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Sleep and Your Gut Bacteria

Updated: Jun 15, 2021

How does your gut bacteria impact your sleep and vice versa?

Most people don't make the connection between what goes on in their gut bacteria with the health of their brain. Maybe because an off-balance of gut bacteria is subtle and often not painful enough to draw attention for us to connect the dots. I had never thought that low grade inflammation in your belly can affect your sleep. But I've learned that our body is a "holistic" system that is interconnected and not one organ system is isolated from the others.

I remember drinking kefir for the first time about seven years ago. At the time, fermented foods (even though they've existed for a very long time) were not very popular within my circle. 'Probiotics' were new terms and 'Prebiotics' were very new concepts (we didn't have probiotics sold at many pharmacies back in those days). So you can imagine how strange it was for my friends and family to hear about fermented milk! I had gotten some milk kefir grains from my aunt who apparently got them from friends who got them from Tibet. After making it myself and drinking it daily for about a week, I noticed that my stomach was much calmer and I slept better than ever! It lowered anxiety that I didn't even know existed in me at the time! When you've been living with a condition for so long, especially one that is chronic but not painful, you may not remember how it feels like to be free of it.

In fact, at present, when I don't drink kefir for a while, I long for that calm and soothing feeling which is my cue to make more kefir!

Gut bacteria can affect our sleep, but the reverse is true too! Did you know that our quality of sleep can also affect our gut bacteria?

Here's why:

Circadian rhythms are patterns of brainwave activity, hormones, cell regeneration and biological activities that occur on a daily basis. Sleeping well, at the right time each day is essential to keeping the circadian rhythms functioning properly so we function properly, too.

Our microbes are actually the regulators of this function and they need us to rest so they can do their 'job' while we sleep and keep this rhythm in balance.

And that's not all!

Not having the right microbes may be lowering your metabolic rate while you sleep and this can lead to weight gain (refer to mouse study below - UI Carver College of Medicine). Mice with lower beneficial bacteria, had a lower metabolic rate both when resting and when asleep, causing them to gain weight.

So what should you do? Should you work on sleeping better to help the microbes or should you work on your gut health to help you sleep better? The answer is to do both.

Here are a number of strategies that can help.

To help reset your circadian rhythm:

  • Go to bed at a set time and get up at the same time as much as possible

  • Avoid bright lights near bedtime especially blue light from your phone

  • Avoid eating or exercising close to bedtime

  • Sleep in a dark space – light tricks the body into thinking it is time to be awake

  • Develop a relaxing routine before bed whether it is taking a bath, stretching, reading a book, deep breathing exercises, or having a nice cup of herbal tea such as chamomile or valerian

  • Supplement with magnesium and abstain from caffeine close to bedtime

  • For those who have irregular work and therefore, sleep schedules, consider talking to a practitioner about taking melatonin

Diet also plays a role. In another mouse study, both high fat and low fat diets played a negative role in the function of circadian rhythms and they also altered the microbiome. Short-chain fatty acid production was lower, especially butyrate which is essential for circadian rhythm function. Butyrate is produced by beneficial colon bacteria from resistant starch found in complex carbohydrates such as potatoes, wheat, rice, legumes and sweet potatoes.

To improve gut health:

  • Eat prebiotic foods, especially those with resistant starch.

  • Take probiotics which can help melatonin levels which, in turn, help restore circadian rhythms.

  • Incorporate fermented foods into your diet (kefir, miso, sauerkraut, kimchi, kombucha, beet kvass)

  • Reduce sugar, alcohol, chemicals

Sleep is one more example of the potential problems caused by dysbiosis (imbalanced gut bacteria) and why we should be focused on improving our gut health.

Contact us if you need help to rebalance your gut bacteria for quality sleep and overall health!


Ø Mice Study on unhealthy microbiome (gut bacteria) leading to weight gain / obesity by lowering resting metabolism - UI Carver College of Medicine:

Ø Circadian Disorganization Alters Intestinal Microbiota, Robin M. Voigt,1 et al, PLoS One. 2014; 9(5): e97500.

Ø Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Leone V1, et al, Cell Host Microbe. 2015 May 13;17(5):681-9.

Ø Melatonin regulation as a possible mechanism for probiotic (VSL#3) in irritable bowel syndrome: a randomized double-blinded placebo study, Wong RK1 et al, Dig Dis Sci. 2015 Jan;60(1):186-94.

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