It's no secret that antibiotics are an incredible and often life-saving innovation. These powerful, fast-acting drugs fight unfriendly bacteria that cause infections—but do they have a dark side? Current research suggests the answer is yes.
Since antibiotics kill both beneficial and harmful bacteria, they can cause significant damage to the gut microbiome, potentially leading to chronic illness. And overuse of antibiotics can create drug-resistant superbugs that have become a global health concern.
The good news is, we can support the microbiome during and after antibiotic use with tools like diet, lifestyle, and the right probiotics to offset their negative long-term effects. In this post, we’ll:
- Walk through the major changes antibiotics cause in your microbiome
- Demystify how long it takes to restore good bacteria after antibiotics
- Cover how to restore gut health after antibiotics.
Understanding the impact of antibiotic use and recovery
When we use antibiotics for infection, our gut microbiome goes through phases of change. First, antibiotics attack gut bacteria. This results in a gut microbiome that is imbalanced with bad bacteria, followed by a sometimes-long journey back to a balanced, healthy gut, aka baseline. Let's explore these phases in more depth.
Phase 1: Antibiotics attack gut bacteria
Antibiotics don't distinguish between good and bad microbes. That’s why when you take an antibiotic, the amount and different types of bacteria in your gut—that is, the richness and diversity of your gut microbiome—decrease significantly [1]–[4].
Some species may even disappear, either for a short or long period [1], [2].
The drop in richness and diversity depends on different factors. For example, broad-spectrum antibiotics (e.g. ciprofloxacin, cefadroxil) target a wide range of bacteria and have a big impact. Whereas narrow-spectrum antibiotics (e.g. metronidazole, erythromycin) target only a few types of bacteria.
Another important factor is the gut microbiome itself.
The gut microbiome varies considerably among people [5]. Some of us are more resilient to antibiotics than others. One study found that with a 5-day course of antibiotics, most people lost around 10 species, while a few lost around 24 [1].
Phase 2: Rise in unfriendly bacteria
When it comes to the gut microbiome, balance is key.
Almost everybody has a small amount of unfriendly bacteria in the gut. And that’s okay. Beneficial bacteria make sure that these not-so-welcome tenants don’t take up too much space.
The problem is, antibiotics cause a major drop in the levels of gut microbes, disrupting this healthy balance [1]–[3].
During this phase, one specific group of microbes known as drug-resistant bacteria take advantage of the decrease in protective bacteria to grow unchecked.
Studies have shown that after antibiotics, the number of drug-resistant bacteria and the amount of antibiotic resistance genes increase [1], [2], [4], [6]. This is why our Tiny Health Gut Test looks at these bacteria and calculates your antibiotic resistance signature.
Your antibiotic resistance signature can help us track the long-term side effects of antibiotics.
For some people, one of the unfriendly drug-resistant bacteria that may grow unchecked is Clostridioides difficile. If present in your gut, these bugs can cause antibiotic-associated diarrhea [7]–[9].
Phase 3: The journey back to baseline
Some weeks after an antibiotic course, beneficial bacteria repopulate your gut, putting unfriendly bugs in check [2].
But this can be a slow process.
And how long it takes for gut bacteria to recover after antibiotics varies from person to person.
For most people, the composition of the gut microbiome returns almost completely to baseline in one to two months. But for a few, things may not go back to the way they were for quite a long time. Which is when we may see the long-term side effects of antibiotic use.
One study found that six months after antibiotics, some individuals only recovered about 63% of the bacterial species they had before the antibiotic treatment [1]. In another study, friendly species such as Bifidobacterium, Coprococcus, and Eubacterium disappeared with antibiotic use. And continued to be undetected from all participants at 6 months post-treatment [2].
Scientists are still not entirely sure why each person responds to antibiotics differently. Some things to consider that may be important factors:
- The initial composition of the gut microbiome, which varies among individuals [5]
- An adult gut microbiome with low diversity to begin with
- A history of antibiotic use, from which the gut didn't fully recover
How to replenish good bacteria after antibiotics
It may feel overwhelming to restore good bacteria after antibiotics, but the best place to start is with diet.
Eating the right foods can promote gut diversity while boosting the growth of beneficial bacteria.
To restore gut health after antibiotics, try:
- Eating more foods high in fiber and/or polyphenols, such as fruits, vegetables, nuts, legumes, and whole grains.
- Adding more fermented foods to your diet. These include yogurt, kefir, sauerkraut, kombucha, and kimchi.
- Avoiding excess saturated fats, artificial sweeteners, and processed meats.
Can you take probiotics and antibiotics at the same time?
Yes. In fact, doing so during and after antibiotic treatment can help protect against infection caused by the overgrowth of drug-resistant bacteria like C. difficile [10]–[12]. It’s important to note that if you have suffered from a C. difficile infection in the past, you are at higher risk of a recurrent infection when taking a new course of antibiotics [13]. In such cases, we strongly recommend taking probiotics to support the restoration of the gut microbiome.
Another case in which we strongly recommend taking probiotics along with antibiotics is in babies who have gone through previous courses of antibiotics. Studies have shown that each new course of antibiotics adds to the risk of developing a chronic immune-mediated disease such as asthma and eczema [14]–[17].
Track your recovery after antibiotic use
In this article, we’ve covered the three phases of antibiotic impact to the gut microbiome and how to restore gut health after antibiotics. It may take some time for good bacteria to repopulate the gut, but the first step is trusting in your body's ability to heal. The second is taking action with a plan and expert guidance.
You can do this with Tiny Health gut microbiome tests, which:
- Give you the ability to detect antibiotic-resistant species
- Help you gauge responsiveness to antibiotics in the future
- Show whether you still need probiotic support
- Reveal any antibiotic signatures that are linked to an increased risk of developing eczema or allergies during pregnancy and a baby’s first year
Interested in taking control of your family’s microbiome health and reducing the likelihood of future illness? With Tiny Health’s tests for babies, children, and adults, we teach you about your microbiome and give you unbiased recommendations to put your family on the path to better lifelong health.