What impact does short-term sleep restriction have on gut microbiome?

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In a recent study published in the journal Scientific Reports, researchers in the United States examined the effects of sleep restriction on the composition of gut microbiota and intestinal permeability.

The gut microbiota has been increasingly implicated as a mediator of adverse health effects related to disrupted/inadequate sleep. For example, sleep deprivation and fragmentation in rodents can change the gut microbial composition and cause inflammation, gut barrier damage, and intestinal permeability. However, the extent to which such effects occur in humans remains unclear.

One study observed alterations in gut microbiota composition and an increase in markers of hypothalamic-pituitary-adrenal (HPA) axis activation, inflammation, and intestinal permeability after total sleep deprivation for 40 hours in adults. However, other studies reported no or minimal changes in gut microbiota composition following sleep restrictions.

Study: Severe, short-term sleep restriction reduces gut microbiota community richness but does not alter intestinal permeability in healthy young men. Image Credit: Design_Cells / ShutterstockStudy: Severe, short-term sleep restriction reduces gut microbiota community richness but does not alter intestinal permeability in healthy young men. Image Credit: Design_Cells / Shutterstock

About the study

In the present study, researchers determined the effect of short-term, severe sleep deprivation on intestinal permeability and gut microbiota composition in adults. Inclusion criteria were healthy adults aged 17 – 45 with a body mass index lower than 30 kg/m2 and a regular sleep pattern of 7 – 9 hours per night, without using antibiotics in the past three months or a history of neurologic disorders, cardiometabolic, and gastrointestinal diseases.

Consumption of probiotics and dietary supplements was prohibited for two weeks before and throughout the study. In addition, the researchers implemented a randomized crossover design involving two conditions for three days: adequate sleep (AS) [7-9h sleep/night] and sleep restriction (SR) [2h sleep/night].

Order of (SR/AS) completion was randomized, and phases were separated by a 21-day washout period when SR preceded AS and a seven-day washout period when AS preceded SR. Participants were provided a diet ensuring energy balance and completed low-intensity exercises during both phases. Stool samples were collected after 48h of AS/SR to examine microbial composition.

DNA was extracted and quantified, and 16S rRNA sequencing was performed. Intestinal permeability was tested using a dual sugar absorption test after 72h of AS/SR. Subjects consumed a beverage comprising mannitol and lactulose dissolved in water, and urine produced in the next five hours was collected and assessed.

Sugar concentrations were measured using high-performance liquid chromatography (HPLC). Fasting blood samples were obtained in the morning of SR days 1 and 4 and AS day 4. High-sensitivity C-reactive protein (hsCRP) and cortisol levels in the serum were quantified. Serum biomarkers, α-diversity, and intestinal permeability between AS and SR were assessed using linear mixed models.  


Twenty-four males were randomized, and 19 participants were included in the study. The self-reported mean weekday wake time was in agreement with actigraphy data. Data showed that participants slept for 125 min/night during SR and 449 min/night during AS. The average energy intake was slightly more during SR than during AS. However, there were no differences in the estimated energy balance between conditions.

No participant consumed any beverage/food other than those provided. Serum cortisol levels declined from SR days 1 to 4 and remained lower on SR day 4 compared to AS day 4. The hsCRP concentrations were not different between SR days 1 and 4 or between SR and AS day 4. Urine volume was not different by sleep condition; mannitol or lactulose excretion and lactulose-to-mannitol ratio were not different between AS and SR.

Stool consistency was similar between conditions. Stool samples produced a median of 39,195 reads, which was not different by condition. Reads were assigned to 3275 unique amplicon sequencing variants (ASVs) of 12 phyla and 98 genera. The principal coordinates analysis (PCoA) of unweighted and weighted UniFrac distances and Bray-Curtis dissimilarity indicated no shifts in microbial community composition due to SR. 

α-diversity was 21% lower during SR than during AS. At the same time, there were no differences in Simpson and Shannon diversity indices between conditions, implying that SR decreased community richness, but evenness was unaffected. Nine ASVs, three genera, and zero phyla in the differential abundance analyses showed no significant differences in relative abundance.

Notably, one ASV within Ruminococcaceae was significantly different after adjusting for the false-discovery rate, suggesting that lower richness during SR might be attributed to the loss of rare taxa. Differences in serum cortisol levels between conditions correlated with the corresponding difference in the lactulose-to-mannitol ratio; there were no additional correlations. 


To summarize, the study demonstrated that restricting sleep to 2h/night for three consecutive days can lower community richness of the gut microbiota without affecting intestinal permeability or relative abundances of prevalent taxa. The decrease in community richness might be due to the loss of rare taxa. This is concerning for populations with repeated sleep restrictions since the loss of taxa reduces the functional repertoire of gut microbiota.

Journal reference:
Tarun Sai Lomte

Written by

Tarun Sai Lomte

Tarun is a writer based in Hyderabad, India. He has a Master’s degree in Biotechnology from the University of Hyderabad and is enthusiastic about scientific research. He enjoys reading research papers and literature reviews and is passionate about writing.


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