Should I Take Probiotics with Antibiotics? The Ultimate Guide to Probiotic Supplements, Part 4

We are back with the fourth part of our probiotic series. In this installment, we’ll answer the question: Should I take probiotics with antibiotics?

Earlier in this series, we learned what probiotics are, when to take probiotics, and if probiotics are good for IBS and IBD. So if you missed those, make sure to check them out.

Have you ever wondered if taking probiotics with antibiotics will interfere with antibiotic effectiveness? 

Or if the antibiotics will wipe out all those good probiotics anyway, so what’s the point? 

If so, this blog is for you! 

These are completely reasonable questions, by the way. And if you don’t feel like reading all the fascinating facts below, I’ll give you the spoiler: 

YES, you should take probiotics with antibiotics. And as we learned in the first blog of the series, they need to be strain specific!

Antibiotics can be lifesaving and are often a medical necessity. But there is no sugar coating that antibiotics can decimate the microbiome, the unique microbes that are intricately entwined with all aspects of human health. 

Because antibiotics affect the gut, they also create side effects ranging from mild to, in rare cases, life-threatening. So, let’s learn precisely how probiotics can help protect your microbiota and prevent unwanted side effects. 

Should I take probiotics with antibiotics? Yes, to prevent antibiotic-associated diarrhea.

Antibiotic-associated diarrhea occurs in up to 35% of people who take antibiotics (1). This is usually just mild diarrhea, but in some rare cases, it can progress to colitis and bacterial infection and become lethal.

Many studies on probiotics and antibiotics focus on antibiotic-associated diarrhea because it is such a concern, especially in children. 

Abundant research supports the use of probiotics to prevent antibiotic-associated diarrhea. A 2021 meta-analysis of 36 studies concluded that probiotics could reduce the incidences of antibiotic-associated diarrhea by 38% (2). 

Strain-specificity, discussed in part one of this series, is critical here. Simply grabbing any probiotic off the shelf may not give you those protective effects. 

A 2017 randomized controlled trial on healthy volunteers found that taking Saccharomyces boulardii CNCM I-745 with the antibiotic amoxicillin/clavulanate had a protective effect on gut microbiota and significantly reduced antibiotic-associated diarrhea (3). 

In this study, the researchers examined microbiota changes with a course of antibiotics or antibiotics plus probiotics. They found altered gut bacteria in those taking antibiotics alone, resulting in an overgrowth of the Escherichia genus (E. coli)—this overgrowth correlated with diarrhea. 

But those who took probiotics had significantly less change in gut flora and less overgrowth of Escherichia, which aligned with a reduced rate of diarrhea (3). 

The 36-study meta-analysis mentioned above supports the protective effects of probiotics against antibiotic-associated diarrhea. It found that the probiotic Lactobacillus rhamnosus GG was equally effective. The authors also note that taking a probiotic early during antibiotic treatment was vital, and taking it within two days of beginning antibiotics provided the best results. 

You can find Saccharomyces boulardii CNCM I-745 in the brand name probiotic Florastor and Lactobacillus rhamnosus GG in Culturelle. 

Should I take probiotics with antibiotics? Yes, to normalize gut flora.

The great thing about antibiotics is that they swiftly and effectively kill pathogenic bacteria. But this is a double-edged sword—they are capable of killing good bacteria as well. 

The collateral damage to your gut flora generally depends on the type of antibiotic prescribed and the frequency of use. Some are broad-spectrum killers, while some target specific bacteria. And the more frequently antibiotics are taken, the more damage can occur.

It can take weeks to years for your gut microbiota to normalize after a course of antibiotics. And in certain situations, it may never return to normal. 

Along with disrupting good gut bacteria, antibiotics significantly reduce the short-chain fatty acids produced in the gut. Short-chain fatty acids are byproducts, also called metabolites, of healthy gut bacteria. They provide abundant health benefits, including anti-inflammatory and immune-boosting effects. 

Fortunately, taking the right probiotic can help protect your good gut bacteria from being wiped out, helping your baseline microbiome recover more quickly and allowing the good guys to produce short-chain fatty acids. 

A 2021 randomized controlled study demonstrated the protective effects of Bifidobacterium animalis subsp. lactis BB-12 on the gut flora of healthy individuals taking a 7-day course of amoxicillin/clavulanate antibiotics (4). 

In this study, the probiotic group ate yogurt containing Bifidobacterium animalis subsp. lactis BB-12 along with the seven days of antibiotics and continued with the yogurt for the following week (14 days total).

The yogurt group’s microbial diversity and short-chain fatty acid levels were compared with a group that only received antibiotics (4). 

The results of this study were pretty impressive. Both groups experienced a diminished microbial diversity, but the reduction was significantly less pronounced in the probiotic group resulting in a more stable microbial population over 30 days (4). 

The short-chain fatty acid acetate was also reduced by antibiotics, dropping by 20% on the final day of antibiotic administration and then continuing to drop by 30% on day 14. At day 30, 23 days after antibiotic cessation, participants’ acetate level was still reduced by 25% (4). Yikes!

But let’s take a closer look at what happened in the group that ate the probiotic yogurt with their antibiotics…

On day 7, the end of antibiotics, the average acetate level was reduced by 15% (compared to 20% in the non-yogurt group). On day 14, that had dropped to only 9.7% (compared to 30%), and by day 30, the group’s acetate level was back to normal (4)! 

Are you thinking, “Damn, how can I get my hands on this fancy yogurt?!” 

Unfortunately, the exact yogurt used in this study was developed by Penn State and is probably not available to the general public. 

However, you can find the exact strain (Bifidobacterium animalis subsp. lactis BB-12) in Nancy’s yogurt, which is available at many grocery stores. 

If you aren’t a yogurt fan, this strain can also be found in the probiotic capsule Solgar Advanced Multi-Billion Dophilus. 

Should I take probiotics with antibiotics? Yes, to prevent C. difficile infection.

Clostridioides difficile (C. diff) is a bacteria that is a member of a healthy gut ecosystem, but when given the opportunity, it will multiply, leading to a stubborn bacterial infection. 

C. diff infection is often present in antibiotic-associated diarrhea and can be a big reason why this side effect occurs and sticks around.

In susceptible individuals, C. difficile can lead to inflammation of the colon and severe infection that may be lethal. A 2012 analysis in the journal Gastroenterology named C. difficile as a leading cause of death from gastrointestinal causes, ranking 9th behind various GI cancers and liver failure (5). 

C. difficile infection is linked to antibiotic use because antibiotics disrupt healthy gut flora. 

When too many good bacteria are wiped out, it gives opportunistic pathogens like C. diff the chance they need to thrive and multiply. Once someone experiences a C. difficile infection, they have a 20-30% chance of getting it again, which only increases with each new infection (6). 

Between 2001 and 2012, the incidences of C. diff infection increased by 42.7%, and the incidences of recurrent C. diff increased by a jaw-dropping 188% (7)!

This massive change is attributed to the evolution of the C. diff bacteria and the increased use of antibiotics and proton pump inhibitors (7), both of which make users more susceptible to the risk of infection from multiple pathogens. 

A 2020 systematic review looked at the effect of several strain-specific probiotics on recurrent C. diff and concluded that the most promising strain was Saccharomyces boulardii CNCM I-745 (8). This is the same strain mentioned above for preventing antibiotic-associated diarrhea and is found in Florastor probiotics. A 2017 Cochrane review* determined that probiotics effectively prevented C. difficile during antibiotic use and were safe for those with healthy immune systems (9). 

Additionally, a study published this month, in October 2022, conducted by Seres Therapeutics shows promising results for using specific probiotic therapy for recurrent C. difficile.

Seres used a new probiotic called SER-109, which has been granted Breakthrough Therapy designation by the FDA to expedite development. This means preliminary results are so good that they want to get the ball rolling. 

SER-109 is composed of purified Firmicutes spores that target C. difficile, strengthen the gut barrier, and help restore microbial balance. The October 2022 study found that eight weeks of SER-109 reduced C. diff infection by 40%, compared to 12% in the placebo group (10). 

In addition to treating recurrent C. diff, Seres Therapeutics is conducting preliminary research on the use of other forms of SER and how they may benefit ulcerative colitis and balance the immune system in specific populations of immune-compromised folks. You might see these probiotics show up in future blogs.

*Cochrane reviews are some of the most thorough and conservative reviews in the research world. They rarely err on the side of effectiveness when evaluating an intervention, like probiotics in the 2017 review mentioned above. This is a big deal!

Should I take probiotics with antibiotics? Yes, to reduce antibiotic side effects.

If you’ve taken antibiotics, you may know they can cause uncomfortable side effects like nausea, bloating, abdominal pain, and skin rashes. 

Fortunately, probiotics may prevent some of these side effects. A 2008 randomized, placebo-controlled trial showed that taking Lactobacillus rhamnosus GG with antibiotic therapy during H. Pylori eradication significantly reduced antibiotic side effects like nausea, taste disturbance, and diarrhea (11). 

Saccharomyces boulardii CNCM I-745 has also been shown to be very effective at preventing antibiotic-induced side effects. A 2017 study found that taking this strain with antibiotics significantly reduced abdominal discomfort, nausea, bitter taste, and diarrhea (12). 

You may be familiar with these specific strains, but if you need a refresher, they are found in the probiotic supplements Culturelle and Florastor, respectively. 

Should I take probiotics with antibiotics? Or prebiotics?

Prebiotics are non-digestible fibers that increase the population of certain gut bacteria. They are basically like fuel that only feeds our helpful gut bugs. 

Including prebiotic-rich foods in the diet is generally a good idea when working on gut health because they can help restore healthy gut flora. And they’re an excellent counterpart to probiotics—some may argue that a prebiotic-rich diet can often do more good than most probiotics. 

So far, we have determined that you should take probiotics with antibiotics. But if you want to go above and beyond, you should also take prebiotics. While there isn’t a lot of research on this topic, what little exists shows promising results. 

A 2005 placebo-controlled study found that oligofructose, a type of inulin, was effective when combined with antibiotics to treat C. difficile infection. In this study, the rate of diarrhea relapse after antibiotic treatment occurred in only 8.4% of those in the prebiotic + antibiotic group versus 34.3% of those in the placebo + antibiotic group. 

Taking a prebiotic also significantly increased levels of Bifidobacterium, an important genus of bacteria associated with numerous health benefits (13). 

Because prebiotics nourish your beneficial gut flora, including them in your post-antibiotic diet can be a great way to help restore your gut ecosystem. 

Prebiotic-rich foods include asparagus, Jerusalem artichokes, chicory, dandelion, leeks, garlic, onions, green bananas, and beans.