165: Before You Say No To Antibiotics, Consider This

It’s pretty common to be afraid that antibiotics will wreck your gut microbiome.

That fear is pervasive thanks to the many health marketers who’ve convinced people (including myself at one point) that antibiotics were something to avoid at all costs.

Unfortunately I’ve found that this approach leads my clients (and those in this community) to feel confused and to avoid treatment when it might actually be the best thing.

I find myself sharing this exact information with clients every single week, so I thought I’d share this with you too to help you make better decisions for your skin and health.

So before you pass on antibiotics prescribed by your doctor because of what you’ve heard or read, here’s what you should consider first!

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In this episode:

  • Understanding the fear driving antibiotic use
  • Will antibiotics totally wreck your gut?
  • How to make a decision about whether (or not) to use antibiotics
  • Six questions to ask yourself before taking antibiotics
  • Situations when antibiotics might be the better option
  • How to take probiotics during a round of antibiotics so that they’re effective


Long-term exposure can reduce gut bug diversity and increase the likelihood of opportunistic overgrowth (like Candida).

We’ve been heavily marketed to through many wellness influencers that antibiotics completely wreck your gut and should be avoided at all costs.

Woman thinking about whether or not to take anti-biotics

Before You Say No To Antibiotics, Consider This (FULL TRANSCRIPT)

Welcome back to episode #165 of the Healthy Skin Show!

In today’s episode, I want to talk about whether you should take or avoid antibiotics from my clinical nutritionist perspective.

The reason is that a lot of people have a fear of taking antibiotics. We’ve been heavily marketed to through many wellness influencers that antibiotics completely wreck your gut and should be avoided at all costs.

Lots of information has been presented in such a way that I believe overly simplifies what ultimately is a complicated topic.

And a topic that doesn’t actually have a straight-forward answer.

It’s my hope that this will help you make a decision that is right for you if you are faced with the option of taking antibiotics.

Just as a reminder, I’m not a doctor so this discussion is purely informational based on my clinical experience and research. Ultimately, the decision to take antibiotics is between you and your doctor who has prescribed them.

Woman with gut pain

Won’t Antibiotics Wreck My Gut?

It’s not uncommon that about once a week, a client is faced with making the decision of whether they should take antibiotics.

It could be for a positive H.pylori test or for some other type of bacterial issue.

Sometimes it’s due to a bacterial skin infection like Staph Aureus or Strep.

90% of the time, there’s a lot of resistance to the idea of taking antibiotics due to many of the things they’ve read online or seen in documentaries.

Typically they’ll say something like “Won’t the antibiotics totally wreck my gut and wipe out all of my good bacteria?”

Before I answer that question, it’s important to know two things:

First, I used to think that everyone had low levels of healthy gut flora from years of antibiotic use. But my clinical experience has shown me that this isn’t always the case.

Having an overgrowth of gut bacteria is actually a more common trend in my clinical practice!

Second, I totally understand the concern of antibiotics’ potential harm to your microbiome.

I used to be very against the use of antibiotics because of the issues with antibiotic resistance and the damage they can cause to your permanent microbiome.

But my work within my clinical practice has made me rethink this hard NO.

Ultimately, that stance is unfair to my clients (because it means I walk into the conversation with an agenda) and it doesn’t account for situations where antibiotics really might be the best choice.

That’s why my clients will never hear me telling them what to do because…

  1. A) I’m not a doctor so I can’t advise anyone on how to take prescribed medication.
  2. B) I’m a firm believer that you ultimately should make your health decisions after gathering all of the evidence.

Health decisions need to be based on your own health values… not mine.

I focus on laying out all the options so that they can ask better questions of their doctors so that they can make more informed decisions.

Doctor holding antibiotics

Why I’m No Longer Anti-Antibiotics

What do I say when someone asks me if I’m against antibiotics?

It depends.

Yes, antibiotics impact the permanent microbiome that you establish within the first 2 years of life in a negative way.

Long-term exposure can reduce gut bug diversity and increase the likelihood of opportunistic overgrowth (like Candida).

But with most things in life, there are both pros and cons.

Guests of the Healthy Skin Show have talked about the anti-inflammatory impact of antibiotics.

Certain skin conditions like perioral dermatitis may respond better to antibiotics than to just anti-microbial herbs from my clinical experience.

I’ve even discussed on the Healthy Skin Show how rosacea can improve with the antibiotic rifaximin.

There have been instances when clients have discovered serious infections in the GI tract through comprehensive stool testing (like C. difficile).

Or their symptoms are so uncomfortable and so dramatically impacting their quality of life that getting relief is their main priority.

And that’s significant given the reality is that antimicrobial herbs and protocols often work much more slowly. It doesn’t mean they’re bad or less than… it’s just worth considering this given whatever situation you’re in.

I’m reminded of a client who had severe asthma (and was using 2 different inhalers daily), bad heartburn, and severe allergies with lots of itchiness that was wrecking her sleep.

We discovered through stool testing that she had high H.pylori and she ultimately decided to take the triple antibiotic with PPI therapy (which I supported).

Within a week of doing this prescribed antibiotic regimen from her doctor, she didn’t need her inhalers nearly as much, the heartburn was gone, her itchiness was much more manageable and she felt substantially better.

The point is that her quality of life was drastically improved so that she could continue to work on the other root causes underlying her eczema, asthma and allergies.

This is just one example of many from my practice where the antibiotics made sense!

Sure, this client could have opted for antimicrobial herbs appropriate for what was going on, but the severity of her situation is what took precedence in deciding what was right for her.

Especially because an antimicrobial herb regimen would likely take her up to 2 months to hopefully get relief.

That’s a long time when your quality of life is really compromised.

Woman wondering about her skin infection

What If I Have A Skin Infection?

I’ve talked before about the necessity of learning to distinguish between a skin flare and a skin infection. We’ll talk more about this in the coming months on the show.

For now, you can check out this episode on Staph skin infection symptoms!

Skin infections can really impact your quality of life and ability to sleep and function (especially the worse that they get).

This is why I often tell clients to go back to their dermatologist to get a skin culture if what they’re describing to me sounds anything like an infection.

A skin infection can turn ugly with severe consequences the longer it is allowed to carry on.

If a client does have a skin infection, I fully support their doctor’s recommendations (which often includes antibiotics).

In the case of clients who are uncomfortable taking oral antibiotics, I will suggest they ask the doctor if topical antibiotics would be an option instead.

The level of relief from the burning, pain and deep itchiness that clients get really improves their daily quality of life (and sleep).

AND, it means they can stick to an integrative protocol better because they aren’t suffering.

Woman considering pros and cons of antibiotics

What To Consider Before Taking (Or Not Taking) Antibiotics

If you’re on the fence about antibiotics or your doctor has prescribed them to you, these are the following questions to consider:

  1. How much is your quality of life being compromised + how severe is the infection?
  2. Could taking the antibiotics actually help you out in some other way (ie. positively impact gut dysbiosis)?
  3. Knowing that the road ahead to addressing your skin (or gut) could be a long one, could getting more immediate relief help you stay the course once you make the shift to antimicrobial herbs?
  4. Do you have a state of gut bug overgrowth or a gut infection better eliminated with antibiotics?
  5. What antibiotic is being recommended and are you okay with the potential side effects associated with that particular medication? (ie. Cipro and other Fluoroquinolones that have a Black Box Warning from the FDA)(1,2)
  6. If you have a skin infection and you’re nervous about oral antibiotics, are topical antibiotics an option instead?

And if you choose to take the antibiotics (and probiotics are appropriate for you), ask your practitioner to recommend the right probiotic supplement to help counter the negative impacts of the antibiotics.

Bacterial probiotics should be taken 2-3 hours after every dose of antibiotics so that they aren’t neutralized by the antibiotic.

If you start to experience looser stools, Saccharomyces Boulardii (a friendly fungal organism) can be helpful to firm things up.

So I hope you can see now why I take a much more comprehensive approach to antibiotics.

A hard NO to antibiotics is overly simplistic and based on sweeping generalizations.

You are not everyone else.

Your situation is unique.

At the end of the day, you have to evaluate the situation based on where YOU are and what’s best for YOU with the help of your practitioner and doctor.

Now’s your turn — Leave your thoughts, experiences, and questions in the comment section below!

If this perspective makes sense to you, share this episode with people who would also find this helpful! It’s so important to approach everything with an open-mind and have balanced conversations like this.

I personally believe that this will allow for you to make the best decision for yourself based on multiple unique facets of your case rather than just based upon generalized fear-filled marketing.

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

Woman looking at reference books in library


  1. https://www.fda.gov/drugs/drug-safety-and-availability/fda-warns-about-increased-risk-ruptures-or-tears-aorta-blood-vessel-fluoroquinolone-antibiotics
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483892/

Long-term exposure can reduce gut bug diversity and increase the likelihood of opportunistic overgrowth (like Candida).

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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