By Courtney Sperlazza, MPH
Reviewed by Emily Gonzalez, ND for Scientific Accuracy

Article at a Glance:

  • Your gut flora are the microorganisms that line your digestive tract, help digest your food and play a role in everything from your immune system to your weight.
  • Antibiotics, sugar and even stress can throw your gut flora out of balance and do a number on your digestive health.
  • Small steps, like taking specific strains of probiotics, eating prebiotic foods and cutting back on sugar, can help restore healthy gut flora as soon as possible.

You have a gut feeling that your digestion is out of whack. Maybe you have to take a course of antibiotics, you feel gassy after eating or you’ve been extra stressed and turning to rich foods and comforting sweets (hey, you’re human). Now you’re wondering how to restore healthy gut flora. Good news: You can take steps to support digestive health and balance your gut microbiome. Keep reading to find out how.


You have a world of microorganisms living in your digestive system. This collection of microorganisms is your gut flora, also known as the gut microbiota—a complex ecosystem that consists of approximately 300 to 500 bacterial species. That’s nearly 10 times the number of cells in the human body.

Our knowledge of the interaction between gut health and overall health is still in its early stages. We do know that colonies of beneficial bacteria help you digest and absorb your food, fight off germs that make you sick and even make a large portion of your serotonin, which helps keep your moods level.

Science is continuing to discover ways that gut bacteria are directly linked to your health. We know that it’s normal to have balanced populations of beneficial gut bacteria and “bad” bacteria, and a healthy gut is able to keep the bad guys in check. But researchers are just now beginning to understand what happens when other factors—like antibiotics, diet and stress—tilt the scales in the wrong direction


Here’s one of the hallmarks of a healthy gut: a thriving population of beneficial microbes, and a diverse mix of them. These good guys support overall human health, but they also prevent the bad microbes from taking over—aka the harmful bacteria that can contribute to inflammation and changes to your weight.

What does that mean for you? Be mindful when you’re dealing with factors that can impact your healthy bacteria. Some factors, like age and getting sick, aren’t in our control. But you can take positive steps with other factors, like what you eat after taking antibiotics, the amount of sugar in your diet and how you manage stress. Below, we’ll expand on a few of these, plus general tips to restore gut flora. As always, maintain open communication with your healthcare provider.


Antibiotics target all bacteria—the good ones and the bad. You can take certain actions to replace the good bacteria while you’re on antibiotics, and help nurture them back into balance after the course is over.

Back in the day, doctors used to think that a healthy body was a sterile body, and that our immune systems were constantly fighting the microbes we came in contact with. Once antibiotics were invented, millions of lives were saved as people were protected from bacterial infections.

Now, the medical community understands that there’s a whole world of beneficial organisms living within your intestines, and as long as we keep them balanced, we’ll stay healthy. Unfortunately, this means that antibiotics are one of the biggest threats to gut health.

Antibiotics kill off the bacteria responsible for infection, but they also kill the friendly gut bacteria and microbial diversity you want to nurture. In the best case, you might have gas and diarrhea for a few days. In the worst case, it can get so bad that the balance of your microbiome shifts, and you can end up with problems like malapsorption, changes to your digestion, candida (yeast) overgrowth and even changes to your mental health.

There’s certainly a time and a place for antibiotics. For aggressive infections, surgery and other instances, you have to have them, and we’re lucky to have access to medicine. It’s also best to have a few preventive measures in your back pocket to keep your gut strong while you’re on antibiotics. That way, you can get back in balance faster when you’re finished.


You are what you eat—at least when it comes to your gut flora. Alcohol and highly processed foods can all negatively impact gut health, but we’re going to focus on one of the biggest players: sugar.

A diet high in sugar can feed the bad bacteria in your gut, creating an optimal environment for the not-so-good microbes to thrive. That’s because high sugar intake seems to change the balance of bacteria in your gut, increasing populations of microbes that contribute to inflammation and gut permeability (or “leaky gut”).

Switching to artificial sweeteners isn’t any better—rodent studies indicate that saccharin, sucralose and aspartame cause shifts in gut microbiota and contribute to intestinal dysbiosis, or an imbalance of microorganisms

What about stress and sleep? Here’s the long and short of it:

  • Stress and gut health: Mental stress—that’s anything from work to the news to family life—can interfere with the communication between your gut and your brain, aka the gut-brain axis. This missed connection contributes to symptoms like nausea, bloating and even the health of your gut bacteria.
  • Sleep and gut health: Losing sleep (or chronic low-quality sleep) can negatively change the ratio of bacteria in your gut, increasing the risk of insulin resistance, increased gut permeability and even sugar cravings.


You don’t have to sit around and just wait for your body to readjust. Read on to find out how to restore your gut flora so you bounce back and feel your best with a rockstar gut microbiome.


Probiotics are your good gut bacteria—the ones that support healthy digestion, produce nutrients and get rid of toxins and pathogens, among other key roles. A diet rich in probiotics (like what you find in kefir, sauerkraut, kombucha and kimchi) can help good microbes colonize in your gut and keep the unfriendly ones at bay.

Heads up: Fermented foods like miso and conventional yogurt don’t work for everyone. Get the details about histamines in fermented foods.


Every dose of antibiotics wipes out a large portion of bacteria throughout your entire body, including the good guys. After that, the good microbes and the unfriendly ones slowly rebuild, and if all goes well, they come back into balance. But, it takes time, and they don’t always colonize in harmony.

To keep one strain of gut flora from taking over, take a probiotic supplement while you’re taking antibiotics. The friendly probiotic bacteria may not colonize in the gut, but they can still help you through a course of antibiotics.

If you time your probiotic dosage right, the good bacteria that are just passing through will be able to do their job and keep the bad guys in check. A few will even survive and be able to continue to keep the balance until the next dose of antibiotics wipes them out.

  • Timing and type are crucial: Make sure to take your probiotics at least two hours before or after antibiotic doses. Also, if you are sensitive to probiotics, avoid strains that might generate histamines, like Lactobacillus caseiLactobacillus reuteri and Lactobacillus bulgaricus. Instead, opt for Lactobacillus plantarum, Bifdocaterium lactis, Bifdocaterium infantis and Bifidobacterium longum. These strains lower histamine levels, reduce inflammation and improve digestion.
  • Take S. boulardiiS. boulardii is a beneficial yeast, not a bacteria, so antibiotics can’t touch it. In several studies, researchers found that S. boulardii prevented antibiotic-associated diarrhea (AAD) when they administered it with antibiotics.


Probiotics are essential, but in order for good bacteria to thrive, they need to eat. That’s why you need prebiotics in your diet. Prebiotics are compounds that feed beneficial gut bacteria. Well-fed, friendly bacteria populate the gut lining, helping to nurture a healthy biome. This helps restore and maintain the integrity of your gut lining.

You can get prebiotics from chicory root, artichokes, leeks, whole grains and foods that are high in resistant starch—a type of starch that resists digestion. It ferments in your digestive tract and feeds the beneficial bacteria in your gut. Sources of resistant starch include unroasted cashews, raw green bananas, raw plantain flour and raw potato starch. It can cause digestive distress in some people, so start slow and build up to a few tablespoons.

Here’s a simple way to get prebiotics in your diet: Take a prebiotic supplement. Bulletproof InnerFuel Prebiotic contains a diverse blend of plant-based prebiotics to support healthy digestion. It mixes easily in hot or cold liquids, so it’s an easy daily add-in to coffee, smoothies and shakes.


A diet high in refined sugar, artificial sweeteners and even natural sugars (including fruit!) can all throw your gut flora out of balance, so you want to limit your sugar intake—especially around antibiotics.

Without bacteria to keep them at bay, fungi have the opportunity to get busy during a course of antibiotics. You can attribute a lot of the problems that you experience after antibiotics—like diarrhea and infections down south—to fungal overgrowth, particularly yeast. One problematic strain of fungus is candida albicans, which is especially prone to going haywire after antibiotics.

Candida thrive on sugar and simple carbohydrates (like bread and pasta) that your body quickly turns into sugar. Candida will flourish if it gets sugar from the food you eat and bacteria aren’t present to fight back. To keep it from taking over, keep your sugar and carb intake to a minimum. They won’t get very far if they don’t have a substantial food source.


The bacteria that line your digestive tract protect the membranes that keep intestinal contents on the inside where they belong. As they wear away, fungi have the chance to colonize in their place. When fungi grow, they shoot out hyphae, thin filament-like roots that dig into the intestinal walls. Essentially, they poke holes in your intestines which allow partially digested food particles to seep outside of the digestive tract and cause problems.

So, what can you do? Make sure you’re eating foods that support strong connective tissue, like bone broth and collagen-rich foods. Collagen is the protein that holds your membranes together, and taking collagen peptides will give your cells all of the amino acids they need when it’s time to make your intestinal walls stronger and more resilient

You can’t make collagen without vitamin C, so it’s a good idea to boost your vitamin C intake when supplementing with hydrolyzed collagen. (That’s why Bulletproof Collagen Protein contains vitamin C, too.)


When a large portion of bacteria gets wiped out, they rebuild slowly. As with any population competing for resources, it’s a bit of a race to repopulate. While this is happening, you want to feed the good guys and starve the bad guys.

Cutting sugar will only take you so far. While you’re closing down the bar on the yeast party, why not serve the welcome guests whole foods? The gut microbes that help you digest and absorb your food love vegetables. Makes sense, because they eat the portion of the veggies that humans do not break down, and convert those portions into nutrients that you wouldn’t otherwise get.

Pile your plate with the whole foods that friendly microbes eat, and more of the good guys will colonize your gut. In particular, look for brightly colored vegetables (like dark leafy greens and vibrant cruciferous vegetables). In addition to gut-friendly fiber, these vegetables are sources of polyphenols—plant-based antioxidants that may help increase the population of good gut bacteria. Talk about a great side effect.

And for an extra serving of polyphenols in your diet, try Bulletproof Polyphenomenal—a daily antioxidant supplement that features a diverse blend of polyphenols from berries and botanicals like pomegranate, blueberries and green tea.