Did you have a good night’s sleep last night? Was it restful? I hope so because when you sleep so do your microbes, but that is not all there is to it.  Sleep and the quality and amount of good gut bacteria are intertwined.

This may explain why I am having some intestinal distress from time to time. Restful sleep is my nemesis. I am stressed. I am busy and in my household, people keep waking me up. And sometimes I wish I did not have to sleep so I could get all my work done. I say to myself “If only I was not so darn tired, I could keep working, I could get this done and free up some time for fun”. Sound familiar?

circadian rhythmApparently, it is not all about us and what we do. We have some other players weighing in on how we sleep. Good gut bacteria levels help us sleep well. And poor sleep lowers good bacteria levels. It is a catch-22.

As if we did not have enough to worry about when we sleep, now we have think about one more thing – whether we have enough good microbes to sleep well.

The good news is that the microbes are doing the thinking for us. The microbiome regulates our circadian rhythm pattern. They determine how we sleep because when we sleep, they sleep, too. However, they are not wasting time while they sleep. They are working away on our behalf.

When we sleep, we go to be bed with one set of microbes and wake up with another. Whether the new set is more helpful or not, depends on how well we sleep. When we sleep well, it aids the good bacteria to continue in the right numbers and protect us. When we sleep badly, it tips the scales toward dysbiosis.

Do not panic. If you do not have dysbiosis, then this balance can easily be restored the next night, if you get a good night’s sleep. So don’t worry about last weekend when you partied all night – as long as it is not a habit, you are probably okay.

However, when you have dysbiosis, not only does a bad night sleep make it worse but now the research seems to be suggesting that the less-then-ideal microbes may be the reason why you do not sleep well.

Circadian rhythms are patterns of brainwave activity, hormones, cell regeneration and biological activities that occur on a daily basis. And sleeping well 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 sleeps 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.

I know what you are thinking. Now we have to worry about gaining weight while we sleep?

Well, you shouldn’t be worrying as that is not helpful for your gut microbes either.

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
  • Avoid eating or exercising close to bedtime
  • Sleep in 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 bed, 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 and why we should be focused on improving our gut health.


  1. Circadian Disorganization Alters Intestinal Microbiota, Robin M. Voigt,1 et al, PLoS One. 2014; 9(5): e97500.
  2. 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.
  3. 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.