UK +44 (0)1865 849841
Malaysia +603 2731 9335

5 Ways Sleep And Microbiome Are Interrelated With Immunity And Cognition

The effect of sleep on the microbiome of the host has been a topic of interest among researchers for the past several years. Studies have yielded opposing results in how short sleep affects the microbiome. While some showed a significant change in Firmicutes to Bacteroidetes ratio, others found no microbial change following short-term sleep restriction.

To find a definite answer, a recent study by Smith et al. (2019) tackles the effect of sleep on microbiome composition in 26 healthy men. They were observed over one month; which is why the researchers of this study believe it was incongruous with other similar studies (they documented short-term observations of the human microbiome following sleep restriction).

The study also accounts for the interrelation among the immune system and cognition in addition to the sleep physiology and microbiome of the host.

Sleep measures were collected using actigraphy whereas stool swabs and saliva samples were taken for the microbiome, interleukins (IL-1β, IL-6), and cortisol testing. The researchers conducted neurobehavioral testing using cognition and emotion test batteries to assess complex cognition, sensorimotor speed, psychological well-being, and stress among other domains.

This article presents a summary of the above-mentioned study with a focus on five main findings.

1. Sleep efficiency influences gut microbiome diversity

Three microbiome measures were used to determine a variety of species – richness, Shannon diversity, and inverse Simpson diversity. All of them showed a positive correlation with sleep efficiency. However, only Shannon diversity was strongly negatively correlated with waking after falling asleep and only inverse Simpson diversity was significant when total sleep time was assessed.

This finding may suggest that gut flora variety helps promote efficient, restorative sleep.

2. Microbiome and sleep are linked to the interleukin-6

Interleukin-6 (IL-6) is known for functioning as a cytokine (supporting inflammation) and myokine (alleviating inflammation). Interleukin was accounted for in this study because the gut flora communicates with it. The amount of IL-6 was previously found to be increased at the time of the beginning of sleep.

The researchers found IL-6 to be positively related to all three microbiome diversity measures used in the study as well as with time spent in bed and sleep time.

3. Microbiome, sleep, and interleukin-6 influence abstract thinking, vigilance, risk decision making, and other cognitive aspects

Microbiome diversity and sleep efficiency showed to have a positive effect on abstract thinking, while richness improved risk decision making.

Cytokine IL-6 increased subjects’ vigilance and perceived rejection, while it seemed to worsen working memory and the feeling of purpose. The authors mentioned a relevant 2005 study which has also shown IL-6 connection with a decline in cognitive and emotional functioning.

4. Certain gut bacteria phyla correlate with abstract thinking, sleep, and IL-6

When subjects slept efficiently, they had an increase in Bacteriodetes richness and diversity. This increase further influenced IL-6 and abstract matching.

Firmicutes had an increase in richness followed by better sleep efficiency. There was also a positive correlation between Firmicutes, IL-6 and better results on abstract matching tests.

Poor sleep efficiency was linked to a decrease in Bacteriodete and Firmicute richness, whereas the richness of Actinobacteria increased with the number of awakenings. The decrease in richness of the first two was linked with poorer reaction time. The reason these three were tested is that certain Bacteriodete, Firmicute, and Actinobacteria are known to produce GABA (Gamma-Aminobutyric Acid), a neurotransmitter that inhibits other neurotransmitters, easing relaxation and promoting sleep.

Researchers also found a positive association between Proteobacteria richness and IL-6.

Image taken from Smith, R. P. et al. Gut microbiome diversity is associated with sleep physiology in humans.

5. Nodes in the human gut interaction network are related to two gut bacteria phyla

The researchers were interested in the brain-gut-microbiome axis (BGMA). It is known that gut microbes can communicate with the host over nervous, endocrine, and immune signalling mechanisms. A recent study showed that this communication can go as far as the gut microbiome controlling the DNA of the host.

Fifteen taxa from the Firmicutes, seven from the Proteobacteria, and three taxa from the Actinobacteria were found to be related to the nodes in the interaction network. To their surprise, the researchers didn’t find node correlation with the Bacteriodetes genera.


This latest study sheds new light on how sleep correlates with our “second brain”, and how the gut microbiome and interleukin-6 respond to and influence the quality of our sleep. The research shows us even more than that, bringing the cognitive aspects into the equation. Although there was no correlation with stress marker cortisol and gut microbiome, this study supports findings from the 2017 study by Takada et al. which shows how sleep can be improved by gut bacteria modulation.


Kristina Miladinovic is a writer and researcher at



The 7th Microbiome and Probiotics R&D and Business Collaboration Forum is now a fully interactive virtual conference. Find out more here.

Leave a Reply

Subscribe to Our Newsletter

Get free reports and resources from our world class speakers.
  • This field is for validation purposes and should be left unchanged.