Worst Antibiotics for Your Gut: What You Need to Know Before You Pop That Pill
Written by: Vincent Pedre M.D. | August 19, 2025 | Time to read 7 min
Antibiotics save lives. No debate there.
But they’re not precision weapons—they’re carpet bombs. They take out the bacteria causing your infection, but they can also wipe out huge swaths of your gut microbiome in the process. And in the gut health world, that’s a big deal.
Some antibiotics are worse than others when it comes to collateral damage. If you care about your gut health (and you should—those microbes affect digestion, immunity, mood, and even metabolism), it’s worth knowing which ones pack the biggest punch to your microbiota.
Why Antibiotics Can Wreck Your Gut
Your gut is home to trillions of microbes—bacteria, fungi, and other microorganisms.
A healthy microbiome is diverse and balanced. Research has shown that diversity in our gut microbiome translates to lower inflammation in our bodies. This is why I call gut microbiome DIVERSITY the HOLY GRAIL of health. Antibiotics disrupt that balance by:
Killing beneficial bacteria along with harmful ones
Allowing opportunistic pathogens (like Clostridioides difficile & Candida) to thrive
Reducing microbial diversity, which can take months—or years—to recover
Some antibiotics hit a narrow range of bacteria (narrow-spectrum) and cause less disruption. Others go broad, nuking everything in sight.
The Worst Offenders for Gut Health
1. Clindamycin
Gut impact: Infamous for causing C. difficile infections.
Why it’s bad: Clindamycin is very broad-spectrum, especially against anaerobic bacteria (many of your good gut microbes fall into this category). Even short courses can drastically shift your gut ecosystem. Only take if absolutely necessary and there’s no better option. For some reason dentists like to prescribe this antibiotic, and it makes me cringe.
Red flag: Strongly linked to antibiotic-associated diarrhea. Question your doctor or dentist whether there is a suitable alternative if you have an infection that needs to be treated.
2. Fluoroquinolones (e.g., ciprofloxacin, levofloxacin, moxifloxacin)
Gut impact: Broad-spectrum with a tendency to alter gut bacterial composition for long periods. Sometimes you can’t get away from it, so if you have no choice but to take a course of these types of antibiotics, make sure to do gut restoration in tandem.
Why it’s bad: Research shows changes to the microbiome can persist for over a year after just one course.
- Extra concern: Linked to tendon damage and nervous system side effects—so it’s gut-wrecking and potentially body-wrecking.
3. Cephalosporins (e.g., ceftriaxone, cefuroxime, cephalexin)
Gut impact: Broad activity against both Gram-positive and Gram-negative bacteria, meaning lots of friendly gut microbes get hit, like your friendly Lactobacilli.
Why it’s bad: High risk of antibiotic-associated diarrhea and C. difficile overgrowth, but much less risk than Clindamycin.
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Note: Often used in hospitals, where microbiome diversity is already at risk.
4. Amoxicillin-Clavulanate (Augmentin)
Gut impact: More disruptive than plain amoxicillin due to the clavulanate, which broadens its bacterial targets and half-life.
Why it’s bad: Strong diarrhea risk, can trigger long-term microbiome imbalance.
- Fun fact: “Augmentin gut” is practically a meme in medical circles. Sometimes it’s been used to treat SIBO (Small Intestine Bacterial Overgrowth), but I’ve almost never seen it be successful in the long-term.
Bonus: 4 more antibiotics that are NOT friends of your gut
5. Macrolides (e.g., azithromycin, clarithromycin, erythromycin)
Gut impact: Broad-spectrum and disruptive to gut diversity, especially reducing beneficial Bifidobacteria.
Why they’re bad: Research has shown it can take up to 6 months for the gut microbiome to recover from a single, 5-day Z-pack. So, think again, when you’re asking your doctor to give you a Z-pack to knock out that likely viral infection that doesn’t need antibiotics.
Extra note: Frequently prescribed for respiratory infections, so they’re common microbiome disruptors.
6. Tetracyclines (e.g., doxycycline, minocycline, tetracycline)
Gut impact: Reduce gut microbial diversity and can promote the growth of antibiotic-resistant strains.
Extra note: Often used long-term for acne, which extends their gut impact. If you have no other alternative, make sure to take gut protective measures.
7. Sulfonamides + Trimethoprim (e.g., co-trimoxazole / Bactrim / Septra)
Gut impact: Can significantly shift gut bacterial composition and allow fungal overgrowth.
- Extra note: Older class, still used for urinary tract infections (UTI’s) and some respiratory infections. And sometime they’re the best choice for UTI’s, but beware of yeast overgrowth as a consequence of taking them, especially if you are a woman.
8. Carbapenems (e.g., meropenem, imipenem, ertapenem)
Gut impact: Extremely broad-spectrum, used in hospitals for serious infections—they obliterate a wide range of gut bacteria.
Extra note: High risk of C. difficile infection, especially in already vulnerable patients.
Here’s a summary of worst to least worst antibiotics for your gut:
Can You Protect Your Gut While on Antibiotics?
You can’t entirely dodge the microbiome hit, but you can soften the blow:
Ask if a narrow-spectrum antibiotic will work — Sometimes doctors can prescribe a more targeted drug.
Time your probiotics carefully — Take them a few hours away from your antibiotic dose to maximize survival. Studies have shown that taking a probiotic while on antibiotic speeds up gut microbiome recovery post-antibiotics.
Load up on prebiotic fiber — Foods like garlic, onions, leeks, and asparagus feed beneficial bacteria as they regrow.
Stay hydrated and nourished — Your gut lining needs nutrients to recover.
Rebuild diversity after — Fermented foods (yogurt, kefir, kimchi) and fiber-rich plants help restore balance.
If you're looking for a targeted supplement to support gut recovery during and after antibiotic use RESTORE Probiotic is a standout option. This boutique blend delivers 50 billion CFUs across ten clinically researched strains, purpose-built to address microbiome imbalances triggered by antibiotics, stress, diet, or lifestyle factors.
Notably, it includes Bifidobacterium lactis (UABi‑12™) —a strain shown to help protect and restore the microbiome following antibiotic therapy, while also strengthening the immune response. It’s formulated free of common allergens (like dairy, gluten, soy, nuts, etc.) and comes in delayed‑release vegetarian capsules—ideal for both safety and survivability through the stomach acid so that the strains are targeted to where they’re needed most.
How it helps during antibiotic use:
While no probiotic is a magic bullet, adding RESTORE during and after antibiotic treatment can help re-seed beneficial bacteria, support bowel function, and soothe gut inflammation. It’s a practical tool in your gut-support arsenal—especially when paired with dietary fiber, fermented foods, and careful timing.
It’s really sad to me that so many people (and doctors) lack this knowledge. Prescribing probiotics with antibiotics should be the standard of care, but unfortunately, in our one-sided Western medicine, it isn’t. We need to shift the focus into always undoing the damage caused by antibiotics before it builds up and causes chronic gut issues that lead people to seek me for 1:1 care.
By the way, if you have chronic gut (or gut-related health) issues that are unresponsive to any measures you or other health practitioners have tried, you can book a FREE 15 MIN DISCOVERY CALL to find out if we can help you. We welcome challenging cases, and our most successful clients are the ones who are ready to commit to the changes required in order to heal.
Bottom Line
I want to help people live healthier, happier lives by addressing the common root cause of so many chronic health issues — the gut, the gut microbiome, and the gut lining. All of these elements build a strong foundation for your health. And when they are out of sorts, your health and mind will follow.
Antibiotics are sometimes necessary. But some—like clindamycin, fluoroquinolones, cephalosporins, and amoxicillin-clavulanate—are particularly brutal to your gut. If you need them, fine. Just be strategic: discuss alternatives with your doctor, support your microbiome during treatment, and work to restore it afterward.
If you’re considering antibiotics or have questions about your gut health, book a free discovery call with a Dr. Vincent Pedre representative. If you decide to move forward, you will benefit from Dr. Pedre’s expert team and his 25 years of experience as a doctor. Reserve your free consultation here.
Gut health isn’t just about avoiding stomach trouble—it’s about protecting an ecosystem that keeps your whole body running well.
A Happy Gut = A Happy Life
