Your microbiome consists of trillions of microorganisms that live in your digestive system, helping to release nutrients in your food and aid your overall health. Here is a quick program to increase the health of the “good” bacteria in your gut.

How do you know if your internal microbiome is healthy and happy?

“It’s a gut feeling,” says Dr. M. Andrea Azcárate-Peril, a director at the Microbiome Core Facility at the University of North Carolina.

Quite literally. With bacteria and other microbes vastly outnumbering the human cells in our bodies, we’re more bacteria than human. Our bodies can’t function properly without them. They support our immune system, help us process and absorb nutrients, and lower the risk many conditions, including:

  • obesity
  • heart disease
  • diabetes
  • cancer
  • mental health and mood conditions
woman adding strawberries to cereal bowlShare on Pinterest
Design by Andie Hodgson. Photography by Getty Images

Many chronic and autoimmune diseases have also been linked to a microbiotic imbalance — or dysbiosis. This just means: Trust your gut when it’s feeling funny and revisit the state of your health.

Most people already have an idea of how healthy their gut is, according to Dr. Ami Bhatt, an assistant professor and researcher at Stanford University. She says that the intestinal microbiome “really does lend itself to people doing experiments on themselves and figuring out what works for them.”

There are roughly 100 trillion bacteria in the digestive system alone. It may seem like a tall order to change them, but the good news is that your microbiome can quickly change. Research has shown that within days of changing your diet, your gut microbiome can change.

So what are you waiting for? Follow this 3-day fix to build and diversify your gut army and support lasting change for the better.

Montage of legs in black leggings, salad, pillow with 11 pm printed on it, apple (in color with a white checkmark) vs. donuts, cheese, and pork chops (in black and white with a red X)Share on Pinterest
Design by Andie Hodgson. Photography by Getty Images

When to wake up

Let your body wake up naturally

Sleeping in line with your body’s natural circadian rhythm is important for good sleep and a healthy gut.

“The gut microbiota has a circadian rhythm like we do,” said Azcárate-Peril. “Our gut microbiota will fluctuate in terms of composition and abundance based on our rhythm of when we eat and sleep. If that circadian rhythm is disrupted, we are going to have issues. We don’t want to interrupt that cycle.”

What to eat today

Ditch the Western diet

A diet that’s high in animal protein, sugar, and fat, and low in fiber — like the diets full of highly processed foods that are popular in the United States — have been shown to decrease the amount of bacteria in the gut, especially of beneficial Bifidobacterium and Eubacterium species.

The Western diet has also been linked to an increased risk of developing diabetes, heart disease, and even certain cancers.

Go Mediterranean

A 2019 study found that a diet rich in vegetables, fruits, and whole grains with a lower intake of red meat, processed foods and meats, and dairy increased the amount of total bacteria in the gut and supported beneficial bacteria like Lactobacillus and Bifidobacterium.

So why not try the Mediterranean diet, which follows these recommendations?

Stick to one glass of red wine or dark chocolate

Other types of alcohol can harm gut health by decreasing beneficial bacteria, but red wine has been shown to support beneficial bacteria in the gut thanks to its concentration of polyphenols. If you don’t want to drink, indulge in fresh berries or dark chocolate to get the same polyphenol benefits.

What are polyphenols?

Polyphenols are plant compounds that have been linked to health benefits like lowering blood pressure and cholesterol. Many polyphenols aren’t absorbed by the body and instead end up being digested by bacteria in the gut.

What to do today

Try to stop smoking, if you do

A small study from 2013 found that when people stopped smoking, they had more microbial diversity in their gut. A 2022 review of 13 studies confirmed smokers experienced a reduction in species diversity in their gut bacteria. To be on the safe side, halt vaping activities too.

Go for a 30-minute run or workout

Add gut health to the list of reasons you should hit the gym. While the gut-exercise connection isn’t yet clear, many researchers believe that exercise reduces stress hormones, which affect the microbes in your gut.

A 2021 review found higher levels of gut microbial diversity in high level athletes. A 2018 study found that exercise increased the microbes that help reduce inflammation, fight insulin resistance, and support a healthy metabolism.

Once the participants stopped exercising regularly, their microbiomes went back to what they had been at the start.

When to sleep: 11 p.m.

Sleep deprivation has been found to alter the bacteria in your gut. Go to bed early — at least 30 minutes before you normally do on a weekday — for quality sleep.

Share on Pinterest
Design by Andie Hodgson. Photography by Getty Images

When to wake up: 7:30 a.m.

Get up earlier so you’re not preparing your body for a late start on Monday.

What to eat today

Add high-fiber foods to every meal

Fiber is key to a happy gut, especially indigestible fiber. Indigestible fiber, aka prebiotics, boost the bacteria you already have instead of adding new bacteria, like probiotics. Feed the bacteria in your gut with:

  • raspberries
  • green peas
  • broccoli
  • beans
  • lentils
  • whole grains

They’ll help support beneficial bacteria like Bifidobacteria.

Cut added sugar

The microbes in your belly love sugar just as much as you do, but the results aren’t great.

Simple sugars feed bacteria and can lead to overgrowths of less beneficial or harmful bacteria and reduce diversity. Check out the ingredient list in breads, sauces, and condiments and keep your daily intake under the recommended limit of 37.5 grams (g) for men and 25 g for women.

Have a glass of kombucha

Fermented foods contain beneficial live bacteria. Some examples include:

These probiotic foods can help improve intestinal health and digestion by supporting and introducing beneficial microbes. When choosing fermented foods, be sure to pick items that are low in sugar like unsweetened yogurt.

What to do today

“We live in a society that is too clean,” said Azcárate-Peril. “We are not exposed to enough microbes during childhood, so we are not properly educating our immune systems.”

Play with a pet

Older studies have found that exposure to pets as infants and children can:

  • reduce the risk of developing allergies
  • support a healthy immune system
  • encourage a diverse microbiome

Further research is needed to better characterize the effect of pet ownership on the human gut microbiome. But that doesn’t mean that adults don’t benefit from the fuzzy snuggles, too.

Get dirty

Garden. Play outside. Lounge on the grass. Exposure to the natural microbes around us can help replenish our microbiota and encourage diversity.

It’s probably not wise to go around licking subway poles or eating undercooked chicken, but most of us could benefit from a little less ‘cleanliness.’

When to sleep: 11 p.m.

Keep the early bedtime to wake up refreshed tomorrow and stay in sync with your circadian rhythm.

Share on Pinterest
Design by Andie Hodgson. Photography by Getty Images

When to wake up: 6:30 a.m.

Try to get up at least 7 hours after you went to bed to bank a full night’s rest.

What to eat today

Try a meatless Monday

Diets that are loaded with fruits and veggies and low in meat have been linked to more diverse microbiota and an abundance of good bacteria like Prevotella. Meat-heavy diets can increase the abundance and activity of microorganisms that have been linked to inflammatory bowel disease.

Drink two extra glasses of water

Proper hydration is key to keeping food moving through your intestines properly, and this movement is vital for a healthy gut.

What to do today

Throw out your antibacterial toothpaste, dental floss, and mouthwash

Antibacterial chemicals can cause antibacterial-resistant microbes and harm beneficial bacteria in your mouth.


Animal studies have found that stress reduces beneficial bacteria and increases harmful bacteria in the gut.

Chronic stress is particularly dangerous because it may increase intestinal permeability (also known as leaky gut) and allows the gut microbiota to go where they shouldn’t, causing inflammation.

When to sleep: 11 p.m.

Keep up a healthy sleep pattern and go to bed early to wake up sharp tomorrow. Even partial sleep deprivation can alter your microbiome, and recent findings suggest that these changes reduce your cognitive function.

A healthy, low stress lifestyle with an emphasis on sleep, exercise, and plant-based foods is the best way to support good gut bacteria. But if you’re only going to stick with one thing: Change your diet to include more whole foods and vegetables. This will have the single biggest impact.

For the rest of the week:
  • Mix it up and try new foods. Eating diverse foods leads to a happier gut and a more diverse microbiota.
  • Skip harsh, aggressive cleaners like bleach and use natural cleaners like soap and water instead.
  • Take antibiotics only when absolutely necessary.
  • Exercise regularly.

While your microbiome may change quickly with what you eat, there are no quick fixes or overnight miracle workers for a healthy gut. Instead, it’s about sticking to the small changes that add up.

“Our microbiome is a mirror of our lifestyle,” said Bhatt. “We need to enact healthy lifestyles over the long term if we are going to see that reflected in our microbiome.”

Mandy Ferreira is a writer and editor in the San Francisco Bay Area. She’s passionate about health, fitness, and sustainable living. She’s currently obsessed with running, Olympic lifting, and yoga, but she also swims, cycles, and does just about everything else she can. You can keep up with her on her blog and on Twitter.