Does Your Gut Know What Time It Is?

By Stephanie Rubino, ND

Are tossing and turning keeping you up at night? A restful night’s sleep is the foundation for an active and productive day, giving the mind and body time to rest and recuperate. However, studies indicate 6% to 48% of Canadians experience different levels of insomnia, and from 2007 to 2015, symptoms of insomnia increased by 42% among Canadians 18 years and older. [1]

Moreover, the impact on sleep quality because of the COVID-19 pandemic has been widespread. A 2020 study by the University of Southampton found that the number of people suffering from sleep problems rose from one in six to one in four, while another study revealed Canadians, especially females, experienced lowered sleep quality and efficiency and greater symptoms of insomnia. [2,3]

Sleep disruptions influence our physical and mental health and can be the result of factors such as stress, hormonal imbalance, irregular work schedules, and poor sleep habits. Lesser known is the relationship between sleep quality and the gut microbiota.

About the gut

The gut is home to a community of trillions of micro-organisms such as bacteria, viruses, and fungi, collectively known as the gut microbiota. Research continues to unravel the microbiota’s role in health, but we do know that this organ is involved in producing digestive enzymes, supporting immune function, synthesizing certain nutrients, reducing infection risk, and maintaining the integrity of the intestinal barrier. [4]

The microbiota also plays an important role in the gut-brain axis – the two-way communication between the enteric (intestinal) and central nervous systems. Through this connection, the brain can impact intestinal activities and the gut can impact mood, cognition, brain development, sleep, and the circadian rhythm. [5–7] The intestinal microbiota can regulate brain function through immunoregulatory, neuroendocrine, and vagus nerve pathways. [8]

How does the microbiota influence sleep?

Although the mechanisms are still unclear, it appears that changes in the microbiota and the intestinal barrier are associated with sleep disturbances. [7] In one study, mice were treated with a cocktail of antibiotics that depleted gut microbes. [9] Researchers found differences in more than 200 metabolites between the groups, and the pathways involved in making neurotransmitters were most impacted by the antibiotic treatment. Mice with depleted microbiota were not able to make serotonin, an important chemical that supports functions such as mood, sleep, and digestion. It is well-known that gut bacteria produce about 95% of the body’s serotonin supply. [10] Deficiency in vitamin B6 metabolites needed for serotonin and dopamine production, and frequent switching between sleep-wake stages, were also noted in the microbiota-depleted mice.

It has also been suggested that disruptions in the circadian rhythm and loss of sleep because of stress and other factors can cause changes in the microbiota, leading to inflammation, metabolic disorders, and concerns with immune function. [8,11] As a result, this can cause changes in neurotransmitter metabolism resulting in impaired nervous system function and sleep problems. [8]

Get a restful night’s sleep

For better sleep, it’s important to support the gut microbiota and the nervous system. Changing the gut microbiota with the consumption of probiotics and prebiotics may help to improve sleep quality. [12,13] One of the most clinically researched probiotic strains, Bifidobacterium longum subsp. longum BB536 has been shown to provide consistent health benefits. [14] With a proven safety record, this clinically effective strain is bioavailable and stable and has been shown to restore gut microbiota balance, alleviate gastrointestinal disorders, and modulate immune function. Bifidobacterium longum subsp. longum BB536 is in 3 Brains The Gut-Brain Strain.

Healthy sleep promotion can also be achieved with sedative herbs, such as passionflower, California poppy, skullcap, and linden, which can be found in 3 Brains Restful Sleep. By reducing anxiety and/or relieving pain, these traditional herbs help promote calmness to support better sleep and can work synergistically with probiotics to support gut health so you can sleep without tossing and turning.

Stephanie Rubino, ND, is a licensed naturopathic doctor, mom, and trusted health educator who strives to guide her patients and other health enthusiasts to achieve their optimal health.     


  1. Chaput JP, Yau J, Rao DP, et al. Prevalence of insomnia for Canadians aged 6 to 79. Health Rep. 2018; 29(12):16-20.
  • Falkingham JC, Evandrou M, Qin M, et al. Prospective longitudinal study of ‘Sleepless in Lockdown’: Unpacking differences in sleep loss during the coronavirus pandemic in the UK. BMJ Open. 2022; 12(1):e053094.
  • Guadagni V, Umilta’ A, Iaria G. Sleep quality, empathy, and mood during the isolation period of the COVID-19 pandemic in the Canadian population: Females and women suffered the most. Front Glob Womens Health. 2020; 1:585938.
  • Hemalatha, R. Diet and gut microbiota in human health. Proc. Indian National Sci. Acad. 2016; 82.
  • Appleton J. The gut-brain axis: Influence of microbiota on mood and mental health. Integr Med (Encinitas). 2018; 17(4):28-32.
  • Smith RP, Easson C, Lyle SM, et al. Gut microbiome diversity is associated with sleep physiology in humans. PLoS One. 2019; 14(10):e0222394.
  • Neroni B, Evangelisti M, Radocchia G, et al. Relationship between sleep disorders and gut dysbiosis: What affects what? Sleep Med. 2021; 87:1-7. 
  • Li Y, Hao Y, Fan F, et al. The role of microbiome in insomnia, circadian disturbance and depression. Front Psychiatry. 2018; 9:669.
  • Ogawa Y, Miyoshi C, Obana N, et al. Gut microbiota depletion by chronic antibiotic treatment alters the sleep/wake architecture and sleep EEG power spectra in mice. Sci Rep. 2020; 10(1):19554.
  1. Terry N, Margolis KG. Serotonergic mechanisms regulating the GI tract: Experimental evidence and therapeutic relevance. Handb Exp Pharmacol. 2017; 239:319-42.
  1. Wang Z, Chen WH, Li SX, et al. Gut microbiota modulates the inflammatory response and cognitive impairment induced by sleep deprivation. Mol Psychiatry. 2021; 26(11):6277-92. 
  1. Marotta A, Sarno E, Del Casale A, et al. Effects of probiotics on cognitive reactivity, mood, and sleep quality. Front Psychiatry. 2019; 10:164.
  1. Bowers SJ, Summa KC, Thompson RS, et al. A prebiotic diet alters the fecal microbiome and improves sleep in response to sleep disruption in rats. Front Neurosci. 2022; 16:889211.
  1. Wong CB, Odamaki T, Xiao JZ. Beneficial effects of Bifidobacterium longum subsp. longum BB536 on human health: Modulation of gut microbiome as the principal action. Journal of Functional Foods. 2019; 54:506-19.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s