Sleep and gut health: how they affect each other

Many people notice that a bad night’s sleep and an unsettled stomach seem to go hand in hand. Science is starting to explain why. Sleep and the gut are linked through your body clock, the trillions of microbes living in your gut, and the nerves that connect your gut to your brain.

How much sleep do adults need?

The American Academy of Sleep Medicine and the Sleep Research Society recommend that adults sleep 7 or more hours a night on a regular basis [1]. Regularly sleeping less than this is linked with a range of poorer health outcomes [1].

Your gut runs on a body clock

Your body has an internal 24-hour clock, known as the circadian rhythm. It doesn’t only control when you feel sleepy. Your gut microbes follow a daily rhythm too, changing in make-up and activity over the course of the day, partly shaped by when you eat [2].

In a study published in Cell, researchers found that jet lag disrupted these daily rhythms in the gut microbes of mice. They also found changes in the gut microbes of two people after a long-haul flight. When microbes from the jet-lagged mice or people were transferred into mice, the mice gained more weight and handled sugar less well [2]. Most of this work was in animals and the human part was very small, but the study showed how closely the gut and the body clock are tied together.

Sleep and your gut microbes

In a small study of 26 healthy men who wore sleep-tracking watches for 30 days, those with a more diverse range of gut bacteria slept more efficiently, slept for longer and woke less during the night [3].

A much larger 2026 study in Nature Communications looked at almost 7,000 adults in the Netherlands. Poorer sleep quality, a later “night owl” body clock and “social jet lag” (sleeping at very different times on work days and days off) were all linked with lower gut microbe diversity [4]. The analysis suggested that sleep habits may shape the gut microbes more than the other way round, although studies like this can’t prove cause and effect [4].

What happens in the gut when we don’t sleep?

Research in animals has explored what severe sleep loss does to the body. A 2020 study in Cell found that in fruit flies and mice deprived of sleep, harmful molecules called reactive oxygen species built up in the gut [5]. This is early laboratory research, but it suggests that the gut may be one of the places where a lack of sleep takes its toll.

The gut–brain connection at night

Your gut and brain are in constant two-way communication through the gut–brain axis, and the vagus nerve is its main pathway. The vagus nerve is the core of the “rest and digest” side of your nervous system [6].

Sleep changes this balance. As you move from being awake into deeper, non-dreaming (non-REM) sleep, “rest and digest” activity gradually increases, which researchers can measure through heart rate variability [7]. During dreaming (REM) sleep, the balance swings back towards the body’s more alert “fight or flight” side [7].

Simple habits for better sleep

The NHS recommends a few practical steps that can help [8]:

• Keep regular hours: go to bed and get up at similar times every day, including weekends.
• Wind down: avoid screens for an hour before bed, and try reading, slow breathing or calming music.
• Watch what you eat and drink: avoid large meals close to bedtime, cut down on caffeine, and avoid alcohol and nicotine in the hour or two before bed.
• Make your bedroom sleep-friendly: keep it quiet, dark and cool.
• Don’t force it: if you’re still awake after about 20 minutes, get up, do something relaxing and go back to bed when you feel sleepy.
• Stay active: regular exercise helps sleep, ideally earlier in the day.

If poor sleep or gut symptoms are affecting your daily life, speak to your GP or pharmacist.

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References

1. Watson NF, Badr MS, Belenky G, et al. Recommended amount of sleep for a healthy adult: a joint consensus statement of the American Academy of Sleep Medicine and Sleep Research Society. Journal of Clinical Sleep Medicine 2015;11(6):591–592.
2. Thaiss CA, Zeevi D, Levy M, et al. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell 2014;159(3):514–529.
3. Smith RP, Easson C, Lyle SM, et al. Gut microbiome diversity is associated with sleep physiology in humans. PLOS ONE 2019;14(10):e0222394.
4. Wu J, Andreu-Sánchez S, Peng H, et al. The interplay of sleep characteristics with health factors and gut microbiome. Nature Communications 2026;17:2731.
5. Vaccaro A, Kaplan Dor Y, Nambara K, et al. Sleep loss can cause death through accumulation of reactive oxygen species in the gut. Cell 2020;181(6):1307–1328.
6. Bonaz B, Bazin T, Pellissier S. The vagus nerve at the interface of the microbiota–gut–brain axis. Frontiers in Neuroscience 2018;12:49.
7. Tobaldini E, Nobili L, Strada S, et al. Heart rate variability in normal and pathological sleep. Frontiers in Physiology 2013;4:294.
8. NHS Every Mind Matters. Fall asleep faster and sleep better.