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Sleep & The Gut Microbiota: Is Your Gut Keeping You Up at Night?

It’s safe to say most people like to get more sleep. Yet modern lifestyles often push us towards late nights, exposure to bright screens, irregular eating patterns, and high stress.  Sometimes it can even feel like a badge of honour to survive on minimal hours of sleep. However, consistently poor sleep can negatively affect almost every aspect of our health – from mood and concentration to immune function, metabolism and even gut health. 

The circadian rhythm, sleep and the gut microbiome are interconnected in a bidirectional relationship.

The gut microbiome exhibits its own diurnal rhythm, influenced by feeding and sleep patterns which can, in turn, affect our circadian clock and sleep duration. Disruptions in any one of these systems – circadian rhythm (e.g. from jet lag or shift work), sleep quality or the gut microbiome – can negatively impact the others, potentially leading to gut dysbiosis (i.e. an imbalance), metabolic dysfunction and an increased risk of various diseases. 

 

With the clocks changing this weekend, it’s a timely reminder to think about how sleep and our gut microbiota are interconnected. For healthcare professionals, understanding these interactions is increasingly important with altered sleep patterns shown to have an impact on gut microbiota composition – which could have implications for metabolic health, immune regulation and overall wellbeing.  

Your internal clock and circadian rhythm

Our bodies are governed by an internal “biological clock”, also known as the circadian rhythm. This is a roughly 24-hour cycle that regulates many processes, including sleep and wakefulness, hormone release, digestion and even how our immune system functions. 

Light is the most powerful cue for this rhythm. In the morning, exposure to daylight signals our brain to increase alertness, while at night, darkness helps trigger melatonin, the hormone that prepares us for sleep. But it’s not just the brain that follows these rhythms. Nearly every organ, including the gut, has its own “local clock,” and together they work in synchrony to keep us functioning at our best. When the clocks change or when our lifestyle disrupts these rhythms (e.g. night shifts, jet lag or late-night scrolling), our internal systems can become misaligned. 

The gut microbiota and circadian rhythm

Interestingly, research shows that our gut microbes also have their own daily rhythm, when it comes to functions, composition and location in the intestines.1 Over half of our microbial composition fluctuates in a rhythmic pattern over a 24-hour cycle.2 

Studies have shown that disruptions to your circadian rhythm is associated with changes in gut microbiota composition. For example, a higher ratio of Firmicutes to Bacteroidetes has been linked to sleep deprivation.3  

 

Does working night shifts impact the gut microbiome?

Night shift work affects over a quarter of the UK population and has been shown to alter the composition and function of the gut microbiome. These microbial alterations have been associated with higher risks of metabolic syndrome, gastrointestinal complaints and mood disturbances in shift-working populations. Emerging reviews and studies continue to investigate these links, underscoring the gut microbiome as a critical mediator of circadian disruption. 

A recent meta-analysis of five studies found reduced gut microbiome diversity and higher levels of pro-inflammatory bacteria such as Escherichia/Shigella, Blautia, and Dialister, in night shift workers.4 These changes were linked to gastrointestinal symptoms and indicators of cardiometabolic dysfunction. 

Therefore, shift work can be associated with significant alterations in gut microbiome composition that may negatively impact health. 

However high-quality long-term studies are required to fully understand this link and the underlying mechanisms.  

One small study investigated the differences in the gut microbiota of rotational shift workers when working the day versus night shift. A reduction in Bacteroidetes and an increase in Actinobacteria and Firmicutes during the night-shift period was observed, compared to working the day shift. These microbial differences in night-shift workers were linked to a cardiac rhythm disturbance which, in turn, could increase risk of metabolic syndrome in these individuals.5  

Overall, further research is needed on how shift work affects gut microbiota composition and diversity, as well as the potential role of probiotics in restoring the gut microbiota of shift workers.

Diet, circadian rhythm and sleep

Dietary patterns can also impact circadian rhythm. Dietary stressors such as alcohol or high-fat meals can exacerbate the gut microbiome disturbances and reduction in diversity caused by circadian disruption.1

Additionally, research in this area suggests that altered sleep/wake cycles can also influence meal timings and food choices, which can in turn affect circadian alignment and microbial diversity.  

Top tips for to support sleep (and the gut microbiota)

Encourage patients to: 

  • Aim for a regular bedtime and waketime as this is associated with better health outcomes and helps to regulate the circadian rhythm.6  
  • Avoid caffeine before bed – caffeine interferes with the sleep-regulating hormone melatonin and has been shown to reduced total sleep time and sleep efficiency.7 
  • Keep the bedroom cool, 16-18 degrees is optimal.  
  • Where possible, avoid heavy meals, large amounts of fluid or intensive exercise before bedtime.  
  • Avoid or limit screentime in the lead-up to bedtime (e.g. phones, laptops, TVs) as the blue light from devices mimics daylight and can suppress melatonin production.8 
  • Keep the bedroom associated with sleep. Avoid working, entertainment and eating in it.  
  • Try using an eye mask and ear plugs if light or noise is negatively impacting sleep.  

As research advances, targeting the microbiome alongside circadian health could offer new ways to protect and support those most affected by irregular sleep schedules. 

If you would be interested in booking a workplace talk to hear about the latest gut microbiome research, get in touch with the Yakult Science team today at science@yakult.co.uk. 

References

  1. Parkar, S.G., Kalsbeek, A. and Cheeseman, J.F. (2019). Potential role for the gut microbiota in modulating host circadian rhythms and metabolic health. Microorganisms, 7(2), p.41.  
  2. Lotti, S., Dinu, M., Colombini, B., Amedei, A., and Sofi, F. (2023). Circadian rhythms, gut microbiota, and diet: Possible implications for health. Nutrition, metabolism, and cardiovascular diseases : NMCD, 33(8), 1490–1500.  
  3. Matenchuk, B.A., Mandhane, P.J. and Kozyrskyj, A.L. (2020). Sleep, circadian rhythm, and gut microbiota. Sleep medicine reviews, 53, p.101340.  
  4. Grasa-Ciria, D., Couto, S., Samatán, E., Martínez-Jarreta, B., Cenit, M. d. C., and Iguacel, I. (2025). Disrupted Rhythms, Disrupted Microbes: A Systematic Review of Shift Work and Gut Microbiota Alterations. Nutrients, 17(17), 2894.  
  5. Mortaş, H., Bilici, S. and Karakan, T. (2020). The circadian disruption of night work alters gut microbiota consistent with elevated risk for future metabolic and gastrointestinal pathology. Chronobiology international, 37(7), pp.1067-1081.  
  6. Chaput, J. P., Dutil, C., Featherstone, R., Ross, R., Giangregorio, L., Saunders, T. J., Janssen, I., Poitras, V. J., Kho, M. E., Ross-White, A., Zankar, S., and Carrier, J. (2020). Sleep timing, sleep consistency, and health in adults: a systematic review. Applied physiology, nutrition, and metabolism, 45(10 (Suppl. 2)), S232–S247. 
  7. Gardiner, C., Weakley, J., Burke, L. M., Roach, G. D., Sargent, C., Maniar, N., Townshend, A., and Halson, S. L. (2023). The effect of caffeine on subsequent sleep: A systematic review and meta-analysis. Sleep medicine reviews, 69, 101764.  
  8. West, K. E., Jablonski, M. R., Warfield, B., Cecil, K. S., James, M., Ayers, M. A., Maida, J., Bowen, C., Sliney, D. H., Rollag, M. D., Hanifin, J. P., and Brainard, G. C. (2011). Blue light from light-emitting diodes elicits a dose-dependent suppression of melatonin in humans. Journal of applied physiology, 110(3), 619–626.