How To Heal Your Gut After Antibiotics

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?


I suggest taking the probiotics you started during your course for at least a month following the antibiotics. If you were taking a single strain supplement like Florastor, you might consider adding a probiotic supplement that has a couple strains like VSL #3 just to bring in some other strains. You can continue taking this supplement for a few months (consult with your practitioner for advice on this).

You’ll also want to focus on including plenty of probiotic-containing foods for the next few months (you should always include these in the diet, but it’s especially important 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 I’m eagerly awaiting the release of Fermented by Jill Ciciarelli. This is one of the most fun ways to experiment in the kitchen, so get fermenting!


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)

As of this writing, only three substances fit this definition (though there are certainly other substances that need more research). Below is a list of the only true prebiotics, where to find them, and what supplements contain them. It’s crucial to consume prebiotic substances after antibiotic treatment as it helps to fix the dysbiosis created.

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. If you choose to supplement, I recommend Pure Encapsulations FOS powder.

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 Jarrow Formulas Yum Yum GOS syrup.

3) Lactulose: Again, you won’t find this one in any foods, so you’ll need to supplement if you want to give this one a shot. Lactulose is more commonly known as a laxative, and in the United States you’ll need a prescription for it. The dose shown to be bifidogenic is 10 grams per day. (6)

You don’t need to supplement with all of these (nor should you). If you’re going to supplement, just choose one.

***Please note: if you are sensitive to FODMAP foods, it is not recommended that you consume these supplements (or foods containing them).

***Also note that if you are supplementing with any these, you’ll want to introduce them very slowly and work your way up to a higher dose over time. You’ll also want to split up your dosage (i.e. take it 3 times a day vs. once a day).

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.


Join my newsletter to download my 5S Protocol to Optimize Digestion at Mealtime. In it, I’ll teach you how to stimulate the production of digestive enzymes and stomach acid, calm your system so it’s in “rest and digest” mode, and slow down to allow the proper breakdown and absorption of your nutrients.

Making sure you are optimizing your digestion is a great first step in improving your gut health!

Click here to download my 5S Protocol


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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