Can You Sleep Your Way to a Healthy Microbiome?

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There’s a bidirectional relationship between sleep quality and the gut microbiome. Poor sleep, like other stressors, can negatively affect the flora in our GI tract. When we don’t get enough rest, our sleep is interrupted, or our sleep cycle is out of sync with the light-dark cycle, our body can enter a state of stress.


This stress can lead to an imbalance in the gut microbiome, increasing the amount of harmful flora while decreasing the population of health-promoting microorganisms. In what becomes a vicious cycle, this imbalance in the gut can then bring on stress responses that can result in health issues ranging from sleep problems to weight management.


While the exact mechanisms underlying the connections between sleep and the gut microbiome remain a mystery, scientists have come to certain understandings. Read on for insights into what they do know, plus tips for bolstering your own sleep and health.

Sleep stress harms the gut microbiome

For a 2017 study, soldiers were exposed to four days of sleep restriction.1 Afterwards, their gut microbiomes changed in ways consistent with an unhealthy state. In a similar study, mice spent two weeks in total darkness, which completely disrupted their circadian rhythms. The result was an increase in the amount of the harmful bacteria, Clostridia, in their small intestines. 

The gut microbiome changes throughout the day

The two main types of gut microbiota, Bacteroidetes and Firmicutes, shift in quantity from day to night.2 During the active phase of the light: dark cycle, levels of bacteria are higher than during the inactive phase. Disrupting the day-light cycle (by placing experimental subjects in total darkness, for example) disrupts these natural oscillations. 

Flora diversity and certain varieties linked with better sleep

A more diverse microbiome is associated with more and better sleep. Plus, scientists have found a correlation between certain microorganisms and improved (or compromised) shuteye. For instance, having more Lactobacillaceae, Actinobacteria, Verrucomicrobia, and Lentisphaerae seems to be associated with higher quality sleep, whereas having more Lachnospiraceae, Corynebacterium, Bacteroides multiforme, Enterococci, and Ruminococcaceae appears to be linked with lower quality sleep.* By pinpointing the flora associated with ideal and non-ideal sleep, researchers hope to be able to devise medical solutions to sleep problems.

Poor sleep can compromise the gut barrier

When sleep quality is low, the GI lining can become more permeable. With a compromised barrier, harmful flora and their byproducts can enter the liver, pancreas, muscle, and fat, resulting in a state of inflammation. As scientists know, inflammation is associated with many health issues. 

The role of sleep hormones

Flora in the GI tract produce neurotransmitters that can positively impact sleep, including melatonin and gamma-aminobutyric acid (GABA). Melatonin, sometimes called the sleep hormone, is a key part of the body’s sleep-wake cycle, though its exact role remains unclear. Meanwhile, scientists know that activating GABA receptors favors sleep.

Boost your sleep

By improving your sleep, you’ll cultivate the health of your gut microbiome—and your entire body. Here are some tips to strengthen your shuteye.

Tweak your routine


  • Sleep seven to eight hours per night. To determine your bedtime, figure out what time you need to wake up, then work backwards. Always go to bed at the same time, even on the weekends.

  • Avoid caffeine, ideally within six hours of your chosen bedtime. Instead, towards the end of the day, sip on herbal tea (like calming chamomile) or even warm milk.

  • If you’re a napper, cap your session to 20 minutes. Any longer could affect your sleep.

  • Ideally, within one to two hours of your bedtime, do something relaxing, like reading, stretching, or calling a close friend. During this time, dim the lights, so your body knows it should prepare to segue to sleep mode. If you plan to use devices, wear blue light-blocking glasses or put your electronics in “night shift” mode.

  • If your feet tend to get cold while you sleep, wear cozy socks. Or, if you get really hot, think about buying cooling pajamas, sheets, and pillows.

  • When you wake up in the morning, immediately spend a few minutes outside to expose your body to sunlight and sync up with the light-dark cycle. Or, if you live in an area without lots of morning sunlight, try a 10,000-lux light therapy lamp.

Enhance your bedroom

  • Set the thermostat at a temperature between 60-67 degrees F, which experts deem ideal for sleep. 

  • Invest in a pillow that supports your sleeping position, such as side- or back-sleeping.

  • Place a nightlight in your hallway in case you need to use the bathroom in the middle of the night. Install blackout shades to block the morning light (or wear a comfortable eye mask). 

  • To drown out sirens or your noisy neighbors, rely on a sound machine. Don’t forget to turn off or silence your phone. 

  • If you can, don’t work in your bedroom. That way, you’ll associate your place of rest with sleep, sex, and relaxation, rather than stress.

  • During trips, request a hotel room away from the ice machine and elevator. If you don’t want to tote along a sound machine, use a white noise app on your phone. 

Probiotics might help

Researchers have found that taking probiotics, like Lactobacillus, Bifidobacterium, and Enterococcus, could help decrease the body’s stress response brought on by poor sleep*. If you’re experiencing sleep issues, consider asking your doctor or a naturopath whether these supplements could be right for you.


1 Karl, J.P. et al (2017). [Study on stress, intestinal permeability and changes in microbiome composition]. American Journal of Physiological Gastrointestinal Liver Physiology, PubMed. gov   

2 Liang, X. et al (2015). [Study on intestinal microbiota rhythmicity and regulation by gender and circadian clock]. 

Li, Y. et al. (2018). [Microbiome and insomnia, circadian disruption and mental health]. Frontiers in Psychiatry, Pubmed Central.

Smith, R.P. et al. (2019). [Gut microbiome diversity and sleep physiology]. PLoS One, PubMed Central.  

Karl, J.P. et al. (2017). [Intestinal microbiota changes and increased intestinal permeability in young adults under stress]. American Journal of Physiology, Gastrointestinal and Liver Physiology,

Pacheco, D. (2022). The Best Temperature for Sleep.

Suni, E. (2022). Melatonin and Sleep.

Gottesmann, C. (2002). [GABA and sleep]. Neuroscience,

Wu, G. (2022). [Cooling pajamas to help with night sweats].