6 Important Questions to Ask Your Doctor if They Prescribe Antibiotics (and how to restore gut health if you really need them)

If you think twice before taking antibiotics or giving them to your children, you are not alone.

On the one hand, they are excellent for helping kill or control the growth of harmful bacteria and have saved countless lives.

On the other hand, there are risks involved in taking any type of antibiotics, even if you need them.

I can’t tell you how many patients I see whose health has been derailed by the use of antibiotics—even if they were indicated at the time.

Antibiotics destroy bad and good bacteria—this is not good news for our microbiome, which relies on a robust and healthy balance of friendly bacteria to support our immunity, digestion, mental health, and more.

Like any intervention, antibiotics come with side effects.

Some of the more common side effects of antibiotic use include:

  • Destruction of beneficial gut bacteria and a change in the gut microbiome (that can persist for over 2 years!)
  • Yeast or Candida overgrowth in the mouth or vagina
  • Antibiotic associated diarrhea
  • Clostridium Difficile infection
  • Kidney and liver toxicity
  • Allergic reactions that can be serious or fatal
  • Interaction with other medications
  • And others

Plus, the overuse of antibiotics is partly to blame for the increase in antibiotic-resistant infections which are responsible for thousands of deaths in the United States annually.1 The Centers for Disease Control (CDC) and World Health Organization considers antibiotic-resistance an “urgent global public health threat.”2

So, what should you do if your doctor prescribes antibiotics for you or your child?

In my opinion, it’s all about weighing risk versus benefit, and using safer alternatives when they exist.

This is why educating yourself about the pros and cons of taking antibiotics is essential.

In this article, you’ll learn six questions to ask your doctor to help protect you and your family from unnecessary antibiotic use while avoiding life-threatening situations.

We’ll also cover how to restore your gut health should you truly need a course (or more) of antibiotics.

Why Everyone Should Question an Antibiotic Prescription

As an integrative functional medicine physician specializing in chronic disease and gut health, I’ve become incredibly selective about my professional and personal approach to antibiotics.

That doesn’t mean I’m anti-antibiotic!

Sometimes the right antibiotic given at the right time for the right purpose is the right course of action.

However, we know that antibiotics are overprescribed in some cases.

According to the CDC, 1 in 3 antibiotic prescriptions are unnecessary. 3  Most of these unnecessary antibiotics are prescribed for respiratory illnesses—including the common cold, sore throat, sinus and ear infections—which are usually caused by a virus (meaning they will not respond to antibiotics).4

That doesn’t mean your doctor doesn’t care about your health, but sometimes, not prescribing antibiotics puts them at risk.

For example, an urgent care doctor who sees you for fever and cough with no follow-up puts him or herself at greater liability risk by not prescribing antibiotics in case your fever and cough develops into full blown bacterial pneumonia.

Same thing if you take your child to a healthcare provider other than their primary care provider for an ear infection. Chances are, the ER or urgent care doctor will be more likely to recommend antibiotics in case that ear infection develops into something more serious or fails to resolve on its own.

There is also evidence that older doctors prescribe antibiotics more frequently (probably because that was the standard of care for so many years) and that doctors will be more likely to prescribe if they feel expectations are high (like a concerned parent asking for a prescription).5

However, studies have also shown clinicians may not accurately perceive parental expectations.

Which is why it’s so important to ask questions and communicate clearly, even if you think your doctor knows what you expect.6

Another comparative study published in the American Journal of Medicine showed that non-physician clinicians are more likely to prescribe antibiotics than physicians in outpatient settings. At the same time, resident physicians are the least likely to prescribe antibiotics. 7

I’m not trying to throw any of my colleagues under the bus (Lord knows, it’s not easy to treat patients you’ll never see again) nor to suggest every doctor over 50 over-prescribes.

However, I think patients should be aware of this information to better advocate for themselves and their families, and to decrease misunderstandings about expectations with your provider.

Bottom line: it’s essential only to use antibiotics when truly necessary to avoid the negative effects on the gut microbiome and overall health.

This means avoiding antibiotics for conditions that can be treated with other methods, such as viral infections, mild bacterial infections (in some cases), or minor cuts and scrapes.

It’s so important to be your own advocate in a healthcare setting, and sometimes the best way to advocate for yourself is by asking questions.

6 Important Questions To Ask Your Doctor if they Prescribe Antibiotics

It can be hard for some people to question their doctors, especially if they’re feeling sick and scared.

However, any doctor worth their salt should be happy to answer your questions and honestly discuss risks versus benefits and potential alternatives.

Of course, this may not be possible if you’re very sick, and they must act immediately to save your life!

However, in normal circumstances, your doctor should always take the time to answer your questions with honesty and compassion.

Plus, asking some simple questions could save you unnecessary prescriptions and side effects.

Research has shown that good patient-provider communication is the most effective way to avoid unnecessary antibiotics.8

With that in mind, here are six questions to ask your doctor before you fill that prescription.

#1: How strongly do you feel I need an antibiotic?

This may seem like a silly question if your doctor just told you, “I’m writing you a prescription for antibiotics,” but it’s a great way to open up the conversation.

If your doctor seems taken aback, just calmly explain you’ve read a lot about the negative side effects of antibiotics and/or the drug-resistant epidemic and want to make sure this is absolutely necessary.

Then move on to question two.

#2: Are there red flags to indicate that I absolutely need an antibiotic right now?

This question will give you valuable information on your condition and/or make your doctor rethink their original recommendation.

However, make sure they answer your question!

If they say things like, “Well, if we don’t treat this, it could develop into pneumonia, meningitis, a kidney infection, etc.”, then they’re not really answering your question.

In that case, ask them again, “So, am I displaying any red flags indicating I could go in that direction quickly?” and “What are the chances I could develop that type of infection given my age and overall state of health?”

If their answers indicate you’re at very low risk of a serious complication, ask if you can wait a few days and do a follow-up.

#3: What are the risks of not taking an antibiotic?

In some cases, the benefits of antibiotics are absolutely worth the risk.

For example, if they tell you that your bladder infection may be spreading to your kidneys which could result in sepsis, then you’d better take that antibiotic!

However, if the risk of foregoing an antibiotic is minimal, move on to the next question.

#4: Would it be safe to wait another 3-5 days before starting an antibiotic if I agree to return for an exam?

This question is GOLD because many conditions, such as ear infections, sinus infections, and others, often resolve on their own within a few days.

Doctors refer to this as a “watchful waiting” period, which is now the recommended approach in many cases, including for many types of ear infections. 9 10

If you have a mild to moderate infection, your doctor may be comfortable delaying treatment if you agree to a follow-up.

However, make sure you do follow up!

Even if you’re feeling better, it’s a good idea to get checked out to ensure progress is being made.

#5: Are laboratory investigations indicated? And if so, can antibiotic treatment be delayed until infection is confirmed?

Laboratory investigations are not always used to diagnose infections for various reasons.

For example, the only way to determine a viral vs. bacterial ear infection using lab work requires puncturing the eardrum to get a sample. This is rarely worth the trauma to a child who is already in pain.

However, in some cases doctors will either skip labwork because they’re confident in their diagnosis based on symptomology and history, or prescribe an antibiotic before they get the results back.

In any case, it’s worth asking the question.

#6: Are there any alternatives to taking antibiotics for my condition?

To be honest, in many cases, unless you’re seeing an integrative doctor or practitioner, you’ll probably get a “no.”

However, it’s still worth asking.

For example, pink eye can often be treated with over-the-counter eye drops and chamomile tea bags 11; some mild bladder infections may respond to natural remedies when caught early; and during an appropriate watchful waiting period, heat, garlic mullein oil, homeopathics, over-the-counter pain medication, and other home remedies may ease discomfort from ear aches.

So, even if you think you know what your doctor will say, it’s worth asking about alternatives.

Finally, if you and your doctor determine that you do need an antibiotic, ask if a shorter course might be appropriate in your case.

Although shortening courses of antibiotics has been generally frowned upon, new evidence has shown that shorter courses can be appropriate in certain circumstances.

A recent perspective in the Medical Journal of Australia argued that discontinuation of antibiotic treatment once symptoms have resolved is a reasonable course of action in many situations, and is not likely to lead to relapse or promote antimicrobial resistance.12

This may not be appropriate in all situations, but be sure to ask about it and share this information with your doctor.

Note: There is a lot of information online about “natural antibiotics,” like herbs. I love recommending herbs in my practice and use them extensively at home.

However, although certain herbs have demonstrated antibacterial properties, I do not advise attempting to substitute herbs for antibiotics when there is a genuine need. People have gotten very sick or even died trying to do this when prescription antibiotics were warranted.

Bottom line: do avoid antibiotics when they’re not necessary. However, do not try to use herbs in place of antibiotics if you or your child really need them.

How to Protect, Replenish, and Heal Your Gut During & After Antibiotics

If, after going through all these questions, you and your provider decide that you really do need to take antibiotics (which nearly everyone will from time to time), there are several steps you can take to replenish good bacteria after antibiotics, support your gut microbiome during treatment, and help minimize potential side effects.

First, Eat Prebiotic-Rich Foods To Feed Friendly Bacteria

Prebiotics are non-digestible carbohydrates found in various plants and starches.

Prebiotic-rich foods include:

  • Onions
  • Garlic
  • Asparagus
  • Sunchokes
  • Artichokes
  • Leeks
  • Chicory
  • Green bananas
  • Cooked and cooled rice
  • Cooked and cooled potatoes and sweet potatoes
  • Potato starch
  • Plantains
  • Legumes and beans

Prebiotic foods, like onions and garlic, can be added to your favorite dishes. And green bananas are a great smoothie hack (peel and freeze them when green)!

You can also take a prebiotic supplement, such as MegaPre from Microbiome Labs. This is a professional supplement line, so use the code “Maren” to access products.

Second, Replenish Good Bacteria During and After Antibiotics with Probiotic Foods and Supplements

Probiotics are live bacteria and yeast found in fermented foods.

Probiotic-rich foods include:

  • Cultured vegetables
  • Sauerkraut
  • Kimchi
  • Kombucha
  • Yogurt (organic dairy for those who tolerate it or plant-based, natural and unsweetened, no added sugars, etc.)
  • Kefir (organic dairy for those who tolerate it or plant-based, natural and unsweetened, no added sugars, etc.)
  • Tempeh
  • Miso

Most doctors will tell you to eat yogurt while taking antibiotics because it contains natural probiotics, which help replenish the good bacteria killed off by the antibiotics.

Probiotics in yogurt have been shown to help prevent side effects, such as antibiotic-induced diarrhea.13

I typically recommend prioritizing cultured vegetables, sauerkraut, or kim chi over yogurt because these products tend to contain a greater variety of probiotic cultures.

Nearly anyone on antibiotics will benefit from taking a probiotic supplement in addition to eating probiotic-rich foods.

However, patients often come to me completely confused about if and how to take probiotics with antibiotics.

Common questions include:

  • “Should I take a probiotic to replenish good bacteria while taking the antibiotic? Won’t the antibiotic just kill them off?”
  • “What type of probiotic should I take during and after?”
  • “How long do I have to take a probiotic after taking an antibiotic?”
  • “Does taking probiotics really make a difference?”

Here’s what you need to know from a functional medicine perspective.

Q: Should I take a probiotic to replenish good bacteria while taking an antibiotic?

Yes! Although it may seem counterintuitive to ingest beneficial bacteria while taking an antibiotic, research shows it makes a difference.

For example, the probiotics Lactobacillus rhamnosus and Saccharomyces boulardii have been shown to help prevent Clostridium difficile infection (CDI), an intestinal infection caused by antibiotics, when used proactively.14 15 16

You’ll have the best results with a spore-form probiotic or one that contains the friendly yeast called Saccharomyces boulardii. We’ll discuss this next…

Q: What probiotic should I take during and after?

Although many good probiotics are available, we must be conscious of choosing probiotics that encourage diversity and have been shown to benefit the gut during and after antibiotic use.

Why does this matter? Because research has shown, it is gut microbiota diversity that creates a healthy gut microbiome.

I often use the example of comparing a mono-crop field of genetically-modified corn or soybeans versus an organic, regenerative farm with gardens, various crops, bees, forests, and livestock.

Which ecosystem do you think is healthier and more naturally resistant to pests?

The regenerative farm, of course.

It’s the same principle for your gut. More diversity equals more resilience and strength.

Therefore, I recommend taking a combination of spore-forming probiotics with prebiotics to encourage the proliferation of multiple gut bacteria.

Ideally, you should take these during and after antibiotic use.

My favorite probiotics include:

  • Microbiome Labs MegaSporeBiotic: This is a spore-based formula with five clinically researched strains of Bacillus species. Spore-based probiotics are preferable because they’re more stable/have a better shelf-life than non-spore probiotics. They also survive gastric juices, which means they actually make it to your gut, where they can seed, proliferate, and repopulate the microbiome.

You can order it directly from Microbiome Labs using the patient direct code Maren, or from my online dispensary.

  • Saccharomyces boulardii: S. boulardii has been shown to prevent Clostridium difficile infection (CDI), an intestinal infection caused by antibiotics, when used proactively. This makes it ideal for anyone with a history of antibiotic-induced diarrhea or CDI. 17

Klaire Labs or Seeking Health both have high-quality Saccharomyces boulardii (S. boulardii) supplements and can be found on FullScript.

Note the right probiotic and the right amount of probiotics for you may depend on the state of your gut health. If you have SIBO or other gut or digestive health issues, check with your doctor first and check out: How to Choose the Best Probiotic Supplement.

Q: “How long do I have to take a probiotic after taking an antibiotic?”

I recommend taking probiotics during and after antibiotic use for several reasons; one of the biggest is they’ve been shown to reduce your need for future antibiotics long-term.18

So, if your goal is to rehab your gut and help reduce your dependency on antibiotics in the future, continue taking probiotics for at least 3 – 12 months.

Research has shown it can take 8-31 months for your gut health to return to baseline after taking antibiotics!19

So, three months minimum and up to a year, or even 31 months, if you can, in addition to the other lifestyle recommendations discussed.

Third, Take Serum-Derived Bovine Immunoglobulins

Supplementing with Serum-Derived Bovine Immunoglobulins (SBI) in addition to pro- and prebiotics after antibiotics is a lesser-known recommendation, but a powerful one.

Serum-derived bovine immunoglobulins are proteins derived from bovine sources that help support intestinal barrier integrity.

They can be used effectively post-antibiotics to help restore gut function, taken for gut-related chronic conditions, or used to support overall microbiome health.

Specifically, studies have shown SBI can support gut function by binding to and excreting unproductive microbes, resulting in: 20 21

  • Reduced gut barrier permeability (aka: Leaky Gut Syndrome)
  • Increased nutrient absorption to help restore homeostasis in the gut
  • Decreased intestinal inflammation
  • Immune activation in the gut

Research has also shown the antibodies in SBI can bind specifically to c. difficile, making it a great treatment option for c. difficile diarrhea. 22

Clinically, following a course of antibiotics I see patients with a low secretory IgA, which represents the gut immune system. This is a major opportunity to replenish that IgA and help rebuild the gut using SBI supplements.

The serum-derived bovine immunoglobulin supplements that I recommend are:

Side note: these are also available through the pharmacy as a product called EnteraGam.

These are bovine-derived, so they’re not appropriate for strict vegans/ vegetarians or those allergic to beef, but are otherwise well-tolerated.

You can even take them daily to help support and maintain gut health and immunity (I do!).

Fourth, Focus on Diversity for your Microbiome

Probiotics and good nutrition are essential to rebuilding gut health after antibiotics.

However, they only represent two tools in nature’s microbiome-diversification toolbox.

Getting outdoors and exposing yourself to nature’s diverse microbe-rich ecosystems, for instance, is equally crucial.

Breathing in the fresh air, for example, exposes you to more oxygen and beneficial airborne microbes which support your lung microbiome.23

Spending time in the forest exposes you to phytoncides, natural immune-boosting essential oils emitted by trees.24

And digging in the dirt or “earthing” (walking around outside barefoot) inoculates you with precious soil microbes that enter your body via the skin and help repopulate your microbiome.

Some soil microbes have even been shown to help with depression via the gut microbiome.25

Plus, getting outdoors is one of the best ways to lower stress, get centered, and get your body moving—all of which are essential to rebuilding a healthy gut.

It’s important to remember that the gut microbiome is a complex and dynamic community of microorganisms.

Thus, the diversification of gut bacteria is the goal when healing your gut.

And you can’t achieve that by simply taking a one-strain probiotic, never getting outdoors, and/or eating sterile, processed foods.

Research shows that although we can get close to baseline, we cannot fully restore our gut microbiome to exactly how it was pre-antibiotics.

That’s okay, so long as there is a diverse and robust ecosystem of beneficial microbiota to build on.

And the only way to achieve that is by taking a multi-prong approach like the one outlined here.

As a side note for all you animal lovers, pets have been shown beneficial for building gut diversity too!26

And Finally, Fifth: Support your Liver

Any time you take medication, be it antibiotics or an over-the-counter pain medicine, it’s important to give your liver some extra support.

Why? Because your liver bears the brunt of what’s required to neutralize and filter out drugs and other toxins.

There are lots of great ways to support your liver, including eating plenty of dark leafy greens, brassica vegetables, and drinking lemon water.

In addition, liver-supportive and protective herbs, like Milk Thistle, can make a big difference after antibiotics use.

I like Designs for Health Milk Thistle which you can access via my online dispensary.

I’m also a fan of Castor Oil Packs for gentle liver support and comfort (use code DRMAREN10 for a discount).

To Recap:

Antibiotics can be necessary and life-saving, but they are widely over-prescribed and come with short-term and long-term risks, especially for the gut microbiome and your future risk of certain diseases.

Therefore, it is always wise to ask your doctor whether antibiotics are truly necessary versus a watchful waiting approach with follow-up.

It’s also wise to know which types of conditions may respond to natural treatment so that you can discuss options with your provider.

Finally, if you truly need to take antibiotics, rest assured that you can protect and repair your gut microbiome through diet, supplementation, and enjoying the great outdoors.

Always take the full course of antibiotics and do NOT attempt to substitute natural remedies when an antibiotic is truly needed (this is not safe and can be life-threatening).

With what you’ve just learned in this article, you are now fully equipped to avoid unnecessary antibiotics and protect yourself when you do need to take them.

Get Customized Supplement and Prescription Recommendations

Ready to start rebuilding your gut health after antibiotics?

When using supplements, choosing pharmaceutical-grade, physician-recommended supplements is essential.

You can find most of the supplements recommended here at a discount through our online dispensaries at:

  • Fullscript: Saccharomyces boulardii, Milk Thistle, serum-derived immunoglobulins
  • Microbiome Labs: Probiotic supplements, prebiotic supplements, and serum-derived immunoglobulins
  • WholeScripts/Xymogen: Note: Xymogen products are only available through WholeScripts.
  • Quicksilver Scientific: Liver support herbs and full body detox
  • Metagenics: Milk Thistle and other liver-supportive herbs

Get easy access to these links, and others, on the Trusted Products page of our website.


  1. https://www.cdc.gov/drugresistance/about.html
  2. https://www.cdc.gov/drugresistance/about.html
  3. https://www.cdc.gov/media/releases/2016/p0503-unnecessary-prescriptions.html
  4. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9449220/
  5. https://www.apa.org/news/press/releases/2017/02/antibiotics-expectations
  6. https://www.aafp.org/pubs/afp/issues/2016/0801/p200.html
  7. https://pubmed.ncbi.nlm.nih.gov/15922696/
  8. https://pubmed.ncbi.nlm.nih.gov/27325869/
  9. https://publications.aap.org/pediatrics/article/131/3/e964/30912/The-Diagnosis-and-Management-of-Acute-Otitis-Media
  10. https://www.cdc.gov/antibiotic-use/pdfs/WatchfulWaitingEar-P.pdf
  11. https://www.nei.nih.gov/learn-about-eye-health/eye-conditions-and-diseases/pink-eye/treatment-pink-eye
  12. https://bpac.org.nz/bpj/2015/june/symptoms.aspx
  13. https://www.pharmacytimes.com/view/study-probiotic-in-yogurt-may-protect-against-antibiotic-associated-diarrhea
  14. https://pubmed.ncbi.nlm.nih.gov/29725956/
  15. https://pubmed.ncbi.nlm.nih.gov/27688016/
  16. https://www.cochrane.org/CD004827/IBD_probiotics-prevention-antibiotic-associated-diarrhea-children
  17. https://pubmed.ncbi.nlm.nih.gov/29725956/
  18. https://www.medicalnewstoday.com/articles/323082
  19. https://academic.oup.com/jac/article/74/3/782/5173727
  20. https://link.springer.com/article/10.1007/s10620-015-3726-5
  21. https://link.springer.com/article/10.1007/s10620-015-3726-5
  22. https://nyaspubs.onlinelibrary.wiley.com/doi/abs/10.1111/nyas.13958
  23. https://pubmed.ncbi.nlm.nih.gov/22278670/
  24. https://pubmed.ncbi.nlm.nih.gov/16873099/
  25. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868963/
  26. https://pubmed.ncbi.nlm.nih.gov/32185142/

About Dr. Maren

Christine Maren D.O., IFMCP is a board-certified physician and the founder of a virtual functional medicine practice in Colorado, Michigan, and Texas.  She is best know for her work in thyroid, gut and reproductive/ preconception health. Dr. Maren is board-certified by the American Board of Family Medicine and is an Institute for Functional Medicine Certified Practitioner (IFMCP)

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