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How your Gut Impacts Sleep

Updated: Apr 10, 2020

Sleep and Your Gut Bacteria

I’ll be honest with you, sleep has always been my lowest priority when it comes to my health, but that’s also been one of my biggest health mistakes! I’ve binged on Netflix, stayed up way too late chatting with friends, or got distracted with who knows what and all of a sudden it’s midnight. Whoops! But then I got a fitness tracker and used it to track my deep sleep (this is where you do the most repair and rejuvenation of the body) and I noticed that the later I went to sleep the less deep sleep I got, even if I still managed to get 7 hours of sleep, my deep sleep suffered by going to bed so late. Once I started going to bed more consistently, around the 10 pm mark, my deep sleep got better. Moral of this story is that good sleep is important and your gut can play a role in this too.

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

The fact that our microbes are actually the regulators of this function and that our sleep patterns are an issue for our microbes should not surprise us. They need us to rest so they can do their thing while we sleep and keep their balance as it should be.

There is also more news you might be interested in. Not having the right microbes may be lowering your metabolic rate while you sleep and this can lead to weight gain. This is based on a mouse study at UI Carver College of Medicine which found that mice given a drug that lowers 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. There are 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, set the mood so to speak and dim the lights

Avoid eating or exercising close to bedtime

Sleep in dark space – light tricks the body into thinking it is time to be awake. Black out blinds or a sleep mask can be really helpful.

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

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.

Butyrate supplements are available if you are unsure as to how well you are producing it.

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


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

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.

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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