How to Restore Gut Flora After Taking Antibiotics

By: Courtney Sperlazza, MPH
February 12, 2020

How to Restore Gut Flora After Taking Antibiotics

  • Sometimes, you have to take a course of antibiotics, and you want to restore gut health as quickly as possible.
  • Antibiotics sweep through all the bacteria in their path, even the friendly ones that help you digest your food and protect your intestinal membranes.
  • There are things you can do while you’re taking antibiotics and after, like cutting sugar, drinking bone broth, taking collagen, taking specific strains of probiotics, and more.
  • Read on to find out how to bounce back from antibiotics as soon as possible.

There’s no way around it. For one reason or another, you have to take a course of antibiotics, and you’re worried about the attack on your gut flora. You’ve experienced the side effects of antibiotics before: gas, bloating, headaches, even yeast infections. How do you manage these symptoms while your gut biome rebuilds itself?

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.

How antibiotics impact gut health

Bottle of yellow pills on blue background

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. Colonies of beneficial bacteria in your digestive tract 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.[1] [2] Science is continuing to discover ways that gut bacteria are directly linked to your health.

Antibiotics are one of the biggest threats to our gut health. Antibiotics kill off the bacteria responsible for infection, but they also kill the friendly gut bacteria 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
  • Acid reflux
  • Irritable bowel syndrome
  • Acne
  • Autoimmune diseases
  • Candida (yeast) overgrowth
  • Anxiety
  • Depression
  • Brain fog[3]

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 from antibiotics as quickly as possible.

The bottom line: Antibiotics can kill healthy gut bacteria, causing problems with your digestion, skin and mood.

Take probiotics to restore gut flora

Person pouring pills into palm

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. Probiotics can help bacteria grow back faster and in balance.

  • Supplement with probiotics: To keep one strain of gut flora from taking over, supplement with probiotics while you’re taking antibiotics.[4] [5] 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 casei, Lactobacillus reuteri and Lactobacillus bulgaricus.[6] [7] Instead, opt for Lactobacillus plantarum, Bifdocaterium lactis, Bifdocaterium infantis and Bifidobacterium longum. These strains lower histamine levels, reduce inflammation and improve digestion.[8] [9]
  • Take S. boulardii: S. 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.[10][11][12][13]

The bottom line: To help bacteria grow back faster and in balance, take beneficial yeast and carefully timed doses of the probiotics recommended above.

Related: Everything You Need to Know About Probiotics

Cut back on sugar while you’re on antibiotics, and after

Spoonful of colorful sprinkles

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.[14]

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.[15] 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. Staying away from sugar is always good advice, but it’s especially crucial when you’re taking antibiotics.

The bottom line: Cut back on sugar out when you’re on antibiotics, or troublesome yeasts can take over and cause some serious problems. Yeast thrive on sugar, so less sugar means less likelihood of a yeast infection.

Related: What to Do When You’ve Had Too Much Sugar

Sip bone broth or take collagen peptides

Pot of bone broth

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.

Giving your membranes what they need to stay strong won’t completely prevent fungi from shooting their roots into your intestinal walls, but it will make them more resistant to damage and more resilient when the antibiotics are done and it’s time to heal.

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 patch up the intestinal walls. 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.

The bottom line: Antibiotics compromise the bacteria that line your intestines. Take collagen peptides to support your intestinal membranes.

Related: Your Complete Guide to Collagen Peptides

Eat a lot of veggies

Closeup of rainbow chard leaf

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? 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 foods that friendly microbes eat, and more of the good guys will colonize your gut.

The bottom line: After antibiotics, feed the good bacteria to help them regrow. They love to eat veggies, so bring on the greens.

Related: How fiber helps your body burn fat and builds a stronger gut

Resistant starch

Person holding bowl of cashews

Resistant starch gets its name because it resists digestion. It ferments in your digestive tract and feeds the beneficial bacteria in your gut.[16] 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.[17]

Sources of resistant starch include:

  • Unroasted cashews
  • Raw green bananas
  • Raw plantain flour
  • Raw potato starch

If you have IBS or Crohn’s Disease, resistant starch may cause digestive distress. Start slow, and build up to a few tablespoons. If you run into stomach trouble along the way, stop taking it.

The bottom line: Resistant starch feeds the good bacteria. If you add resistant starch to your diet, it will ferment in your intestines, making a tasty snack for the good guys.

Related: Resistant Starch 101: A Complete Beginner’s Guide

People who pop over-the counter and prescription pills for every minor thing are doing it wrong. With all the havoc pills cause in the gut, you and your doctor need to be judicious about using them.

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.

Join over 1 million fans

Sign-up for the Bulletproof mailing list and receive the latest news and updates!