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Bad Sleep Messes With Your Gut: Here Are 5 MD-Approved Tips To Help

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December 3, 2019

Poor sleep affects everything. Maybe you drink too much coffee to kick-start your day. Or your temper is shorter, so you easily snap at your kids or significant other. It makes even simple tasks at work feel like a struggle, and your entire day just feels off.

What you might not realize is this: Whether it's difficulty falling asleep, staying asleep, or both, when you miss out on good sleep, you're messing with your body's delicate internal rhythms. And that includes your gut. 

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What is sleep fragmentation?

Sleepless nights throw off your gut rhythm by adversely affecting the balance of favorable and unfavorable bacteria1 and compromising the gut wall. This can lead to things like constipation or diarrhea in the short term, and over time can even affect insulin signaling2.

But even if your circadian rhythm seems normal and you are spending eight hours a night in bed, if you are waking up during the night, the overall quality of your sleep suffers. Scientists call this poor-quality sleep "sleep fragmentation." Just as missing out on sleep affects the gut, sleep fragmentation can also adversely affect the gut microbiome.

In other words, when something is off—in this case, sleep—your gut feels the impact. 

How poor sleep affects health.

What affects your gut affects your entire body. This is because the gut microbiome doesn't exist in a vacuum. This complex system interacts with inflammatory, metabolic, and circadian clock systems. So, your behaviors, food choices, and lack of proper sleep hygiene can all have drastic consequences on not only your gut health but your overall health.

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Hormone balance

Poor (or lack of) sleep affects your hypothalamus3, the master control center in your brain of hormones like cortisol, epinephrine, and norepinephrine. When these hormones are out of balance, it can trigger sugar and carb cravings, making you more likely to choose foods that create gut imbalances, further upsetting gut health.

Not getting enough sleep can also lead to poor eating decisions by messing with your hunger hormones4. Poor sleep causes ghrelin, which tells your brain to eat now, to increase, and leptin, which tells you to put down your fork, to decrease. Translation: You're hungry and probably not for wild-caught salmon and Brussels sprouts. Studies have shown5 sleep deprivation leads to cravings for high-calorie, low-nutrient snacks, like candy bars, chips, chocolates, and other desserts.


If your mood is off after a terrible night's sleep, it's not all in your head. Your gut creates most—around 90%, to be precise—of the body's serotonin. While this hormone is attributed to your brain's "happy mood," you actually have more serotonin receptors in your gut6. So, when gut health is disrupted by poor sleep, it can affect serotonin production and, therefore, mood.

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Insulin resistance

One study found that just one night of bad sleep—like the four hours you get before catching that 5:30 a.m. flight—could increase the risk of insulin resistance2 in otherwise healthy adults. Repeated nights of poor sleep will have an incremental effect on this process, paving the way for diabetes and other health complications, like heart disease, over time.

5 ways to improve sleep hygiene.

If you want to fix your gut, start with what goes on the end of your fork. But even when you're eating well, poor sleep can thwart those goals. Sleep hygiene really is that important for your gut and overall health. These five healthy sleep habits create a solid foundation to do just that:

1. Create a sleep routine. Regular sleep patterns mean a happier gut, which translates into a better mood and, well, pretty much better life. Consistency is key with routine, as the body and your gut like predictability. One study found that keeping a regular routine could reduce insomnia7. Finish eating at least three hours before bedtime; don't just eat dinner and then lie down to sleep. A full stomach will most certainly disturb your sleep. Find something that helps you unwind before bed. Try meditation, which activates the calming part of the autonomic nervous system, reducing nighttime cravings for sugary or salty snacks and helping you relax before going to sleep. 

2. Pinpoint sleep hijackers. Many patients know having that after-dinner double espresso can keep them wired into the night, but they might not associate a sugary dessert or second glass of pinot noir with sleep problems. In fact, some of them use wine or sugar to lull them to sleep and then wonder why they're wide-awake at 3 a.m. Keeping a food journal can identify these and other key culprits. Bonus: Participants in one study who wrote everything down lost twice the weight compared with those who didn't.

3. Work out earlier in the day. Studies are mixed about whether exercising too close to bedtime can cut into your sleep. I'm not going to deter you from doing that 7 p.m. boot-camp class, but pay attention to your sleep cycle on those nights. Intense exercise can stimulate your nervous system8, keeping you fired up when you should wind down. Knocking out your workout early in the day can feel like "mission accomplished" and inspire you to hit other goals throughout the day, but fitting it in—period—also matters.

4. Step away from screens before bed. The average adult spends about 11 hours staring at screens daily. (Yes, you read that correctly, 11 hours.) But screen time infringes on sleep. The blue light from screens can suppress levels of melatonin, which regulates your sleep cycles. Try to turn off screens two to three hours before bedtime. That can feel challenging, but your gut and your sleep will thank you. That "urgent" email can wait till tomorrow morning, and knowing what your colleague ate for dinner on Instagram isn't worth cutting into your sleep schedule. 

5. Wear blue-light blockers. Let's be honest: Most of us have a tough time peeling ourselves away from our screens into the wee hours of the night. So, if you can't bring yourself to follow my last tip because you just have to answer those last few emails, then let's biohack the blue-light effects on your retinal nerves in your eyes and brain9. It's easy enough to find blue-light-blocking glasses, even by prescription, that can minimize the sleep-disrupting effects of blue light on your brain. But here's the thing—blue-light blockers only work if you wear them! And even if you are turning off your screens, I still suggest wearing the glasses since the lighting in your home can give off blue light. So, make it a point to start wearing blue-light blockers starting at least three to four hours before bedtime, or even as soon as the sun sets. 

If you have insomnia or other serious sleep disturbances, consider working with a sleep specialist who can create a customized protocol for your condition. At the same time, almost everyone can work on improving their sleep patterns. 

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Vincent M. Pedre, M.D.
Vincent M. Pedre, M.D.

Vincent M. Pedre, M.D., medical director of Pedre Integrative Health and president of Dr. Pedre Wellness, is a board-certified internist in private practice in New York City since 2004. He completed his bachelor’s degree in Biology at Cornell University before attending the University of Miami School of Medicine and completed his residency in Internal Medicine at the Mount Sinai School of Medicine. He has appeared on the Martha Stewart Show and ABC and is the author of Happy Gut: The Cleansing Program to Help You Lose Weight, Gain Energy, and Eliminate Pain. Dr. Pedre is a clinical instructor in medicine at the Mount Sinai School of Medicine and is certified in yoga and medical acupuncture.

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