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Gut Health & Sleep

Sleep affects health and the gut and these also affect sleep! In this article, Cliff summarises the research on the gut and sleep.

Key points

  • There is a bi-directional relationship between sleep and the gut
  • Lack of sleep affects the motility of the gut which is likely to affect gut health
  • Lack of sleep influences the microbiota and the microbiota influence circadian rhythms and length and quality of sleep
  • The effects of short-term restriction or extension on sleep in humans are unclear though

It has been suggested that sleep and circadian rhythm dysfunctions affect the microbiome, contributing to an inflammatory state and metabolic diseases.1, 2

It is also thought that metabolites from the gut microbiome (compounds produced by bacteria) help to influence circadian rhythm and help to regulate sleep, metabolism, and body composition and these end products of bacterial species are also able to induce fatigue. Furthermore, probiotic supplementation has been found to improve subjective sleep quality.3

Metabolites from the gut microbiome influence circadian rhythms and help to regulate sleep, metabolism, and body composition

However, the relationship between sleep and gut health is bidirectional. Microbiome diversity is correlated with sleep efficiency and abstract thinking, while several genera including Lachnospiraceae, Corynebacterium, and Blautia are correlated with poorer sleep measures.4

Microbiome diversity is correlated with sleep efficiency and abstract thinking

Sleep quality is also associated with faster cognitive functions and tests results for this (the Stroop test) are related to Verrucomicrobia and Lentisphaerae.5 Good self-reported sleep quality is positively associated with microbial diversity, Firmicutes to Bacteroidetes ratio, and butyrate-producing bacteria (such as Blautia and Ruminococcus), while poor self-reported sleep quality was positively associated with the genus Prevotella.6

Disturbed sleep is known to worsen eating behaviours and thus, may play a further role in the disturbance to the microbiota seen with poor sleep.

Animal and human research have shown that disturbed sleep increases ad libitum food intake and changes the microbiota. This increases highly fermentative Lachnospiraceae and Ruminococcaceae while decreasing Lactobacillaceae families. In mice, this leads to inflammation, insulin resistance, and is associated with colonic epithelium disruption. These results have been confirmed through inoculation of germ-free mice with microbiota from sleep disturbed subjects.7 Antibiotics (which reduce bacteria number and diversity) have also been shown to reduce sleep in mice.8 Research in people with IBS also suggests that gut dysfunction affects sleep.9

Disturbed sleep is known to worsen eating behaviours and thus, may play a further role in the disturbance to the microbiota seen with poor sleep.

However, short term sleep restriction over several days has not been shown to overly influence gut microbiota in either rats or humans.10 Similarly, sleep extension has not been demonstrated to influence the overall gut composition, but better quality sleep was related to a higher abundance of the phyla Tenericutes.11 Finally, in a study of young, active adults (18-35 yrs.) no significant relationship between habitual sleep duration and microbiota diversity was observed.12


1.         Reynolds AC, Paterson JL, Ferguson SA, Stanley D, Wright Jr KP, Dawson D. The shift work and health research agenda: considering changes in gut microbiota as a pathway linking shift work, sleep loss and circadian misalignment, and metabolic disease. Sleep medicine reviews. 2017;34:3-9.

2.         Parekh PJ, Oldfield ECIV, Johnson DA. The Effects of Sleep on the Commensal Microbiota: Eyes Wide Open? Journal of Clinical Gastroenterology. 2018;52(3).

3.         Matenchuk BA, Mandhane PJ, Kozyrskyj AL. Sleep, Circadian Rhythm, and Gut Microbiota. Sleep Medicine Reviews. 2020:101340.

4.         Smith RP, Easson C, Lyle SM, Kapoor R, Donnelly CP, Davidson EJ, et al. Gut microbiome diversity is associated with sleep physiology in humans. PloS one. 2019;14(10):e0222394.

5.         Anderson JR, Carroll I, Azcarate-Peril MA, Rochette AD, Heinberg LJ, Peat C, et al. A preliminary examination of gut microbiota, sleep, and cognitive flexibility in healthy older adults. Sleep Medicine. 2017;38:104-7.

6.         Grosicki GJ, Riemann BL, Flatt AA, Valentino T, Lustgarten MS. Self-Reported Sleep Quality Is Associated With Gut Microbiome Composition in Young, Healthy Individuals: A Pilot Study. Sleep Medicine. 2020.

7.         Poroyko VA, Carreras A, Khalyfa A, Khalyfa AA, Leone V, Peris E, et al. Chronic Sleep Disruption Alters Gut Microbiota, Induces Systemic and Adipose Tissue Inflammation and Insulin Resistance in Mice. Scientific Reports. 2016;6(1):35405.

8.         Lendrum JE, Seebach B, Klein B, Liu S. Sleep and the gut microbiome: antibiotic-induced depletion of the gut microbiota reduces nocturnal sleep in mice. BioRxiv. 2017:199075.

9.         Orr WC, Crowell MD, Lin B, Harnish MJ, Chen JDZ. Sleep and gastric function in irritable bowel syndrome: derailing the brain-gut axis. Gut. 1997;41(3):390.

10.       Zhang SL, Bai L, Goel N, Bailey A, Jang CJ, Bushman FD, et al. Human and rat gut microbiome composition is maintained following sleep restriction. Proceedings of the National Academy of Sciences. 2017;114(8):E1564-E71.

11.       Reutrakul S, So-ngern A, Chirakalwasan N, Saetung S, Chanprasertyothin S, Thakkinstian A, et al. No changes in gut microbiota after two-week sleep extension in chronically sleep-deprived individuals. Sleep Medicine. 2020;68:27-30.

12.       Morales Marroquín FE. Distal gut microbiome association with sleep duration and quality 2018.

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