How your quality of sleep affects your microbiome

For those of you who aren’t aware, our circadian rhythm plays the starring role when it comes to our sleep/wake cycle. It runs on a 24hour clock that has been fine tuning itself ever since the days where we used to hunt for our dinners. The cycle is designed to flow in sync with the rise and fall of daylight. It allows us to wake up naturally as the sun starts to rise and when it starts to become dark our circadian rhythm encourages the cells of our body to slow down, relax and allow the hormone melatonin to rise which helps us to get a good night sleep.

It really is quite impressive what our bodies can do when they are left to keeping us alive.

Unfortunately, even though this process of sleeping and waking is natural to us, in modern times we have made this an increasingly difficult task.

Whether we’re staying up stuck in a scroll hole on Instagram reels, watching old episodes of wife swap on YouTube or just ‘one more‘ episode of line of duty on Netflix, we are all guilty of bedtime procrastination. Filled with regret the next morning we often wonder why we do it to ourselves as our zombie doubles struggle to get to work. However, after our 3rd cup of coffee we seem to forget the pain that was and do it all over again, like the struggle bus that we rode this morning was never as bad as it actually seemed.

But if we continue to turn a blind eye to how little sleep we are actually getting, what are the consequences and are they reversible?

What happens when we don’t get a good night sleep?

When we rest at night it may appear that we are doing absolutely nothing but in fact the cells in our body are working tirelessly to prepare us for the next day. Much like a pit stop at the F1, our cells break down and get rid of anything that is no longer of use to us and replaces it with newer models that work more efficiently. They work to repair any damage done like healing a scab, replacing the tastebuds we burnt off or breaking down what’s left in our stomach. Without sleep our bodies would not be able to work as efficiently as they do. We are left feeling fatigued and foggy minded throughout the day, which can increase our appetite and cravings for foods high in sugar because our bodies need the energy to make up for lost sleep. Continuously not getting enough sleep and eating junk foods to recover creates a bad habit that leads us to even more damaging effects on our health ranging from obesity, high blood pressure and diabetes.

There have been studies which demonstrate how poor quality of sleep negatively impacts the diversity of our gut bacteria. Diversity in gut bacteria is important to maintaining optimal health. Melatonin (the sleep hormone) has shown to contribute to a healthy gut lining and when we aren’t producing enough (possibly due to screen time interference late at night), it can disrupt multiple communications between the brain and the gut by increasing gut permeability which you may know as ‘leaky gut’. This brain/gut connection is crucial to be able to keep our circadian rhythm in working order.

How does ‘leaky gut’ affect my sleep?


Leaky gut can affect the production and synthesis of serotonin – also known as our happy hormone.  Serotonin is also a precursor to our sleep hormone melatonin so if we are running low on our happy hormone, we might find it harder to fall asleep because we will be making less melatonin. This is one reason why it is common for people who suffer with depression to struggle with insomnia.

Low levels of serotonin can affect us in multiple ways from;

  • Increased inflammation throughout our whole body causing stiff joints to a slightly swollen belly and even migraines.
  • Inflammation also affects our skin making us appear red and puffy and not quite ourselves.
  • Brain fog and difficulty concentrating - something we have all experienced.
  • Most famously serotonin is known to affect our mood. Low levels of serotonin may leave us feeling anxious or depressed and cause fluctuations in our daily mood.

Leaky gut also makes us more susceptible to illness because it weakens our immune systems defence. Some studies demonstrate how leaky gut may even be a primary cause of heightened immune reactions such as asthma and eczema.


Not only this but leaky gut may also increase your chances of developing food allergies or intolerances.

What can you do to help support your gut from the effects of poor sleep?

Firstly, put the phone down and close your eyes. Light interference around bedtime confuses your circadian rhythm and delays the release of melatonin. If you’re on your phone all night your brain still registers the light as it being daytime and your circadian rhythm will be thrown off.

Secondly, by working to improve your gut health daily the billions of bacteria that reside there will do all the hard work for you when it comes to telling the brain to go to bed. Making sure you have well balanced microbiome will prevent your gut from becoming ‘leaky’. With a secure and tight wall preventing harmful toxins and bacteria from interfering with your gut’s daily functions, your gut and brain can communicate properly meaning your circadian rhythm will keep you on track for when it’s time to go to sleep.

Taking a friendly bacteria supplement daily greatly improves the diversity of your gut microbiome and supports you in getting a good night sleep by encouraging production of serotonin and melatonin – meaning you don’t have to take the struggle bus every morning.