How To Heal Your Gut After Antibiotics

Now that you’ve learned what probiotics to take while you’re antibiotics, you’re probably concerned with what you should do after you’ve finished your course.

Antibiotics take a toll on our microbiome, destroying lots of our good bacteria and causing overgrowth of others like yeasts. This imbalance of gut bacteria is called dysbiosis. So how do we fix it?

Probiotics After Antibiotics

There is some recent research suggesting that probiotic consumption after antibiotic treatment may delay your microbiome from returning to its normal state, so if you’re not experiencing any digestive complaints after finishing your course of antibiotics, I recommend focusing mostly on prebiotics (see below) as opposed to probiotics.

If, however, you’re struggling with some post-antibiotic digestive woes, you may want to try a probiotic in addition to the other suggestions in this article. If you already began taking probiotics during your course of antibiotics, you can continue that probiotic for a month or two after finishing up your course.

Take a Probiotic Supplement

If you weren’t taking a probiotic during your antibiotic course, you can choose one of the below (which I recommended in my previous article):

  • Saccharomyces boulardii biocodex (now called Saccharomyces boulardii CNCM I-745) is found in the Florastor brand probiotic and helps to prevent C.diff infections (5) and even helps those who tend to have recurrent C.diff infections. (6). This strain does not need to be refrigerated, so it’s very easy to buy saccharomyces boulardii online.
  • Visbiome (a multi-strain probiotic) has also been shown to reduce the incidence of antibiotic-associated diarrhea.(7) Note that if you buy Visbiome online, you should choose a retailer that ships it refrigerated. (Please note: I used to recommend VSL #3 as it was the brand that use the De Simone probiotic formula. However, they have since lost access to the well-researched formula, and now Visbiome has the only rights to it. Make sure you get Visbiome and NOT VSL #3 if you’re looking for the De Simone formula.)
  • Lactobacillus rhamnosus GG (found in the Culturelle supplement) has been shown to reduce the occurrence of antibiotic-associated diarrhea, as well.(8) Like Florastor, it’s easy to buy Culturelle online since it does not need to be refrigerated.

Eat Probiotic Foods

You’ll also want to focus on including plenty of probiotic-containing foods for the next few months (you should always include these in your diet, but it’s especially great to do so right after taking antibiotics). Here’s a list of fermented foods, including (but not limited to) the following:

  • Water or Dairy kefir – fermented water (often with juices or fruit included for flavoring in a “second ferment”) or dairy with kefir “grains”. Click here for a recipes, or purchase at your local natural foods store
  • Kombucha – a fermented tea drink. Click here for a recipes, or purchase at your local natural foods store
  • Kimchi – a spicy fermented cabbage, a Korean staple (and my personal favorite!). Click here for a recipe and try it at a Korean restaurant for a taste. You can often purchase this in tubs at Korean grocery stores as well.
  • Sauerkraut – another fermented cabbage, but a German version this time! Click here for a recipe or you can pick up some Bubbie’s sauerkraut at Whole Foods or other natural foods store
  • Pickles – the deli classic can be made by fermenting cucumbers! Click here for a recipe and keep in mind these are different from the pickles in vinegar you’d find on the shelf of your regular grocery store.
  • Salsa – another classic dish that can take a fermented turn! Click here for a recipe and give it a shot!
  • Beet kvass – a fermented beet juice drink. Click here for a recipe or you can usually find this in your Whole Foods or other natural foods store.
  • Yogurt – if you tolerate dairy, yogurt is a great source of probiotics. Click here for a recipe or of course you can pick some up from your grocery store (choose one that uses a good quality milk though and always buy full fat!)

Keep in mind that you can ferment pretty much anything! My favorite resource for fermentable foods is the book Wild Fermentation by Sandor Katz and you may also want to check out Fermented by Jill Ciciarelli. This is one of the most fun ways to experiment in the kitchen, so get fermenting!

Prebiotics After Antibiotics

Prebiotics are a wonderful thing to incorporate into your diet and supplement routine after antibiotics. A prebiotic is a “nondigestible food ingredient that beneficially affects the host by selectively stimulating the growth and/or activity of one or a limited number of bacteria in the colon, and thus improves host health.” (1) This definition was later revised to include that a prebiotic:

“a) resists gastric acidity, hydrolysis by mammalian enzymes and gastrointestinal absorption;

b)  is fermented by the intestinal microflora;

c) stimulates selectively the growth and/or activity of intestinal bacteria associated with health and wellbeing.” (2)

Supplementing with Prebiotics after Antibiotics

Prebiotics work by selectively feeding your beneficial gut bacteria, which in turn, helps to push out unwanted or “bad” bacteria that might be hanging out in the gut.

You can think of the microbiome as a parking lot — there’s only so many spaces available. Taking prebiotics helps your good bacteria to take more of those parking spots and leaves less spots available for any bad bacteria.

Best Prebiotics:

1) Fructo-oligosaccharides: FOS is found is a variety of foods including Jerusalem artichokes, chicory root, onions, bananas, honey, garlic and leeks. (3) The appropriate dose of FOS is about 10 grams per day (this leads to increases in bifidobacteria and has the least amount of side effects (which tend to be gas and bloating)). (4) Whether you get this dose from food or supplement is up to you, but it will help to correct the dysbiosis caused by antibiotic treatment. My favorite FOS supplement is NOW Foods UltraFlora FOS powder. (P.S. it tastes like cotton candy.)

2) Galacto-oligosaccharides: GOS isn’t found in many foods, so if you’d like to try this one you’ll need to supplement. A dose of 5 grams per day has been shown to be bifidogenic (increases bifidobacteria counts) in most healthy people while consuming it along with their usual diet. (5) Try Klaire Labs Galactomune supplement.

3) Sunfiber (galactomannan fiber or partially hydrolyzed guar gum): Sunfiber is a great choice as it is low-FODMAP and thus typically very well tolerated even by those who are experiencing digestive issues. I recommend 6 grams per day, which has been shown to be a bifidogenic dose. I love Sunfiber so much that it’s the prebiotic I use in my drink company, Gut Power Drinks! Give our Gut Power Matcha a try as an easy way to incorporate both prebiotics (Sunfiber) and probiotics into your routine in a delicious way.

gut power matcha

When starting on prebiotic supplements, it’s important to begin with a small dose and work your way up slowly. It’s normal to experience a bit of extra gas or bloating when increasing your dose, but it should dissipate within a couple days.

Incorporate High Polyphenol Foods Into Your Diet

Polyphenols, a type of antioxidant that gives our food color, actually act as prebiotics in the gut. This means that the more high polyphenol foods you incorporate into your diet (like berries, tea, spices, etc), the better balanced your microbiome will be.

This is another great reason to give Gut Power Matcha a try — matcha is one of the best things you can consume to get lots of gut-healthy polyphenols into your diet!

Because each different polyphenol feeds different classes of healthy bacteria, it’s best to incorporate a wide array of colorful fruits and veggies into your diet.

What if Probiotics and Prebiotics Aren’t Enough?

Because of the intense effect antibiotics can have on our gut flora, sometimes simply adding probiotics and prebiotics doesn’t quite cut it.

Maybe you’ve noticed that your digestion is just off after taking a course (or a few courses) of antibiotics. What do you do then?

Well, a good first step is to have your gut bacterial balance tested.

There are two common imbalances that can result from antibiotic treatment. The first, which we just discussed, is called dysbiosis.

The second is something called SIBO (small intestinal bacterial overgrowth).

Both of these conditions can cause many annoying digestive symptoms and can be difficult to deal with.

You can learn more about both of these conditions and the testing you need to identify them in this blog post.

If you’re experiencing lots of digestive symptoms like bloating, gas, diarrhea or constipation long after being on antibiotics, it’s definitely time to test for SIBO and dysbiosis. (Note: you’ll need to wait at least 2 weeks after being on antibiotics to do these kinds of tests.)

Once you identify these imbalances, you can get to work clearing out bad bacteria and healing your gut. This typically involves an antimicrobial protocol (or antibiotics — but don’t worry, these ones aren’t like the ones that got you here in the first place!), gut-healing supplements, stress management, and a proper diet.

I have an entire 8-week course dedicated to this process called Build Your Biome. If you’re totally overwhelmed by all the research you need to do to kick these symptoms to the curb, I invite you to join me in BYB where I make it all super easy!

Takeaway: By getting probiotics and prebiotics in the diet (or via supplementation), you’ll be helping your gut recover from the traumatic experience of dealing with antibiotics. However, some people may find that they are left with nagging symptoms even after incorporating probiotics and prebiotics. In this case, it’s very important to test for common conditions like dysbiosis and SIBO.


1) Pharmaceutiques, Universitad Catholique de Louuain. “Dietary modulation of the human colonie microbiota: introducing the concept of prebiotics.” Journal of Nutrition 125 (1995): 1401-1412.

2) Gibson, Glenn R., et al. “Dietary modulation of the human colonic microbiota: updating the concept of prebiotics.” Nutr Res Rev 17.2 (2004): 259-275.

3) Chow, JoMay. “Probiotics and prebiotics: a brief overview.” Journal of Renal Nutrition 12.2 (2002): 76-86.

4) Bouhnik, Yoram, et al. “Short-chain fructo-oligosaccharide administration dose-dependently increases fecal bifidobacteria in healthy humans.” The Journal of nutrition 129.1 (1999): 113-116.

5) Davis, L. M. G., et al. “A dose dependent impact of prebiotic galactooligosaccharides on the intestinal microbiota of healthy adults.” International journal of food microbiology 144.2 (2010): 285-292.

6) Bouhnik, Y., et al. “Lactulose ingestion increases faecal bifidobacterial counts: a randomised double-blind study in healthy humans.” European Journal of Clinical Nutrition 58.3 (2004): 462-466.

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