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How to Improve Gut Health Naturally? These 2 Things Are Key

Improve your gut health by getting enough sleep, living in sync with your circadian rhythm, tweaking your diet, exercising, and keeping stress low.
Written by
Jeff Kahn, M.S., Rise Science Co-Founder
Reviewed by
Chester Wu, MD, Rise Science Medical Reviewer
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Updated Regularly
We regularly update our articles to explain the latest research and shifts in scientific consensus in a simple and actionable way.
Woman eating yogurt to help improve her gut health alongside sleep

Even when you’re alone, you’re never really alone. You’ve got trillions of bacteria, viruses, and fungi living in your gut contributing to or sabotaging your overall health. 

When things are going well, these gut inhabitants can help us feel, look, and perform our best. When things aren’t going so well, they may cause us to suffer from low energy, anxiety, depression, digestive distress, and serious health conditions like obesity and diabetes. 

“Gut health” has become a bit of a buzzword. And while you should skip over the ads for supplements promising instant results, there are science-backed ways you can improve it naturally.

Below, we’ll dive into how you can improve your gut health naturally and how the RISE app can help. 

What is Gut Health?

What exactly is gut health? In short, it’s the health of our gut microbiota, the microorganisms that live inside our gut and contribute to everything from digestion to heart health, weight to mood. They can have a profound impact on our overall well-being. 

There are a lot of bacteria, viruses, fungi, and protozoa living in our gut — about 100 trillion of them, in fact. And the more diverse this population, the better our health. 

We inherit some parts of our gut microbiota, but factors like diet, sleep, stress, and antibiotic use may play a more deterministic role in their health and composition. 

Why is Gut Health Important?

Gut health is important for many reasons. Firstly, the gut is where digestion happens. We need food to fuel our bodies, but if our guts are in poor shape and can’t digest this food properly, we won’t get the nutrients we need to feel and perform our best. 

We also need microbiota diversity, or a variety of different species of microorganisms in the gut. Lower microbiome diversity is linked to health conditions like: 

  • Obesity
  • Inflammatory bowel disease (IBD) 
  • Type 1 and type 2 diabetes 
  • Celiac disease 
  • Psoriatic arthritis 
  • Atopic eczema 

A healthy gut has also been linked to a healthy immune system. But gut health isn’t just important for keeping health problems at bay. It may play a role in how much energy we feel. Your gut microbiota may influence how much energy your body makes and how this energy is used. 

Beyond physical health, your gut can also affect your mental health. Your gut microbiota communicate with your brain via the vagus nerve — this is called the gut-brain axis. 

When your gut isn’t happy, neither are you. Poor gut health has been linked to anxiety and depression, and changes to diet that improve gut health may help to improve mental health issues. 

Your gut health also impacts your sleep. And as your gut affects your mood and sleep so much, it may be one of the reasons insomnia and depression appear together so frequently. An imbalance in your gut microbiota may even contribute to brain fog

Here are two key impacts of poor gut health you may not have thought about. 

Your Gut Health Impacts Your Sleep  

If you’ve got digestive issues like acid reflux or irritable bowel syndrome (IBS), you may struggle to get the sleep you need at night. But the link between gut health and sleep goes deeper than that. 

Good sleep is needed for gut health. And gut health is needed for good sleep, which is needed for almost everything else in life — energy, productivity, mental and physical health. 

The gut provides about 95% of the body’s serotonin, and serotonin is needed to produce the sleep hormone melatonin. 

A 2019 study found that more diversity in your gut microbiota is linked to increased sleep efficiency (which measures the time spent sleeping in bed), increased total sleep time, and less time awake during the night. A diverse microbiome can even increase how much deep sleep you get. 

Sleep fragmentation and short sleep duration have been linked to gut dysbiosis, or an imbalance in gut microbiota. And probiotic supplements, which boost gut health, can improve subjective sleep quality (although there’s no set definition for sleep quality). 

When you don’t get enough sleep, the end products of the types of bacteria that can grow in your gut when sleep deprived can cause fatigue, as if the sleep loss itself wasn’t making you tired enough. 

Your Gut Health Impacts Your Circadian Rhythm 

Beyond sleep, a healthy gut is important for a healthy body clock. We’re going to dive into the science here, but trust us, it’s important for your gut and overall health. 

First up, what is your circadian rhythm exactly? Your circadian rhythm is your body’s roughly 24-hour biological clock. You have one master clock in your brain that dictates things like your sleep-wake cycle, the production of certain hormones, and your body temperature fluctuations. 

You also have clocks in almost every tissue and organ in your body, including in your gut microbiome. These are called peripheral clocks. 

The master clock and peripheral clocks can get out of sync with each other and with the outside world, and this can lead to a whole host of health problems.

The master clock communicates with your peripheral clocks and can affect their timing. And your peripheral clocks can have an impact on your master clock, too. 

That means if your gut clocks are out of whack, they can alter the timing of your master clock, and therefore your sleep-wake cycle. And if your master clock is out of sync with the outside world, this can throw off your gut’s clocks, and therefore your gut health and digestion. 

What do your gut’s clocks do? Throughout the day and night, microbiota composition and what function they’re doing changes. For example, Bacteroidetes bacteria are higher at night than during the day. Firmicutes bacteria, on the other hand, are higher during the day. 

These circadian rhythms are predominantly affected by your meal times, but also your sleep times. When you live out of sync with your circadian rhythm — by sleeping or eating at odd times, for example — your gut microbiome is thrown out of balance.  

For example, circadian rhythm disruption from working night shifts, for example, can lead to changes in gut mitochondria. This is linked to metabolic syndrome, which includes obesity, high blood pressure, and type 2 diabetes. 

It’s a vicious cycle, too. Sleep loss or circadian misalignment can change your gut mitochondria. These changes can then cause inflammatory reactions, metabolic disorders, impaired immune function, and nervous system dysfunction. These health issues can lead to trouble sleeping and psychiatric problems like depression, which can cause even more sleep loss and gut damage. 

How Do You Know if You Have a Healthy Gut?

It can be hard to tell if you have a healthy gut or an unhealthy gut. But if you suffer from digestive issues, your gut is probably not in the best shape. 

These issues include: 

  • Cramps 
  • Bloating 
  • Constipation 
  • Diarrhea 
  • IBS 
  • Changes in your bowel habits 
  • Pain when using the bathroom 

Other signs you may not think of are poor sleep, poor skin, and brain fog.   

How to Improve Gut Health Naturally?

We’re still learning about the gut and just how much of an impact it can have on other areas of our health. So, more research needs to be done on how we can protect and improve our gut health. Here’s what we do know. 

1. Keep Your Sleep Debt Low 

RISE app screenshot showing how much sleep debt you have
The RISE app works out how much sleep debt you have.

Sleep debt is the measure of how much sleep you owe your body. It’s compared against your sleep need, the genetically determined amount of sleep you need. 

If, for example, your sleep need is 8 hours 30 minutes, but you only get six or so hours of sleep a night, you’ll have built up a lot of sleep debt. This not only tanks your energy levels, it affects your gut health. 

One study found that even just two nights of partial sleep deprivation (defined here as four hours 15 minutes of sleep a night) can change your gut bacteria for the worse. 

It’s not all about duration, though. Sleep fragmentation also affects your gut. When mice had fragmented sleep for four weeks they ate more food and their gut bacterial composition changed, which led to inflammation and changes in insulin sensitivity. 

Sleep disorders like sleep apnea can also mess with your mitochondria composition

More research needs to be done into why sleep affects our gut health so much. It may be that it’s having an impact through other factors. For example, sleep loss can cause stress (sleep deprivation is stressful for the body) and changes to your diet (you’re more likely to reach for junk food and overeat when you’re sleepy). So, it may be that stress and diet changes are causing gut health changes, but we don’t know for sure.

At RISE, we measure your sleep debt over your last 14 nights and recommend you keep it below five hours to maximize your health. 

Got more than five hours? Here’s how you can pay back sleep debt: 

  • Take a nap: Do this during your afternoon dip in energy (check RISE for when this will be each day) to stop naps affecting your nighttime sleep. 
  • Go to bed a little earlier. 
  • Sleep in a little later: Keep this to an hour or two to avoid circadian disruption.  
  • Improve your sleep hygiene: Sleep hygiene habits can cut down the time it takes you to fall asleep and reduce how often you wake up during the night, reducing sleep fragmentation and helping you get more sleep overall. RISE can guide you through 20+ daily behaviors.  

Want to maximize your sleep? We’ve covered the best side to sleep on for digestion here.

RISE users on iOS 1.202 and above can click here to view their sleep debt.

RISE users on iOS 1.202 and above can click here to set up their 20+ in-app habit notifications. 

2. Stay in Sync with Your Circadian Rhythm 

As we explained above, your master clock can get out of sync with the outside world, and it can get out of sync with your peripheral clocks. Both impact your gut’s clocks and how well it functions. This may lead to metabolic disorders such as obesity and diabetes. 

We covered how disrupting your circadian rhythm can wreak havoc with your gut mitochondria. Here’s how to get back in sync: 

  • Keep a consistent sleep schedule: Aim to go to sleep and wake up at roughly the same times each day, even on weekends. 
  • Eat meals at roughly the same times and during the day: Keep regular meal times and avoid eating at night or eating close to bedtime.
  • Go to bed during your Melatonin Window: This is what we call the roughly one-hour window of time when your body’s rate of melatonin production is at its highest. As melatonin primes your body for sleep, going to bed during this window can help you fall asleep, stay in sync, and meet your sleep need.

The RISE app predicts your circadian rhythm each day, showing you when your body naturally wants to wake up, wind down for bed, and go to sleep. You can then sync up your sleep and meal times to it. 

RISE users on iOS 1.202 and above can click here to see their circadian rhythm on the Energy screen.

3. Try Time-Restricted Eating 

Time-restricted eating is when you eat all of your meals for the day within a set window of time. 

More research needs to be done, but when mice fasted for 16 hours, and ate only in an eight-hour window, they had more good bacteria in their guts. 

Earlier research on mice found time-restricted eating promoted more good bacteria and less of the bad bacteria in their guts that can lead to obesity. 

Time-restricted eating may also change how your gut digests certain foods. For example, research from circadian expert Satchin Panda’s lab has shown time-restricted eating in rodents can change how the gut breaks down and absorbs fiber. A large proportion of the sugars are excreted, instead of absorbed. 

More research needs to be done to find the ideal eating window, but you could start with a 12-hour window, which would mean having breakfast at 8 a.m., for example, and being done with dinner by 8 p.m. 

Keeping meals to during the day and not too close to bedtime can also ensure digestion and digestive issues don’t keep you up at night, building up sleep debt and sabotaging your gut health this way. 

4. Eat More Fiber 

Fiber can promote regular bowel movements, prevent constipation, and control blood sugar. And a higher intake has been linked to eating less, having a lower body weight, a reduced risk of heart disease, and lower mortality, especially from circulatory, digestive, and inflammatory diseases. 

High-fiber foods include: 

  • Beans 
  • Berries 
  • Avocados 
  • Lentils 
  • Chickpeas 
  • Oats
  • Quinoa 

It doesn’t take long for your diet to affect your gut health. Your gut mitochondria might see changes within a few days

The food you eat also affects your sleep. We’ve covered the best foods for sleep here.

5. Eat More Prebiotics 

Prebiotics are classified as fiber, but not all fiber is prebiotic. Prebiotics aren’t absorbed in the upper GI tract, they’re fermented in the gut, and they promote growth or activity of good bacteria.

A prebiotic diet has been shown to prevent stress-induced reductions in gut diversity, and increase how much rapid-eye-movement sleep (REM sleep) you get after exposure to stress. REM is important for consolidating memories and regulating emotions. 

Prebiotic foods include: 

  • Leeks 
  • Asparagus 
  • Garlic 
  • Onions 
  • Wheat
  • Soybeans 

6. Eat More Probiotics

Probiotics contain good bacteria to help improve gut diversity. They can be found in fermented foods like: 

  • Sauerkraut
  • Kefir
  • Yogurt
  • Kimchi
  • Kombucha 
  • Miso 

Probiotic supplements may also help improve your gut health, but more research needs to be done to see if these are more or less beneficial than probiotics from foods. 

Probiotic supplements may help if you have digestive issues, however. In those with IBS, probiotic supplements have been shown to ease abdominal pain and bloating, increase pain tolerance, and improve “satisfaction with bowel habits.”

7. Eat More Polyphenols 

Dark chocolate lovers rejoice, it can have some health benefits. It contains polyphenols, a plant compound that improves gut mitochondria function and composition, and it may be anti-inflammatory, too.  

You can find polyphenols in: 

  • Dark chocolate 
  • Green tea 
  • Almonds 
  • Blueberries
  • Broccoli 
  • Artichokes
  • Red wine (although, newer research suggests you would have to drink a prohibitive amount to get the benefits)

8. Eat a Mediterranean Diet

The Mediterranean diet may be able to promote brain function, lower cholesterol, increase weight loss, and prevent premature death, and it may be the best diet for gut health.

Research shows the Mediterranean diet can promote healthy changes in your mitochondria. 

The Mediterranean diet includes: 

  • Fruits 
  • Veggies
  • Nuts 
  • Seeds
  • Complex carbohydrates  
  • Fish 
  • Extra virgin olive oil 
  • Moderate dairy intake 

9. Avoid Sweeteners and Additives

When it comes to what to avoid, skip sweeteners and food additives

Sucralose, aspartame, and saccharin can disrupt the balance and diversity of your gut. And additives found in processed foods may lower the gut’s good bacteria and increase bad bacteria.

Opt for whole foods over processed junk foods. 

10. Keep Stress and Anxiety Low 

RISE app screenshot showing you different guided relaxation techniques
The RISE app can guide you through relaxation techniques.

Stress and anxiety can disrupt microbiota composition. And this is another example of a relationship that may go both ways. Some probiotics in the gut may improve stress response and reduce anxiety.  

Stress can also cause intestinal permeability, or leaky gut, when food and toxins leak from the intestines into the bloodstream. This can lead to bloating, cramps, and food sensitivities. 

Stress can come from daily life, or from not getting enough sleep — a huge stressor on the body. And stress can also keep you up at night, making it even more damaging to the gut. 

Keep stress in check by: 

  • Do a calming bedtime routine: Read, do yoga, journal, or listen to calming music in the run-up to bedtime to help slow your body and brain for sleep. 
  • Do a brain dump: Write down what’s worrying you or, if stress is keeping you up, write out a to-do list, which has been shown to help you fall asleep faster than other forms of evening journaling. RISE’s brain dump feature will remind you of everything you write down the next day. 
  • Try relaxation techniques: RISE can walk you through four science-backed relaxation techniques for sleep including progressive muscle relaxation and diaphragmatic breathing. 
  • Ask for help: Reach out to friends, family members, your healthcare provider, or a therapist to get help managing stress and any mental health struggles. 

Anxious thoughts keeping you up? You can learn more about how to sleep with anxiety here.

RISE users on iOS 1.202 and above can click here to go right to their relaxation audio guide homepage and get started.

RISE users on iOS 1.202 and above can click here to set up their Brain Dump Habit notification

11. Exercise 

Exercise can help you lose weight, fall asleep, and keep your gut healthy and happy.

Research shows exercise can improve mitochondrial diversity, which could contribute to weight loss and help improve gastrointestinal disorders. Moderate endurance exercise has been shown to improve diversity and composition of gut mitochondria, as long as it’s not too intense.

A healthy gut may even help you have more motivation to exercise. Research on mice found those with depleted gut microbes got exhausted earlier and ran less on their wheel. The makeup of your gut microbiome may be a greater predictor of how long you can exercise for and how much you want to exercise than genetic, metabolic, or behavioral traits. 

Just be sure not to exercise too close to bedtime. This can keep you up and throw off your circadian rhythms. We’ve covered the best time to work out here.

12. Cut Down on Alcohol 

For a healthy microbiome, consider cutting down on alcohol. Alcohol can decrease the good bacteria in your gut, cause intestinal damage and leaky gut, and increase your risk of gastric cancer. 

Alcohol can also be a trigger for digestive system issues like acid reflux or IBS. And it can mess with your sleep, which, of course, can mess with your gut health. 

Cut down on alcohol and avoid drinking three to four hours before bed to stop it from waking you up at night. 

We’ve covered more on how long before bed you should stop drinking alcohol here. 

If you need a reminder, RISE can tell you when to have your last alcoholic beverage each day. 

RISE users on iOS 1.202 and above can click here to set up their avoid late alcohol reminder.

13. Quit Smoking 

Smoking can also reduce good bacteria in your gut and cause leaky gut and inflammation in your digestive tract.

Smoking can also cause digestive health issues like acid reflux, gastroesophageal reflux disease (GERD), peptic ulcers, and digestive cancers. 

Smoking can also disturb your sleep. Smokers sleep for shorter periods of time, take longer to fall asleep, and show insomnia-like sleep impairments that non-smokers don’t. But quitting can improve your sleep long term. 

14. Avoid Antibiotics (if Possible) 

Sometimes you need to take antibiotics for an illness, but when at all possible, avoid them for the sake of good gut health. 

Antibiotics can reduce species diversity and change the metabolic activity of your gut. The surviving microbiota can convert antibiotics into chemicals that affect your brain function and cause side effects like anxiety. 

Low-dose antibiotic intake from food (found in some meat and dairy products) may also mess up your gut diversity.

If you need to take antibiotics, increase your probiotic intake to counter the damage. A supplement may be needed, but speak to your healthcare provider or a dietitian before taking one to make sure it’s right for you. 

Pay special attention to getting enough sleep and staying in circadian alignment while taking antibiotics to avoid further damage to your gut health. 

15. Drink Enough Water 

Water helps keep things regular and prevents constipation, it can also improve the health of your gut bacteria. 

A 2022 study found drinking water was linked to more gut diversity and less of the bad bacteria that can lead to gastrointestinal infection. 

How much is enough? Just like with sleep, it’s different for everyone. But, according to the US National Academies of Sciences, Engineering, and Medicine, women should drink about 11.5 cups of water a day and men should drink about 15.5 cups a day. 

You may need to drink more if you do a lot of exercise or live in a hot climate.

16. Enjoy Coffee Wisely 

RISE app screenshot showing when to limit caffiene
The RISE app can tell you when to stop drinking coffee each day.

You don’t need to give up your morning cup of joe to boost your gut health. In fact, it may be helping it. 

One study found drinking three cups of coffee for three weeks increased the amount and the activity of beneficial bacteria in the gut. 

Research from 2022 even found coffee may correct mitochondrial imbalances in your gut caused by sleep deprivation — although don’t let that be an excuse to swap some shut-eye for caffeine!

Just be sure your coffee habits aren’t getting in the way of a good night’s sleep. RISE can tell you when to have your last coffee of the day

Caffeine can be a trigger for digestive issues like acid reflux or IBS, so cut down or cut it out completely if you find it affects you. 

RISE users on iOS 1.202 and above can click here to set up their limit caffeine reminder.

17. Breastfeed (if Possible) 

You can’t do much about whether or not you were breastfed, but if you’re in the position to, breastfeeding your baby can help nurture their gut health. 

Breastfeeding can promote your baby’s healthy gut mitochondria and may help prevent allergies

Beyond gut health specifically, we’ve covered more things that help with digestion here.

Improve Gut Health in Your Sleep 

There are many things you can do to improve your gut health, but two commonly overlooked methods are lowering your sleep debt and getting in sync with your circadian rhythm. 

The RISE app can work out how much sleep debt you have and keep track of it as you pay it back. RISE can also predict your circadian rhythm each day, so you can easily sync up your sleep and meal times to it. 

As well as promoting gut health, you’ll be boosting your energy levels, improving your mood, and looking after your overall health and wellness. 

Summary FAQs

How can I naturally heal my gut?

Heal your gut naturally by getting enough sleep, living in sync with your circadian rhythm, eating a diet full of fiber, prebiotics, and probiotics, lowering your stress levels, and exercising.

How to improve gut health naturally?

Improve your gut naturally by getting enough sleep, living in sync with your circadian rhythm, eating a diet full of fiber, prebiotics, and probiotics, lowering your stress levels, and exercising.

Signs of a healthy gut

Signs of a healthy gut include regular bowel movements, pain-free bowel movements, good sleep, high energy, and not having regular digestive issues like constipation, diarrhea, and IBS.

What foods repair gut health?

Fiber, prebiotics, probiotics, and polyphenols can all repair your gut health. Try to eat fruits, veggies, whole grains, legumes, dark chocolate, onions, garlic, kefir, sauerkraut, and kimchi.

Worst foods for gut health?

The worst foods for gut health are processed foods with additives, artificial sweeteners, high-sugar foods, fried foods, red meat, alcohol, and foods with antibiotics like some meat and dairy products.

How can I improve my gut health at home?

Improve your gut health at home by getting enough sleep, living in sync with your circadian rhythm, eating a diet full of fiber, prebiotics, and probiotics, lowering your stress levels, and exercising.

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