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7 Ways to Replenish Good Bacteria After Antibiotics

Written by Dr. Michael Ruscio, DC on October 28, 2024

Written by Dr. Michael Ruscio, DC on October 28, 2024 — Reviewed by Hannah Wright

Restoring Gut Microbiome Balance in 7 Simple Steps

• Antibiotics & the Gut Microbiome?|
• 7 Ways to Replenish Gut Bacteria after Antibiotics|

Antibiotics can wreak havoc on our gut microbes and cause a lot of uncomfortable digestive side effects like nausea and diarrhea. Repeated rounds of antibiotics can also set us up for some long-term health concerns, by training harmful bacteria to become immune to their antibiotic effects. 

However, antibiotics are a valuable and even life-saving tool when needed, so I don’t want any of us to be overly concerned if we end up having to use them. 

The truth is, antibiotics don’t have to totally disrupt the gut for any length of time. There are a lot of simple strategies that can help to mitigate antibiotic side effects and restore gut homeostasis more quickly.

Before I get into how I go about replenishing good bacteria after antibiotics, allow me to share some background on how antibiotics impact the gut microbiome.

How do Antibiotics Impact the Gut Microbiome?

The human gut is home to more than 1,000 microbial species with 150 times more genes than the entire human genome 1. Your own gut microbiome is unique to you, and it’s a vital organ that impacts every other organ system in your body 2. Maintaining balance and diversity in the gut microbiome seems to translate to better mental and physical health 3.

But the gut ecosystem isn’t an island unto itself—it relies on both internal and external inputs to stay healthy. What we eat, how well we sleep, how stressed we are, and how much we exercise can all impact the balance of microbes in the gastrointestinal tract. 

Certain medications, especially antibiotics, can significantly influence microbial balance 4. I’ll illustrate this with an analogy.

Imagine you’re caring for a beautiful garden with an abundance of flowers, trees, and shrubs (aka your gut microbiome). Let’s say you encounter an invasive plant species (a pathogen) that’s taking over the entire garden. It would be great if you could prune out only the invasive plant, but that’s rarely an option. Most of the time, getting rid of the invader means also harming the beloved plants you want to keep. This is essentially what broad-spectrum antibiotics are doing—they’re killing the harmful bacteria, but in the process they’re also taking out your beneficial bacteria 4.  

Not all antibiotics are equally problematic when it comes to GI disruption, but broad-spectrum options like amoxicillin, ciprofloxacin, and cefprozil may alter the gut microbiome for up to 12 weeks after taking them 4. 

It’s possible to recover decently after one antibiotic exposure, but repeated rounds can end up removing enough beneficial gut microbes to increase the likelihood of long-term dysbiosis. Untreated dysbiosis from antibiotic use puts us at risk of:

• Clostridium difficile infection—a potentially serious infection that can cause mild to extreme chronic diarrhea 4
• Developing antibiotic-resistant bacteria 4
• Reduced numbers of certain beneficial bacteria for an extended period of time 4
• Shifts in the entire balance of the bacterial community 4
• Chronic, inflammatory diseases 5

This may all sound pretty scary, but rest assured that we have a lot of control over the health of our gut microbiome, even if we have to take antibiotics. Let’s get into 7 strategies I recommend to my clients so they can both prepare their microbiome to withstand antibiotics and replenish good bacteria afterward.   

7 Ways to Replenish Gut Bacteria After Antibiotics

If you’ve ever taken a course of antibiotics, your original symptoms probably improved dramatically, but you may have ended up with uncomfortable side effects like diarrhea, nausea, or even a vaginal yeast infection. Those symptoms probably result from the antibiotics altering your gut microbial balance. 

So, is there any way to prevent these side effects from happening in the first place, or to improve them once they happen? The answer is—absolutely! 

Let’s dig deeper into the 7 strategies I teach my clients to help them recover well from antibiotic use.

1. Supplements

Probiotics are my first choice for combating the negative impacts of antibiotics on the gut microbiome. 

Probiotics, especially multi-strain, can reduce antibiotic-associated diarrhea 6 and help to restore the gut flora after taking antibiotics 7. Here’s the research:

• A 2012 meta-analysis of 63 studies showed that people who took probiotics had a 48% lower risk of developing antibiotic-associated diarrhea 6.
• A 2014 systematic review of 63 trials found that 83% of probiotics used in the studies restored the gut microbiota in clients with dysbiosis 7.

One small study found that probiotics colonized the gut really well after antibiotic use, but they delayed the return of the normal (pre-antibiotic) gut microbiota 8. This might sound bad, but which beneficial microbes come into play first doesn’t really matter, as long as they’re there and improving your symptoms.  

If you have side effects during or after antibiotic use, and probiotics mitigate those side effects, that’s what matters. As a clinician, I’m much more interested in how you’re feeling than the ratios of specific bacteria in your gut.

So, which probiotic is best? Any high-quality probiotic supplement will likely be beneficial. In the clinic, we’ve found a triple-therapy approach (a combination of the three most effective categories of probiotics) to be the most helpful for all kinds of gut issues, including antibiotic-related dysbiosis. 

And research supports using these different categories of probiotics—Lactobacillus and Bifidobacterium blends, Saccharomyces boulardii, and soil-based probiotics—to reduce gut problems during and after antibiotic treatment. For example, a 2021 meta-analysis of 42 randomized controlled trials found 9:

• A 46% reduction in the risk of antibiotic-associated diarrhea when participants used a high dose of mainly Lactobacillus and Bifidobacterium strains with and after antibiotics.
• The probiotic yeast, Saccharomyces boulardii, was also highly effective, reducing the risk of antibiotic-associated diarrhea by 36%.
• The soil-based probiotic, Bacillus clausii, reduced the risk of antibiotic-associated diarrhea by 39%.

Soil-based probiotics haven’t been studied as long as Lactobacillus and Bifidobacterium strains or Saccharomyces boulardii, so that last figure was based on only one study. However, other strong research supports soil-based probiotics for treating diarrhea. For example:

• A 2018 meta-analysis of 6 randomized controlled trials showed that combining soil-based probiotics helped to reduce acute diarrhea and hospital stays in children 10.

Overall, these findings support a multi-strain probiotic approach but also refute the old adage that we need to avoid probiotics while taking antibiotics.

In my clinical experience, starting probiotics as soon as you start an antibiotic course is a great way to support the gut microbiome during the process, and it may even help the antibiotic work better. For example, two meta-analyses of randomized controlled trials have shown that probiotics added to antibiotics can boost eradication rates of the digestive system pathogens Helicobacter pylori and Clostridium difficile 11 12.

The probiotic protocol we currently use in the clinic consists of taking all three categories of probiotics during and after antibiotic use, for at least 2–3 months.

Once the round of antibiotics is complete, prebiotic supplements (dietary fibers that feed gut bacteria) may help to increase levels of beneficial bacteria 13 14 15 16. Just a note of caution: Too many prebiotic supplements or prebiotic foods (like Jerusalem artichokes, onions, leeks, wheat, asparagus, and oats) may aggravate symptoms in people with dysbiosis or irritable bowel syndrome (IBS). 

If, after a trial of probiotics and possibly prebiotics, my clients are still having gut symptoms, then antimicrobials (including the antibiotic rifaximin and herbal varieties) can be helpful. A gentle, localized antibiotic like rifaximin, or alternatively, herbal antimicrobials with ingredients like oregano oil and pau d’arco, can correct dysbiosis of the small intestine and related conditions, like IBS. 

Rifaximin, which requires a doctor’s prescription, temporarily reduces the levels of several types of gut bacteria 17 18 and helps improve IBS and SIBO (small intestinal bacterial overgrowth, a type of dysbiosis) 19. Herbal antimicrobials can function in a similar capacity to rifaximin 20, and given a little more time, they can help improve SIBO, IBS, constipation, and indigestion 21.

The next way to replenish gut bacteria after a round of antibiotics is by eating a gut-friendly diet.

2. Diet Therapy

In general, a more diverse gut microbiome means better overall health, but antibiotic use (especially repeated rounds) can reduce gut microbiome diversity 3. 

Since food has a significant impact on gut microorganisms, I coach my clients to harness their diet to help restore their microbial community after using antibiotics. 

Everyone has a unique set of microbes, so there’s no one-size-fits-all diet for promoting a healthy gut microbiome 3 23. As I discuss in Healthy Gut, Healthy You, it’s important to consider the following when figuring out what diet to eat for gut microbiome health. Does the diet:

• Control inflammation?
• Control and balance blood sugar?
• Allow for personalized carbohydrate and prebiotic fiber intake?
• Eliminate or reduce food allergens and intolerances?

Eating a variety of different plant types tends to equate to greater gut microbiome diversity 24. In generally healthy people, a Mediterranean or Paleo diet may be a great option for restoring gut microbiome balance after antibiotics. Both of these diets focus on whole foods and a lot of plant variety. 

But plants can be a double-edged sword for some people. Plants tend to be fiber-rich, and fiber feeds gut microbes. However, higher-fiber diets can be helpful for some GI issues, but problematic for others—the key is to adjust fiber intake based on symptoms 25. And here’s how we do that in the clinic:

If our clients notice digestive discomfort when they eat plants and plant-based foods, we do a trial of a low-FODMAP diet. A low-FODMAP diet restricts certain carbohydrates that gut bacteria love to ferment, a gas-producing process that can create symptoms for some people. There’s a lot of evidence for using this diet to improve IBS symptoms 26.

How does it work? A low-FODMAP diet can increase the density of enteroendocrine cells 27, which regulate digestive function. People with IBS tend to have lower levels of enteroendocrine cells, so bumping their numbers is one way a low-FODMAP diet can improve symptoms. 

A low-FODMAP diet may also make people feel better by reducing inflammation, leaky gut, and histamine levels 28 29 30 31 32 33. 

Not only that, but research also shows that a low-FODMAP diet is beneficial for curbing SIBO infections and symptoms, especially when the diet is combined with probiotics 34. 

Generally, a low-FODMAP diet excludes certain plants, like broccoli, cabbage, onions, garlic, cashews, beans, apples, pears, and wheat. But it includes a wide array of other plants (plus meats, certain grains, and some kinds of dairy) that shouldn’t provoke symptoms in sensitive people. 

And for clients who like Paleo or Mediterranean diets but just need to tweak a few gut-upsetting foods, they can mix and match to personalize a diet that makes them feel best.

Here’s a snapshot of what to enjoy on a low-FODMAP diet:

In addition to a personalized diet, layering in some intermittent fasting may help to balance the gut microbiome during and after antibiotics, and it could aid with weight loss and metabolic health, too 35.

3. Exercise

You probably already know that exercise is good for your heart, bones, and brain. But research also confirms that exercise benefits the gut microbiome 36 37 38. 

Going back to what I mentioned earlier about creating the right type of environment for gut microbes, exercise can improve general health and encourage healthy microbes to thrive. I discuss this in more detail in Healthy Gut, Healthy You, but exercise might provide its gut microbiome benefits by:

• Modulating toll-like receptors (TLRs). TLRs are sensors for the contents in the gut and help prevent the immune system from attacking things it shouldn’t, such as food, good bacteria, and the intestinal lining 39.
• Stimulating the growth of healthy bacteria that produce short-chain fatty acids (SCFAs). SCFAs may have numerous gut-health benefits like reducing inflammation, supporting immune system function, and providing us and our microbes with energy. Athletes tend to have more of the bacteria that make SCFAs 22 36 37.
• Increasing microbial diversity 39. 
• Supporting the gut-muscle connection to regulate metabolism and the types of bacteria living in the gut 22.

You may be wondering what type of exercise is best for the gut, particularly when you’ve just taken antibiotics. As with diet, there isn’t one perfect exercise routine for the gut microbiome. It’s important to listen to your body and do what works for you. But a 2023 systematic review suggested that moderate-to-high intensity exercise (cardio or a combo of cardio and strength) lasting for at least 30 minutes, 3 times per week, may help to improve the gut microbiome 37. 

Having said that, balance is key. Too much and too little exercise can both be problematic for the gut. For our clients who are new to exercise, we coach them to build a foundation by walking as much and as often as they can to start. As they advance, they can experiment with different types and intensities of exercise.

4. Stress Management

It’s probably no surprise that stress can have a negative impact on our gut microbes, especially when we’ve just had antibiotics. When we’re stressed, our fight-or-flight hormones can disrupt the way our gut bacteria function 40. In fact, under stress, bacteria that would normally produce SCFAs may end up altering the way the body regulates mood-related chemicals and the protective gut barrier 40. 

Of course, we can’t get rid of all of our stress—and antibiotics themselves are a type of internal stress—but we can learn techniques to help us better manage it so it’s not so detrimental. 

We often recommend that clients learn mind-body practices like meditation and mindfulness-based stress reduction to help control their stress response, reduce inflammation, and support a healthy gut 40. 

I’m also a huge fan of spending time in nature, and we have plenty of evidence touting its health benefits. A 2020 systematic review found that being in nature was associated with 41:

• Lower perceived stress  
• Reduced activity in brain regions related to stress 
• Improved cortisol and blood pressure levels 
• A calmer autonomic nervous system

Overall, spending time in nature seems to have a calming effect 41 42. And walking in nature may be especially beneficial for stress, attention, and mood 43 44 45, especially while recovering from antibiotics. If you’re into habit-stacking to maximize your time, walking in nature is one way to cross both exercise and stress management off your list for the day. 

But it’s not necessary to go for a hike in the woods to reap the benefits of nature—living close to natural greenery, and even looking at photos of nature can improve mood and reduce stress 46 47.

5. Restful Sleep

Sleep is another factor that affects the internal environment. The quality and quantity of sleep can alter the bacteria living in the gut and may help or hinder the rate of recovery from antibiotics. Good sleep seems to create a more supportive environment for good bacteria. Poor sleep doesn’t allow the body to recover from daily stressors, which may harm helpful bacteria and support problematic ones 48. 

Here are some of my favorite tips to help clients optimize their sleep:

• Reduce exposure to bright lights at night
• Sleep in a dark, cold, quiet environment
• Avoid stressful activities, like exercise or arguments, before bed
• Aim to be in bed by 10 pm, asleep before 11 pm, and to sleep for 7–9 hours
• Address sleep problems like sleep apnea

6. Sun Exposure

We don’t know much about how sun exposure directly affects the gut microbiome, particularly with respect to antibiotic use. But sun exposure could help protect against digestive tract diseases and inflammation 49 50 51. 

In addition, a 2019 clinical trial found that women with low vitamin D levels had significant changes to their gut microbiota when exposed to UVB light that raised their vitamin D levels 52. This suggests that sun exposure may influence the digestive tract by improving vitamin D levels, but it’s not clear that just taking vitamin D supplements has the same effects 53 54 55.

When it comes to specific sun exposure recommendations, we advise that clients with darker skin or who don’t burn easily get 25–40 minutes of direct sun exposure (without sunscreen) on their hands, face, forearms, and lower legs, on most days, whether or not they’re taking antibiotics 56. People with lighter skin can aim for the same bodily exposure for 9–13 minutes a day, most days, antibiotics or not 57. But again, it’s important to do what’s right for your body and skin type—make sure not to burn 58 59! 

7. Social Connection

Spending time with people we care about is a great way to manage stress 60. Close relationships also seem to influence our gut bacteria more directly, regardless of the food we eat 61. 

One 2019 microbiome study suggested that the closeness of our relationships may matter a lot when it comes to the gut microbiome. In this study, married couples tended to have more similar and more diverse gut bacteria (remember, diversity is good) than siblings did, especially if the married couple felt very close to each other. In fact, their sense of closeness seemed to have a stronger effect on their gut bacteria than even their genetics or early environment 61.

So, among the many reasons it’s great to have close social connections in life, recovering well from a round of antibiotics may be yet another one.

In case it’s helpful to have it all in one table, here’s a recap of my top 7 strategies for helping people replenish good bacteria after antibiotics. As always, consult with your healthcare provider before making significant changes to your health routine.

Restoring gut microbiome balance requires building and maintaining a healthy foundation. Most of these strategies are free and don’t take a huge time commitment, plus there’s a lot of leeway with how to implement them.

Antibiotics Don’t Have to Derail the Gut Microbiome

Antibiotics are a very important tool we have for fighting bacterial infections, but they can reduce gut microbial diversity, leading to dysbiosis and negative downstream effects. I don’t think any of us should fret over having to take antibiotics if we need them, especially when we can use simple strategies to create a robust gut microbiome and help it recover more quickly after antibiotics. 

Multi-strain probiotics, taken with and after a course of antibiotics, are very effective at combating antibiotic-associated diarrhea and restoring the gut microbiome from dysbiosis. And if probiotics don’t have the desired effect, herbal antimicrobials or rifaximin (with a clinician’s support) can be helpful options.

Additional foundational strategies, like eating a wholesome diet, getting regular exercise, sleeping well, managing stress, spending time in the sun, and creating a close social network, may help to restore balance to gut microbes after antibiotics. With gut health back on track, continuing to practice these science-based strategies can make it easier to recover well from any future antibiotic use. 

All that said, if you’ve tried these 7 simple steps and still feel poorly after antibiotics, we’d love to help you troubleshoot. My book, Healthy Gut, Healthy You, includes a complete step-by-step gut healing guide, and we also offer virtual appointments at the Ruscio Institute for Functional Health.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.