Gut Microbiome And Sleep

Last updated: September 17, 2019

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All of the microbes that live in our intestines are known as the gut microbiome. Some even call it our “second brain” because it influences so many processes (not just breaking down food) – our mood, mental health, hormone production, and sleep, to name a few.

Taking special care of your gut health can have great effects on the quality of your sleep. This is true even if you are going through a stressful period which would normally disrupt your sleep length and quality. On the other hand, taking care of your sleep will keep your gut microbiome well-balanced and fully functional.

This means that one will suffer if the other is disrupted. The gut microbiome has a circadian rhythm (biological clock) just like our brain does. Our gut microbes change for worse if we don’t have a healthy sleep schedule. They are responsible for the production of some of the sleep-inducing chemicals so we may fall into the vicious cycle of bad sleep and poor microbiome negatively affecting each other.

The good news is that you can improve your microbiome by consuming delicious fermented foods, exercising, and practicing good sleep habits.

How are sleep and microbiome connected?

Scientists have started paying more attention to the gut microbiome and its connection to sleep fairly recently. We know that sleep affects microbes but we don’t know exactly how. Here’s some of the information research has given us so far.

Sleep, microbes, and cognitive flexibility

A study conducted among the elderly has shown that better scores on the Stroop test depend not only on good sleep but also on certain microbial composition.

Stroop word color test
Figure 1. The Stroop Word-Color Test

Better sleep showed an increase in Verrucomicrobia strain which is believed to be linked with better cognitive function. Those who slept poorly had lower levels of the said microbes.

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Study authors hope that improving gut microbiome could lead to a new way of cognitive decline treatment in older adults.

Microbiome and circadian disturbance

Our gut microbes seem to express fluctuation throughout the day. This fluctuation is regulated by certain genes. Sleep deprivation can alter gene expression – in this case, circadian gene expression can be seen through the presence of certain microbes. Long-term sleep deprivation may cause long-lasting epigenetic changes which can be observed though our microbiome.

Circadian Rhythm and gut microbiota
Figure 2. Circadian rhythm, gut microbiota, and metabolism. Source: Parkar S.G, Kalsbeek A. Potential Role for the Gut Microbiota in Modulating Host Circadian Rhythms and Metabolic Health.

This also means that the microbiome of shift workers or those who change time zones a lot is probably in dysbiosis (imbalance).

One study has found a link between circadian disruption and leaky gut, especially in those who frequently consume alcohol.

Insomnia, depression and gut microbiome

Insomnia and depression often come together. When we don’t sleep well, we may become more susceptible to stress, anxiety, bad mood, and pessimism. A particularly sad life event can disrupt our sleep so it works both ways.

What many people don’t know is that our gut microbes are responsible for about 90% of the serotonin (our “feel good” neurotransmitter) produced in the body. They also produce GABA which relaxes us by inhibiting stress. Low levels of GABA mean more stress and less chance to fall asleep.

People with insomnia and depression usually don’t have the right balance of microbes or their microbes don’t work properly.

Long-term sleep deprivation and gut microbiota

Chronic sleep deprivation not only changes the microbiome but it also causes tissue inflammation and insulin resistance, according to a study conducted on mice.

The tissue inflammation is directly caused by an imbalance in the microbiome. The reason lies in that some of the more fermentative bacteria have shown an increase whereas lactic acid bacteria have decreased.

Melatonin production

Melatonin is also known as the “darkness hormone”. Its main function is to make us sleepy. Apart from being produced in the brain as a response to the outside darkness, our gut also produced melatonin.

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Healthy gut prevents stress and maintains good sleep

You could be doing yourself a huge favor if you eat your yogurt regularly. Students who took Lactobacillus casei-rich dairy on a daily basis showed better sleep quality even during a stressful exam period.

The Japanese study authors wanted to see the effect of taking small doses of a probiotic drink on students who experienced academic stress. The placebo group showed worse and shorter sleep as the exam day was nearing whereas those who took 100ml of fermented milk enjoyed much more of the restorative deep sleep.

How can I improve my gut microbiome?

You can help your gut by sleeping well, eating healthy and exercising.

If you have poor sleep habits, you should change them. The first step is to recognize what you are doing wrong and substitute it with good sleep practices.

Foods that are good for your microbiome include:

  • Unprocessed food. Unprocessed food contains more nutrients and fiber, which is excellent for gut microbes.
  • Fiber. Brocolli, artichoke, wholegrain, bananas are just a few fiber-rich foods. Be careful with packaged snacks and cookies that advertise as being high in fiber – if they are processed, they probably aren’t.
  • Eat all the fruit and vegetables. Good bacteria love various plants and herbs. Make a huge salad containing as many veggies as possible. Make fruit your regular snacks instead of energy bars that are usually full of sugar.
  • Fermented dairy – yogurt and kefir. These are very rich in probiotic cultures and are very helpful with supplementing your gut with more of the friendly bacteria.
  • Kimchi. Kimchi is another excellent source of bacteria. You can have it with any meal.
  • Supplements – prebiotics and probiotics. Prebiotics are generally food for good bacteria (probiotics). If you are taking antibiotics, it is advisable to take both probiotics and prebiotics. This is because antibiotics don’t only kill the bad bacteria in the body, they also kill the extremely important gut bacteria.

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Additional resources

  1. A preliminary examination of gut microbiota, sleep, and cognitive flexibility in healthy older adults. Sleep medicine. https://www.ncbi.nlm.nih.gov/pubmed/29031742
  2. The Role of Microbiome in Insomnia, Circadian Disturbance and Depression. Frontiers in Psychiatry. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6290721/
  3. Chronic Sleep Disruption Alters Gut Microbiota, Induces Systemic and Adipose Tissue Inflammation and Insulin Resistance in Mice. Scientific reports.  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5064361/
  4. Beneficial effects of Lactobacillus casei strain Shirota on academic stress-induced sleep disturbance in healthy adults: a double-blind, randomised, placebo-controlled trial. Beneficial Microbes. https://www.wageningenacademic.com/doi/pdf/10.3920/BM2016.0150
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