How Antibiotics Mess Up Your Gut

How Antibiotics Mess Up Your Gut [+ What To Do About It]

As a physician, I've seen the life-saving power of antibiotics firsthand. They’re incredible tools for battling serious infections. Yet, every medication has its trade-off, and the gut impact of antibiotics is a prime example of this.

Let me paint a picture. You've been under the weather, a nagging sinus infection just won't let up. You’ve tried using a neti pot, steaming, and cold compresses to the face, but the pressure just keeps building up. The doctor prescribes antibiotics and voila, the infection subsides, your sinuses start to clear up, but your gut isn't singing the same victory tune. Instead, you're now dealing with digestive issues, like bloating, discomfort, and loose stools. You traded one problem for another, except the new problem could last for months if you don’t address it properly.

The connection? It lies within your gut microbiome, a thriving community of bacteria, both “good” and “bad,” residing within your digestive tract. When you take antibiotics, they do their job, yes, but they do it a bit too well, leading to something we call “dysbiosis.” I talk a lot about this in my newest book, The GutSMART Protocol. Antibiotics aren’t like highly trained attack dogs; instead, they act like a bull in a china shop, demolishing both the harmful bacteria causing your infection and the beneficial bacteria helping to maintain homeostasis in your gut. In their wake, they leave a scorched field that requires repair.

The result is an imbalance in your gut microbiome, leading to the unpleasant digestive issues you're probably now experiencing. Not to mention, some antibiotics come with great risks to your health. Let’s take two examples of antibiotics used widely by the dental and medical professions.

First of all, clindamycin! I cringe when I see patients put on clindamycin by their dentists, because of the risk of severe side effects, including a horrible gut infection.


Clindamycin is an antibiotic often used to treat serious infections caused by certain types of bacteria, like the ones found in deep tooth root infections. It works by slowing or stopping the growth of bacteria. However, it carries its own set of risks:

  1. Antibiotic-associated Diarrhea: Clindamycin is the most common antibiotic associated with this type of reaction. It can lead to a severe condition called Clostridium difficile-associated diarrhea (CDAD). CDAD can range from mild diarrhea to severe inflammation of the colon, leading to colitis and megacolon, which can be life-threatening.


  2. Allergic Reactions: As with all drugs, some people may have an allergic reaction to clindamycin, resulting in rashes, itching, difficulty breathing, or swelling of the face, tongue, or throat.


  3. Drug Interactions: Clindamycin may interact with certain other medications, such as erythromycin, which could increase the risk of side effects.

Ciprofloxacin (Cipro) is a fluoroquinolone antibiotic commonly used to treat urinary tract infections and sinusitis. However, it also carries some significant risks:

  1. Tendon Problems: Ciprofloxacin can cause tendonitis or tendon rupture, particularly in older adults, those with kidney, heart, or lung transplants, and those on corticosteroid therapy. The Achilles tendon is most often affected.


  2. Neurological Effects: Some people may experience nervous system effects, such as headaches, dizziness, insomnia, agitation, or even more serious conditions like peripheral neuropathy.


  3. Cardiac Effects: In rare cases, Ciprofloxacin can affect the electrical communication pathways in the heart, potentially leading to serious conditions such as QT prolongation that can result in a life-endangering arrhythmia.


  4. Disruption of Gut Microbiome: Like all antibiotics, Ciprofloxacin disrupts the gut microbiome for up to 12 months, leading to side effects like diarrhea and, rarely, more serious conditions like pseudomembranous colitis caused by C. difficile overgrowth.

To avoid these unwanted secondary side-effects, try to avoid taking antibiotics unnecessarily. However, the truth is you won’t always be able to stay away from antibiotics, as you might find yourself with an infection that needs attention right away. But here's the good news. You can restore harmony within your gut microbiome and get your gut back to homeostasis with the right combination of positive health behaviors.

Here are My Top Five Tips to Help Your Gut Recover From Antibiotics:

1. Go high-fiber.

Good bacteria love dietary fiber. So, if you want to replenish your gut's good bacteria, feed them plenty of fruits, vegetables, legumes, and whole grains. Diversity is the key, and to support a more robust and resilient gut microbiome, aim for 5 - 8 servings (or approximately 40 grams of fiber) daily.


2. Bring on the fermented foods.

Fermented foods, such as yogurt, kefir, sauerkraut, kimchi, kombucha, kraut juice, and vegetable brine drinks are chock-full of beneficial probiotics. These probiotic-rich foods are not only adding a healthy dose of bacteria to your gut, but they’re also helping to support the growth of other favorable bacteria through a process called cross-feeding. Good bugs feed other good bugs and support each other’s growth.


By adding fermented foods to your diet, you can replenish the beneficial bacteria your gut has lost from having been on a course of antibiotics. Aim to eat 2 - 3 servings (2 - 3 cups) of ferments daily to replenish those lost good bugs.

3. Go high on polyphenols.

Polyphenols, including bioflavonoids, are potent plant compounds renowned for their antioxidant properties. Pomegranates, among other fruits and vegetables, are particularly rich in these compounds. Intriguingly, recent research suggests that polyphenols may have a profound impact on gut health, specifically in restoring the gut microbiome and mucosal layer. The gut microbiome interacts with dietary polyphenols, breaking them down into metabolites that may have health-promoting effects. These metabolites can help nurture the 'good' gut bacteria, promoting a healthy and diverse microbiome. Furthermore, polyphenols help to maintain the integrity of the gut mucus layer, a protective barrier that shields the gut lining from potentially harmful substances. By reducing inflammation and oxidative stress in the gut, polyphenols contribute to the regeneration of this vital mucus layer, thereby supporting overall gut health and function. Add in 1 tablespoon of pomegranate arils to smoothies and salads as a way to enhance your polyphenol consumption.

4. Move your body.

A regular exercise regimen can profoundly influence the diversity and composition of the gut microbiota. Research has shown that physically active individuals typically possess a more diverse gut microbiome compared to sedentary individuals. This microbial diversity is generally associated with better health, as a greater variety of bacteria species can contribute to improved digestion, nutrient absorption, immune function, and inflammation control.

Move your body

Exercise also enhances the prevalence of beneficial bacterial species. For instance, certain bacteria such as Bifidobacterium and Akkermansia are found in greater quantities in those who exercise regularly. These bacteria play a critical role in maintaining a healthy gut barrier, which prevents harmful substances from leaking into the bloodstream.

The impact of exercise on the gut microbiome may also extend to mental health. The gut and brain are closely connected through the gut-brain axis, and changes in gut microbiota can affect this connection. Exercise-induced changes to the microbiome may help improve mood and reduce anxiety, although this field of research is still growing.

It's worth noting that the benefits of exercise on the gut microbiome seem to be most profound when combined with a balanced, high-fiber, high-fermented foods, and polyphenol-rich diet (points #1, 2, 3 above). This is because beneficial gut bacteria thrive on these nutrients, and making sure to combine them with an exercise regimen will augment their beneficial effects.

While research is ongoing to uncover the full extent of exercise's influence on the gut microbiome, it's clear that getting regular physical activity can be a boon for gut health, contributing to a diverse and balanced microbiome. So whether it's jogging, cycling, yoga, or even a brisk walk, find a physical activity you enjoy and make it part of your routine for the sake of your gut health.

5. Reach for a high-quality probiotic supplement.

Finally, perhaps the most efficient way to restore your gut microbiome is by taking a high-potency probiotic supplement. I recommend Happy Gut Restore, the supplement I developed to restore your gut's balance quickly and efficiently.

Happy Gut Restore is not your everyday probiotic. It's been carefully formulated to repopulate your gut with a robust variety of beneficial bacterial strains. It doesn't just restore; it enhances, delivering billions of health-promoting bacteria straight to your gut.

If you've used antibiotics or are currently taking antibiotics and are dealing with their gut disruption (gas, bloating, diarrhea, loose stools or floating stools), don't despair. Choose a high-potency probiotic, like the Happy Gut Restore, specially designed to restore your gut health back to baseline, lessen the side effects of antibiotics, and make your gut a happy place once more.

So, give your gut the love and care it deserves. Choose Happy Gut Restore today. Let's say goodbye to bloating, discomfort, and irregularity and say hello to a healthier, happier gut, and a healthier, happier you. Trust me; your gut will thank you.

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