep disorder, obstructive sleep apnoea. This involves shallow breathing and breathing pauses during sleep. Very often, people with obstructive sleep apnoea also snore. In one study, scientists subjected mice to a pattern of disturbed breathing that mimics the effects of obstructive sleep apnoea. They found that the mice that lived with periods of OSA-like breathing for six weeks showed significant changes in the diversity and composition of their microbiome. (5)

Gut health is also significantly related to hormones that influence sleep

The gut microbiome influences hormones responsible for sleep

Gut health is also significantly related to hormones that influence sleep. Melatonin, the “darkness hormone”, is essential for sleep and a healthy sleep-wake cycle. Melatonin is produced in both the gut and the brain, and evidence suggests that melatonin in the gut may operate on a different cyclical rhythm than pineal melatonin produced in the brain. (6)

In addition, cortisol is crucial to the sleep-wake cycle. (7) This hormone is central to the body’s stress and inflammatory response and affects gut permeability and microbial diversity. Rising cortisol levels very early in the day help to promote alertness, concentration and energy. Changes in cortisol that occur within the gut-brain axis are very likely to have an impact on sleep. (8)

Simply put, our gut affects how well we sleep, and sleep affects the health of our gut. By working on both fronts, we can vastly improve the quality of our sleep. With myBioma, you can easily find out if your gut microbiome is in balance and optimise your gut health with appropriate nutritional recommendations.

A closer look at the science of microbiome and sleep

A growing body of research now suggests that the gut’s vast and diverse microbial ecosystem has its own daily rhythms. These microbial rhythms appear to be deeply interwoven with circadian rhythms. (9)

A circadian rhythm, for example, refers to fluctuations in bodily functions that are controlled by exogenous (day-night changes) or endogenous (hormones) influences. Examples are fluctuations in heart rate, sleep-wake rhythm, blood pressure and body temperature. Research suggests that both circadian and microbial rhythms are capable of influencing and disrupting the other, with consequences for both health and sleep. (10)

Diet influences the gut microbiome

According to research, the rhythms of the microbiome are influenced by what and when we eat. A study with mice found that when mice ate a healthy diet, they produced more beneficial bacteria and that the collective activity of microbial life in the gut followed a daily – or diurnal – rhythm. (11, 12)

This rhythm, in turn, supported the animal’s circadian rhythms. Mice fed a high-fat, “Western” diet, on the other hand, produced less optimal microbial life. The bacteria in these mice did not adhere to a diurnal rhythm themselves and also sent out signals that disrupted the circadian rhythm. These mice gained weight and became obese, while the mice that ate a healthy diet did not.

A healthy diet supports the good gut bacteria

Scientists bred a third group of mice without a microbiome. Because they lacked a gut microbiome, there were no bacteria to send signals to the rest of their bodies. Circadian disruptions occurred in these mice, but they did not gain weight or suffer from metabolic disorders, even when fed the high-fat diet. This suggests some important conclusions. First, that microbial activity is key to normal circadian function and thus sleep. Second, that the microbiome, along with diet, plays a key role in regulating weight and metabolism.

Studies of sleep and the microbiome in humans

Research in humans has yielded similar results. The human microbiome appears to follow daily rhythms influenced by the timing of meals and the types of foods consumed, and it appears to exert effects on circadian rhythms. Research has also found that the relationship between these different biological rhythms works both ways. Scientists found that disruptions to circadian rhythms – the kind that occur due to jet lag, whether from actual travel or “social” jet lag – disrupt microbial rhythms and the health of the microbial ecosystem. (13) According to research, people who experience these changes in microbial rhythms as a result of circadian disruption suffer from metabolic imbalance, glucose intolerance and weight gain. (14)

The negative effects of disturbed sleep

We have known about the relationship between sleep, circadian rhythms and metabolic health for some time. Disrupted sleep and misaligned circadian rhythms are strongly associated with higher rates of obesity and with metabolic disorders including type 2 diabetes. This new knowledge about the microbiome and its relationship to circadian function may, in time, provide us with a deeper understanding of how health is affected by sleep and circadian activity. (15)

What helps to influence the microbiome and sleep in a positive way?

Although science continues to explore the complex interactions between the gut microbiome and sleep, the full implications of this relationship are not yet fully understood. What is certain is that the health of our gut impacts our overall well-being. When you begin to positively influence the ecosystem of your microbiome, you are taking a preventative measure to avoid discomfort. Whatever your sleep routine, there are ways you can support your sleep and your gut.

Start by positively supporting your microbiome, learn your status quo and get a complete gut check to improve your overall wellbeing afterwards. Start now with your individual microbiome analysis.


(1) Schwartz, J.R.L. and Roth, T. (2008). Neurophysiology of sleep and wakefulness: basic science and clinical implications. Current Neuropharmacology. 6:4, pp. 367-378. doi: 10.2174/157015908787386050

(2) Martin CR, Osadchiy V, Kalani A, Mayer EA. The Brain-Gut-Microbiome Axis. Cell Mol Gastroenterol Hepatol. 2018;6(2):133-148. Published 2018 Apr 12. doi:10.1016/j.jcmgh.2018.04.003

(3) IY Chen, DC Jarrin, H Ivers, A Rochefort, CM Morin, 0291 ASSOCIATION BETWEEN STRESS-INDUCED AROUSAL AND NOCTURNAL SLEEP, Sleep, Volume 40, Issue suppl_1, 28 April 2017, Pages A107–A108,

(4) Chichlowski M, Rudolph C. Visceral pain and gastrointestinal microbiome. J Neurogastroenterol Motil. 2015;21(2):172-181. doi:10.5056/jnm15025

(5) Moreno-Indias I, Torres M, Montserrat JM, Sanchez-Alcoholado L, Cardona F, Tinahones FJ, Gozal D, Poroyko VA, Navajas D, Queipo-Ortuño MI, Farré R. Intermittent hypoxia alters gut microbiota diversity in a mouse model of sleep apnoea. Eur Respir J. 2015 Apr;45(4):1055-65. doi: 10.1183/09031936.00184314. Epub 2014 Dec 23. PMID: 25537565.

(6) Mukherjee S, Maitra SK. Gut Melatonin in Vertebrates: Chronobiology and Physiology. Front Endocrinol (Lausanne). 2015 Jul 22;6:112. doi: 10.3389/fendo.2015.00112. PMID: 26257705; PMCID: PMC4510419.


(8) Foster JA, Rinaman L, Cryan JF. Stress & the gut-brain axis: Regulation by the microbiome. Neurobiol Stress. 2017 Mar 19;7:124-136. doi: 10.1016/j.ynstr.2017.03.001. PMID: 29276734; PMCID: PMC5736941.

(9) Gutierrez Lopez DE, Lashinger LM, Weinstock GM, Bray MS. Circadian rhythms and the gut microbiome synchronize the host’s metabolic response to diet. Cell Metab. 2021 May 4;33(5):873-887. doi: 10.1016/j.cmet.2021.03.015. Epub 2021 Mar 30. PMID: 33789092.



(12) Roberto Refinetti (2017) Western diet affects the murine circadian system possibly through the gastrointestinal microbiota, Biological Rhythm Research, 48:2, 287-296, DOI: 10.1080/09291016.2016.1254873

(13) Deaver JA, Eum SY, Toborek M. Circadian Disruption Changes Gut Microbiome Taxa and Functional Gene Composition. Front Microbiol. 2018 Apr 13;9:737. doi: 10.3389/fmicb.2018.00737. PMID: 29706947; PMCID: PMC5909328.

(14) Shu-Qun Shi, Tasneem S. Ansari, Owen P. Mcguinness, David H. Wasserman, Carl Hirschie Johnson. Circadian Disruption Leads to Insulin Resistance and ObesityCurrent Biology, 21 February 2013 DOI: 10.1016/j.cub.2013.01.048

(15) Bailey SM, Udoh US, Young ME. Circadian regulation of metabolism. J Endocrinol. 2014 Aug;222(2):R75-96. doi: 10.1530/JOE-14-0200. Epub 2014 Jun 13. PMID: 24928941; PMCID: PMC4109003.


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