215: Probiotic Tips While Taking Antibiotics (from a Nutritionist)

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Have you had that dreaded diarrhea after you start a round of antibiotics?

And maybe you worry that if you take probiotics, doing so while taking the antibiotics will just “cancel them out.”

You’re not wrong to think this because timing is everything when it comes to taking probiotics while on antibiotics!

Thanks to my recent 3-week course of antibiotics after finding a gross blood-filled tick in between my toes, I got a lot of questions about what my probiotic regimen looked like.

That’s why I want to answer your questions about the do’s and don’t’s of probiotic supplementation while taking antibiotics.

And offer you insight into how you can approach probiotics so that they do what they’re supposed to do!

Otherwise, your worst fear (that the antibiotics will kill them all) will come true and you’ll potentially get stuck dealing with that dreaded antibiotic-triggered diarrhea.

Or, listen on your favorite app: iTunes (Apple Podcasts) | Spotify | Stitcher | TuneIn | Subscribe on Android

In this episode:

  • Why you might need antibiotics even though you’d rather not take them
  • How to take probiotics so that antibiotics don’t “cancel them out”
  • Foods to help support your gut flora during antibiotics
  • Are yogurt + other fermented foods enough (or is a supplement better)?
  • Why probiotics taken during antibiotics could be really helpful
  • When taking probiotics with antibiotics might NOT be necessary


If you don’t want your probiotic “canceled out”, take probiotic supplements 2-3 hours before or after a dose of antibiotics.

Probiotics are helpful during a course of antibiotics, but so are the fibers you choose to eat during this time too!

Probiotic foods

Probiotic Tips While Taking Antibiotics (from a Nutritionist) (FULL TRANSCRIPT)

Welcome back to episode #215 of the Healthy Skin Show!

In today’s episode, we’re talking about antibiotics and probiotics!

I get asked frequently for advice on what to do if you DO need to take antibiotics.

It’s understandable to want to avoid antibiotics as much as possible, but sometimes they are necessary.

Maybe you’ve got a pretty bad staph or strep infection on your skin

Or something else happens out of the blue as it did to me when I discovered my foot was swollen from a tick completely ballooned with blood hiding between my second and third toes (a couple of months ago).

In my situation, antibiotics were really important to get started on to potentially halt any issue with Lyme should one of those infections be present.

But also, I did come to discover that the tick carried Rocky Mountain Spotted Fever so starting antibiotics immediately was very much to my benefit.

This course was rather long — 3 weeks!

So I needed to do what I could to help prevent any intense problem with my microbiome (which I’m already aware tends to be more “depleted” thanks to stool tests I’ve run on myself).

I shared in my newsletter as well as on Instagram what I was doing to support my gut during antibiotics, so I figured that I’d share it here on the Healthy Skin Show so that it could help even more people.

So if you find yourself confronted with having to take antibiotics, here’s what you need to know!

Woman thinking about what probiotics to take

How Do You Take Probiotics With Antibiotics

Have you ever been concerned that if you take probiotics while on antibiotics, it will just cancel out the probiotics?

It’s a really common question that I get from my clients.

And frankly, your head is in the right place if you worry about this because we know that antibiotic exposure does decrease even “good” gut bacteria which can include the probiotics that you take.

The answer to this question is YES — if you take antibiotics and probiotics too close together, the probiotics will essentially be canceled out.

So taking them together will not help (and this includes fermented foods like yogurt).

The general recommendation is to take probiotic supplements 2-3 hours before or after a dose of antibiotics.

This timing rule also includes spore-based probiotics like Megasporebiotic.

The only exception to this rule would be S. boulardii (which I’ll talk more about in a moment since it’s fungus, not bacteria).

Kombucha tea with elderberry

Best Probiotics When Taking Antibiotics

My memories of taking antibiotics for most of my life all pretty much look the same — bad diarrhea.

I imagine you might have also had a similar experience at some point.

They don’t always trigger diarrhea for everyone, but it’s the dreaded impact that we have all come to experience quite intimately.

And that’s where probiotics can really help!

Before you pick some up, there are a few things you should know first about probiotics to help inform your purchasing decisions.

Probiotics are not all created equal.

Different strains can have vastly different impacts on the gut as well as your health (and research continually expands our knowledge about this).

Some strains aren’t appropriate for certain situations — especially those with histamine intolerance since some probiotics can increase histamine in the gut exacerbating an already problematic situation.

Some probiotics are bacteria while others are fungal… and sometimes your symptoms can help you determine which is better to take.

For loose stools or diarrhea — Saccharomyces boulardii (or S. boulardii) is probably going to be your best bet (unless you have a known IgE allergy or antibodies (more common in those with IBD) to Saccharomyces cerevisiae).

This fungal organism is available worldwide in local pharmacies (often sold in the US as Florastor (FYI – it contains lactose). It’s well known to help with diarrhea and can firm up soft stools. However, it’s generally not good for someone who is constipated as it will likely make things worse.

You’ll notice that S. boulardii capsules contain much smaller quantities of organisms (typically 3 or 5 billion CFUs) compared to bacterial probiotics. That’s normal. While you might do fine with a bacterial probiotic that’s 50 or 100 or even 250 BILLION CFUs, that’s not appropriate with S. boulardii.

If you take too much S. boulardii, you could end up constipated, so take what you need and talk to your practitioner if you need more than 5 or 6 capsules per day to control diarrhea.

Spore-based probiotics can also be helpful — such as Megasporebiotic. Depending on how dysbiotic (or imbalanced) your gut is, it could help maintain formed stools. I generally don’t start a client on Megasporebiotic if they need antibiotics, but will keep them on it if they’re taking it already.

The reason I don’t start it at this time if someone’s not currently on it is that it’s possible to have a die-off reaction to Megasporebiotic. That’s why you always start taking a lower amount and slowly ramp up over the course of 2-4 weeks. Die-off symptoms are typically a sign of pretty bad dysbiosis.

Multi-bacterial strain probiotics that contain Lactobacillus acidophilus and Lactobacillus rhamnosus GG (found in the probiotic called Culturelle) can be helpful as well.(1)

During my recent antibiotic course due to the tick, I personally used the following probiotics daily:

  • Megasporebiotic
  • Probiotic 225 (Orthomolecular)
  • HMF Bifido powder (Genestra)

Once I finished the Probiotic 225 (as it’s a high dose of 225 Billion CFUs), I shifted to something less potent.

This combo worked well for me, but this is my personal experience based on what I know about my unique gut microbiome and symptoms — and not necessarily a recommendation for you since I don’t know your situation and health status.

And yes as you can see from what I did, you can take different probiotics at the same time!

I opted for powders (you can open the Megasporebiotic capsule) to add to a protein shake since I can’t swallow pills.

Lastly, in terms of how long you should take probiotics for a round of antibiotics, ideally, you will take the probiotics during the entire course of antibiotics.

Generally, it may be best to continue them for at least 2-3 months after you finish the antibiotics (if not longer, but obviously based on your health and gut).

Strawberries and blueberries

Best Foods To Eat When Taking Antibiotics

Even though everyone asks about probiotics if they have to take antibiotics, rarely does anyone ask about foods that can be helpful.

This is crucial especially if you are really serious about tending to healthy gut flora.

The bacteria that live there require sustenance in order to thrive.

So taking probiotics just on their own may not be sufficient enough to encourage what you take (during times of antibiotics or not) to take root.

Keep in mind that generally, probiotics are transitory so what you take only hangs out for about 6 weeks. 

If you stop taking them, just know that their impact will disappear after that 6 week period which is why WHAT foods you eat are a crucial piece of the puzzle.

Gut bacteria ferment fermentable starches found in FODMAP-rich foods.(2)

That’s why I will typically encourage clients while taking antibiotics to also increase high FODMAPs to tolerance (ie. without triggering extra gas, bloating, burping or other GI symptoms).

Foods that I chose to focus on were cauliflower, fresh figs, strawberries, blueberries, asparagus, avocado, chickpeas, brussels sprouts, onions, and garlic.

I also added in hydrolyzed guar gum, also called Sunfiber which is in one of my favorite drink mixes from Gut Power — I love the chocolate. (Use the coupon code HEALTHYSKINSHOW at checkout to get 15% off your order). Sunfiber is considered a SIBO-safe fiber according to Monash University.(3)

I also added in some inulin (which you increase slowly as your gut adjusts to it) starting with ¼ tsp/day and working up to around 1 tsp in my morning protein shake.

I know that high FODMAP foods get such a bad rap as if FODMAPs are inherently bad. For some with overgrowth issues, they can cause gut dysfunction and symptoms associated with IBS. If that’s your situation, then increasing them wouldn’t make sense.

But if you can tolerate them, I highly encourage you to add them in along with probiotics while taking antibiotics.

One last point about using fermented food in lieu of probiotics — I know a lot of people think that yogurt alone is sufficient to take with antibiotics, but I’d argue otherwise. Typically yogurt contains a handful of strains that are likely not at a therapeutic dose.

It’s sort of like trying to put out a raging forest fire with a soaker hose — it will help, but it’s really not all that effective.

The same could be said of fermented foods.

Again, they’re a helpful tool to have in the toolbox if you can tolerate them, but they do not compare to the power of a supplement in this particular situation.

Large crowd of people

Does Everyone Need To Take Probiotics While On Antibiotics

Generally speaking, taking probiotics may be helpful while you’re taking antibiotics for a few reasons.

If you’ve been colonized by C.difficile (aka. C.diff) but don’t yet present with an infection, probiotics may be helpful when taking antibiotics.(4) The stats speak for themselves — if probiotics are recommended along with antibiotics, the risk of developing C. difficile-associated diarrhea is reduced by 60% on average according to a 2017 Cochrane review of 39 randomized trials.(5)

Specifically, S. Boulardii (a friendly fungal probiotic) can be a great option especially if you tend towards soft or loose stools when on antibiotics.(6)

Another concern is if you have had a history of fungal overgrowth or yeast infections because the use of antibiotics can allow the yeast to essentially flourish by reducing the healthy gut flora that’s keeping it in check.

But the truth is, not everyone needs probiotics while taking antibiotics.

Those who are immuno-compromised need to talk to their doctor first about whether it is safe for you to take probiotics, PERIOD.

There are some instances where overgrowth patterns in the GI tract (like small intestine bacterial overgrowth (SIBO)) may make the need for probiotics unnecessary because there’s already too much bacteria present in the GI tract.

Typically I can make a recommendation for the appropriateness of taking probiotics during antibiotics based on a comprehensive stool test. That’s why a more personalized approach can inform the need for probiotic supplementation.

And that’s a significant point here given that most people have been convinced that generally everyone’s microbiome bacteria has been depleted due to antibiotic use. But clinically, I see patterns of overgrowth much more frequently than undergrowth.

Talk to your doctor and other practitioners to decide what’s the best way forward for you. Everyone is different and so you must approach the health of your gut based on your own history, symptoms and concerns.

Not on what I personally did (or anyone else who shares their experience) because you are unique.

It’s my hope that you’ll be able to make better choices about your probiotic options the next time you’re faced with a round of antibiotics.

If you’ve got any questions or thoughts to share about this, leave a comment below so I can address them.

Because this episode can be useful for so many people, even those without skin issues, share this information to help your family and friends make smarter choices when it comes to minimizing the impact of antibiotics on their gut microbiome.

Thank you so much for tuning in and I look forward to seeing you in the next episode!

Woman reading reference books


  1. https://bmcgastroenterol.biomedcentral.com/articles/10.1186/s12876-018-0831-x
  2. https://www.monashfodmap.com/about-fodmap-and-ibs/high-and-low-fodmap-foods/
  3. https://sunfiber.com/fiber-health-benefits/taiyos-sunfiber-earns-monash-universitys-low-fodmap-certification/
  4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335148/
  5. https://www.cochrane.org/CD006095/IBD_use-probiotics-prevent-clostridium-difficile-diarrhea-associated-antibiotic-use
  6. https://pubmed.ncbi.nlm.nih.gov/30689174/

If you don’t want your probiotic “canceled out”, take probiotic supplements 2-3 hours before or after a dose of antibiotics.

Jennifer Fugo, MS, CNS

Jennifer Fugo, MS, CNS is an integrative Clinical Nutritionist and the founder of Skinterrupt. She works with women who are fed up with chronic gut and skin rash issues discover the root causes and create a plan to get them back to a fuller, richer life.

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