The Relationship Between Sleep and Your Microbiome

By Dr Ernst
October 27, 2017

New research is consistently confirming the importance of your microbiome when it comes to everything from digestion to immunity to mental health.

But we now have to add sleep to that list, because it turns out there is a cyclical, feedback loop relationship between sleep and your microbiome.

Very quickly, what is the microbiome?

See, in your gut—mostly your small intestine—you’ve got trillions of bacteria. There are more bacteria in your gut than there are cells in your body. Some people like to say you are more bacteria than human if they want to make a point—and it’s sort of true. But not just because of the sheer number of these little guys.

It turns out that on top of playing a major role in your digestion and immunity, your microbiome has quite a bit to do with WHO YOU ARE!

How is that? Well, first of all, your microbiome influences your hormones—when they are stimulated, suppressed and how much or how little. Your hormones have a pretty big affect on your behavior. They are what make you feel hungry, full, aggressive, peaceful, content, agitated, energetic, tired, etc.

Furthermore, while it is a new field, it turns out your microbiome exerts a lot of influence on your brain. Many are starting to call the microbiome in your gut the “Second Brain” because it actually produces a lot of the neurotransmitters we’ve traditionally considered to be limited to the brain. That includes MOST of our body’s serotonin, about half of the dopamine and, most relevant to this particular discussion, about half of the body’s melatonin– the neurotransmitter that makes you feel sleepy.

Sleep and the microbiome

This discovery has spurned a new branch of psychology called psychobiotics, and there’s research out there disocvering how fixing the microbiome can also fix things like depression and anxiety.

Considering both depression and anxiety are both causes of poor sleep and insomnia, you’ve got your first clue as to how the gut is linked to sleep.

But it goes even deeper. It turns out that the melatonin produced in your brain is different than the melatonin produced in your gut. Researchers aren’t exactly sure what that difference is, or why, but what they do know is that your brain produces melatonin when it gets dark. Your gut produces melatonin around mid-day. It might be to prep for and begin that wind-down process to bedtime and counteract all the testosterone and cortisol that you produce during your active hours—but that’s just speculation.

In any case, this is all related to the Circadian Rhythms. Here is a recent article I did on Circadian Rhythms for reference, but in short, if you are operating as you should be, you get tired at night and you are primed for high activity between 8am and 5pm—ish. Most of us get up in the morning very tired, wake up for a little while (thanks to coffee), get tired again mid-afternoon but power through it, then we’re wide awake late at night. It turns out that your gut bacteria have their own Circadian Rhythms too, and it gets out of whack just like the one in your brain.

The bacteria in your gut also produce tryptophan. You might have heard this as being one of the things you ingest when you have turkey—which is why everyone always feels sleepy after Thanksgiving dinner.

Tryptophan is the chemical precursor to melatonin, so you do need your gut to produce tryptophan before even your brain can make melatonin.

Finally, a healthy gut literally makes you more tolerant to pain, and pain is the most commonly-listed reason people say they can’t sleep. This comes from a 2015 study in the Journal of Neurogastroenterology and Motility that found a link between how the gut bacteria communicates with the brain via the vagus nerve, and how disrupting that makes us feel like everything hurts more than it would if our gut and brain were communicating well. It’s cutting edge stuff!

As you can see, a healthy gut is going to mean a healthy sleep. But most of us don’t have a healthy gut. The next question is why? And how do I fix it?

How you are hurting your microbiome

First on the list. Stress kills the microbiome. Having a bad microbiome compromises the ability to manage stress. Stress compromises sleep. It’s a vicious cycle. Stress also releases the hormone cortisol, that makes you alert and puts you into “fight or flight” mode.

But the two ways you hurt your microbiome are with antibiotics and a leaky gut. Antibiotics are fairly straightforward. They are meant to kill bacteria and your microbiome is made up of bacteria.

The problem is, taking even one round of antibiotics will knock out your microbiome for up to seven years. And unfortunately, until recently, antibiotics were very much over-prescribed. Luckily, doctors are starting to scale back their prescriptions because there is fear of a “superbug” that is resistant to antibiotics, but it helps to save our gut at the same time.

My recommendations would be to learn the antibacterial and antiviral applications of things like coconut oil, garlic, ginger and other natural remedies. Save antibiotics as a last resort solution to an infection.

A leaky gut, sometimes called intestinal permeability, means that over time, the individual cells in your small intestine have spread apart enough that molecules get through into the bloodstream.

Sugar, toxins like pesticides and antibiotics and BPA from plastics, gluten from grains and stress contribute to a leaky gut.

Fix your microbiome

The quickest and easiest way to get rid of a leaky gut is to go on a 4-day bone broth fast. The collagen in the bone broth coats the inner wall of your intestine with a protective layer, giving it time to heal and for the gap junctions to close.

As long as you don’t eat anything during this time, that’s all it takes. And for those of you saying, “Well! I could never NOT eat for FOUR WHOLE DAYS!” I’ve seen hundreds of people do it. Young people, older people, overweight people, skinny people, diabetics, cancer patients and all manner of perfectly normal and sane people who were just willing to go the distance to get their health back.

Other than that, you’ve got to get rid of the things that cause leaky gut. Like I said, no antibiotics. Cut out sugar, grains, GM foods, processed foods, all medications you can, use glass water bottles instead of plastic. Use organic cleaning products and beauty products.

Figure out ways to manage your stress. Meditate, exercise, participate in hobbies you enjoy. If you used to play soccer, join an adult league. If you used to play guitar, pick it up again!

If you can heal your leaky gut, you’ll lose weight (which you’ll love) and your inflammation will go down throughout your body, reducing pain—which helps you sleep.

The next step is just continuously supporting your microbiome. Stay away from processed foods, sugars and antibiotics, but also eat fermented foods to support the healing and growth of your microbiome.

That includes sauerkraut, kimchi, kombucha, lassi, raw yogurt, raw cheese and dairy.

See, you can take a supplement, but it usually only contains a handful of bacterial strains when you need hundreds or even thousands of different kinds of bacteria in your gut. You get more from fermented foods.

Breaking the cycle

Sleep is one of these things that is very much subject to cycles and circular processes. Of course, there’s the Circadian rhythm that ideally fits into the rising and setting of the sun.

But there are other cycles you get into.

Poor sleep damages the microbiome. A bad microbiome hurts circadian rhythms and the ability to sleep. You can’t fix one without the other, and it’s a downward spiral where one feeds the other and you have to break the cycle somehow.

Since you can’t force yourself to sleep without drugs (and I highly recommend you DON’T do that because it’s not real, restful sleep you’re getting). So it’s easier to break the cycle by first healing the gut and microbiome. Sleep will come later.

Or how many of you recognize this cycle? Come home from work, fall asleep on the couch for an hour or two, go to bed way too late because you’re not tired, wake up in the morning for work extremely tired. Repeat.

You’ve got to understand that naps, while sometimes useful and warranted, don’t give you the same health benefits as long, uninterrupted sleep. You need to break this cycle as well. Skip the naps for two weeks. Go to bed earlier. You’ll get more done throughout the day and won’t wake up so tired.


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