How to Take Care of Your Gut While On Antibiotics

I had a solid 5 or so year stretch from high school through college without having any illness that took me out for more than a day or so. And now that I'm graduated/in the real world, I can catch any bug around. I'm a big proponent of asking whether or not you really need antibiotics before jumping into taking them, but I also know that there's a time and place where they're helpful and we all need medical help sometimes. I posted on my Instagram stories/feed over the holidays about gut health while you take antibiotics and got a resounding "YES" when I asked if this should be a blog post, so let's get into it!


Basically, your microbiome is the collection of bacteria/yeast/microbes that live inside your body, doing their little microbe thing. Most to all of the microbes are healthy and are supposed to be there, but sometimes we introduce different strains or proportions based on our lives. We get our microbiome at birth and it changes as we grow up in response to a lot of factors, like stress, what we eat, illness, and medications.

I think of our microbiome like the anthill in A Bug's Life (anthill = our GI tract, ants = microbes). All of the ants/microbes have jobs and they work together to keep the whole operation running. Everything goes pretty smoothly, but when we have to do things like take an antibiotic or have a really stressful period, it's similar to the "bad guy" grasshoppers coming in and wiping out all of the ants. The antibiotic targets the bacteria that's making you sick, which it's supposed to do - but it also gets some of your good bacteria as it works. So with normal, day-to-day activities, your microbiome handles itself - but antibiotics can be an "extreme" circumstance for your gut health and may need some help being guided back to a normal state.

strawberry and granola yogurt parfait

strawberry and granola yogurt parfait


There's two major problems your gut can have on antibiotics: antibiotic-associated diarrhea (AAD) or Clostridium difficile infection (C. diff). C. diff typically occurs to older adults who have been on antibiotics and it's more severe (and has more consequences) than AAD, so read up on symptoms here and talk to your doctor as needed.

AAD is more common/less severe but still not fun. Even without symptoms of AAD, I still think it's worth talking to your doctor about how you can protect your gut health while on your medication.

overhead view of hidden veggie oatmeal cup muffins

overhead view of hidden veggie oatmeal cup muffins


Before we get into how to actually be mindful of gut health while on antibiotics, let's review some quick definitions:

  • A probiotic is a food or supplement that introduces new microbes into your gut - like if a van dropped off a new group of worker ants to the anthill.

  • A prebiotic is a food or supplement that nourishes and fuels the microbes already in your gut - like if the ants got new tools and a filling lunch.

There's plenty of food sources of both out there, and for the most part by allowing natural balance to find us, we can maintain a gut balance as well. Here's where it gets a little tricky, because when we're sick/on antibiotics, that's an important time to consider gut health and whether or not we need some help. It's also a time where certain foods maybe don't sound good or we have food aversions, whether it's from illness or from side effects of medications. So while it's all fine and good to say "eat probiotic foods" here, that may not be realistic for your palate or preferences. And for the sake of efficiency, we're not going to get into prebiotics in this post because probiotics are really the focus when talking about antibiotics (you still need prebiotics, but you can't nourish microbes until you re-populate them).


  • Kefir (yogurt-like dairy beverage. Think Danimals for grown-ups)

  • Kimchi (fermented Korean cabbage/veggie salad)

  • Sauerkraut

  • Miso (you can buy this at the store in paste form to cook with, or just order up soup from Japanese takeout)

  • Yogurt

  • Pickles

  • Kombucha (fermented tea - definitely an acquired taste, but delicious once you find a flavor you vibe with)


If you don't like, don't want, or can't find probiotic foods that work for you, probiotic supplements are available over the counter in the vitamin section of stores. Because antibiotics target bacteria, it may be more beneficial to find one with a yeast strain of probiotics (like S. Boulardii) that won't be as "set back" by your meds as an all-bacteria probiotic would. As always, check with your doctor before beginning any medication or supplement to make sure it's appropriate for you.


Stay well this cold and flu season!