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How Poor Sleep Can Affect Your Gut Health

If you’ve ever spent the night tossing and turning, you already know how you’ll feel the next day—tired, cranky, and probably not at all like your best self. While the occasional restless night shouldn’t cause too much trouble, chronic sleep deprivation can drain your mental abilities and put your physical health at risk.

Why Is Sleep Important?

Sleep is an essential function. It lets your body and mind rest and recharge, leaving you refreshed and alert. However, shortchanging the amount of shuteye you get can impair your ability to think clearly. This make sense since, as you sleep, your brain consolidates memories,  clears toxic waste, and performs essential maintenance to support healthy brain function.1 Routinely getting a good night’s sleep also helps your body stay healthy and fight off disease.2,3 Although experts recommend getting seven to nine hours of sleep a night, studies show that people who regularly get fewer than six hours are at higher risk for diabetes, heart disease, and stroke.4,5 Skimping on the sleep also makes it more likely that you’ll gain weight, thanks in part to higher levels of the stress hormone cortisol.6,7

How Does Sleep Affect Your Gut Health?

The fact that poor sleep can affect your cognitive, cardiovascular, and immune health may not be surprising. But how does sleep impact your gut?

Your body has a 24-hour clock that determines when you wake up and when you sleep. It also regulates many processes in your body, including  your metabolism.8 Research shows that your gut bacteria heavily influences how well your body’s clock works. This same research found that the shift between day and night doesn’t just affect your circadian rhythm, but the rhythm of the gut microbes whose activities depend on your schedule.  Things like jet lag or working the night shift can also disrupt your microbiota, eventually changing the patterns and diversity of the microbes in your gut.9

Even one night of poor sleep can reduce your gut’s bacterial diversity, decreasing beneficial bacteria (like those producing anti-inflammatory short-chain fatty acids, commonly called SCFAs), and increasing potentially harmful, pro-inflammatory microbes, leading to gut barrier issues, inflammation, and a weakened immune response. These changes are all mediated through the gut-brain axis.10

 Guard Your Gut

Even if you prioritize sleep, there will be nights (or maybe several) when those zzzz’s are elusive. Fortifying your microbiome with a clinically-studied probiotic can help guard against the damage that stems from both occasional and chronic sleep problems.

When choosing a probiotic, look for a product that lists the full names of its bacterial strains (genus, species, and strain code), since benefits are very strain-specific and you want types that have been studied in people for gut and immune health.11 A shelf-stable formula that contains well-researched strains, such as Lactobacillus and Bifidobacterium species, will also be more likely to support overall diversity.12 Rather than chasing high CFUs, check that the label guarantees live bacteria through the product’s expiration date. For optimal results, remember that pairing your probiotic with a prebiotic supplement or a diet rich in fiber will give those beneficial microbes the food they need to thrive.

Good sleep and gut health support each other in a helpful cycle: when you sleep well and keep a regular schedule, your body’s internal clock helps guide the timing of digestion, hormone release, and microbial activity in your intestines. This, in turn, can support a more stable and diverse microbiome. In contrast, chronic short sleep, irregular bedtimes, or frequent night shifts can disrupt this rhythm and are linked with changes in gut bacteria, increased inflammation, and higher risks of metabolic issues—all of which may work against your microbiome goals over time. Focusing on consistent sleep and wake times, winding down before bed, and limiting late-night meals or alcohol can create a more restful night, which in turn gives your gut the stability it needs to function and adapt optimally.

References

  1. Eugene AR, Masiak J. The neuroprotective aspects of sleep. MEDtube Science. 2015;3(1):35-40.
  2. Garbarino S, Lanteri P, Bragazzi NL,et al. Role of sleep deprivation in immune-related disease risk and outcomes. Communications Biology. 2021;4:1
  3. Singh KK, Ghosh S, Bhola A, et al. Sleep and immune system crosstalk: Implications for inflammatory homeostasis and disease pathogenesis.Annals of Neurosciences. 2024;32(3):196-206.
  4. Domínguez F, Fuster V, Fernández-Alvira JM, et al. Association of sleep duration and quality with subclinical atherosclerosis. Journal of the American College of Cardiology. 2019;73(2):134-44.
  5. Nôga DA,Meth EDMES, Pacheco AP, et al. Habitual short sleep duration, diet, and development of type 2 diabetes in adults. JAMA Network Open. 2024;7(3):e241147.
  6. Yap Y, Yan Chi Tung N, Shen L, et al. Daily associations between salivary cortisol and electroencephalographic-assessed sleep: a 15-day intensive longitudinal study.Sleep. 2024;47(9):zsae087.
  7. Papatriantafyllou E, Efthymiou D, Zoumbaneas E, et al. Sleep deprivation: Effects on weight loss and weight loss maintenance. Nutrients. 2022;14(8):1549.
  8. Circadian rhythms. National Institutes of General Medical Sciences. 20225. Available at: https://www.nigms.nih.gov/education/fact-sheets/Pages/circadian-rhythms
  9. Lotti S, Dinu M, Colombini B, et al. Circadian rhythms, gut microbiota, and diet: Possible implications for health. Nutrition, Metabolism, and Cardiovascular Disease. 2023;33(8):1490-1500.
  10. Karl JP, Whitney CC, Wilson MA,et al. Severe, short-term sleep restriction reduces gut microbiota community richness but does not alter intestinal permeability in healthy young men. Science Reports. 2023;13:
  11. Hemarajata P, Versalovic J. Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Therapeutic Advances in Gastroenterology. 2013;6(1):39-51.
  12. Spaiser SJ, Culpepper T, Nieves C Jr, et al. Lactobacillus gasseri KS-13, Bifidobacterium bifidum G9-1, and Bifidobacterium longum MM-2 ingestion induces a less inflammatory cytokine profile and a potentially beneficial shift in gut microbiota in older adults: A randomized, double-blind, placebo-controlled, crossover study. Journal of the American College of Nutrition. 2015;34(6):459-69.

This article is for informational purposes only. This article is not, nor is it intended to be, a substitute for professional medical advice, diagnosis, or treatment and should never be relied upon for specific medical advice.