The Complex Relationship Between Antibiotics and the Gut Microbiome


Antibiotics are a powerful tool used to treat a wide variety of bacterial infections 1–6. Hailed as one of the most important medical discoveries of the 20th century, antibiotics are one of the most widely used drugs in the world 1,2,7–9. However, it's becoming increasingly clear that antibiotics can have unintended consequences, particularly in the gut microbiome 3,5,7,8,10–19. The gut microbiome, and the microbes that live there, are crucial for human health, influencing everything from digestion to immune and brain function 9,15,20–31. Microorganisms in the gut are essential for normal digestion and essential functions throughout our bodies, and antibiotics can disrupt this balance by killing both beneficial and harmful bacteria 3,5,7–10,14,15,21,22,27,32–36. In this blog, we'll explore the effects of antibiotics on the gut microbiome, including how the gut can recover from antibiotic use and the risks of repeated exposure to antibiotics.

The Effects of Antibiotics on the Gut Microbiome:

While antibiotics are incredibly effective at killing off bacterial infections, they don't discriminate between harmful and beneficial bacteria. This means that when you take antibiotics, you also kill off some of the "good" bacteria that comprise the gut microbiome, significantly impacting its microbial composition 1,6,7,9,12,14,19,32,34–38. This can result in an imbalance of the gut microbiome, known as dysbiosis, which can negatively affect human health 3,6–8,11,15,21,23,25,26,28,30,31,31,34,39,40.

Generally, antibiotics have been shown to reduce the diversity of the gut microbiome, leading to an overgrowth of certain bacteria and/or a decrease in other bacteria 1,3,5,6,8–10,14,19,34–36,41 21,33. Research also shows that antibiotic-based changes in the gut microbiome may have long-term consequences, with early-life antibiotic use associated with an increased risk of asthma, obesity and Crohn’s disease 6,7,9,36–38,40,42–51. 

Recovery of the Gut Microbiome After Antibiotic Use:

While the gut microbiome is resilient and can recover from antibiotic use, it is not always the same as before. Generally, the gut microbiome should return to its pre-antibiotic state within a few weeks, but this isn’t always the case 5,7,9–13,15,16,19,34,35,42,50,52. In some cases, the gut microbiome may not return to its original diversity, resulting in a permanently altered microbiome 5,6,10,12,13,15,34–36,53. This can lead to long-term issues such as an increased risk of infections, digestive problems and the development of diseases (such as asthma, inflammatory bowel disease, colorectal adenoma, obesity, and C.difficile infections) 7–9,21,23–26,28,31,36,44.

The Risks of Repeated Exposure to Antibiotics:

While the gut microbiome can recover from antibiotic use, repeated exposure to antibiotics can increase the likelihood of negative effects on the gut microbiome 6,7,15,35,36,42,50,53. This is because each round of antibiotics can further disrupt the delicate balance of the gut microbiome, making it harder for it to recover fully 6,15,17,35. In some cases, the gut microbiome may take months or even years to recover fully, and in rare cases, it may never fully recover 12,17,35,36,53,54.

Where does Fecal Microbiota Transplantation fit in?

One promising approach to restoring the gut microbiome after antibiotic use is fecal microbiota transplantation (FMT) 15,50,55,56. FMT involves transferring fecal material from a healthy donor to a recipient to restore the gut microbiome balance 21,26,31,57.

FMT has been shown to be highly effective at treating C. diff, with success rates of up to 90% 50,55,58,58–63,63,64. This is important as studies have shown that antibiotics can increase the risk of developing antibiotic-associated diarrhea, a condition caused by the overgrowth of harmful bacteria like Clostridium difficile 1,3,4,7–9,14–16,19,41,50,65,66.


Antibiotics are an incredibly useful tool for treating bacterial infections, but they can have unintended consequences for the gut microbiome 1–3,3–5,5–8,10–19. While the gut microbiome can recover from a single course of antibiotics, repeated exposure to antibiotics can make it more difficult for the gut microbiome to recover fully, leading to a range of health problems 6,7,15,17,35,36,42,50,53.  It is important to weigh the benefits and risks of antibiotic use carefully and consider alternative treatments or ways to support gut health after taking antibiotics.


At Novel Biome, we're passionate about the importance of the gut microbiome and the transformative potential of Fecal Microbiota Transplantation (FMT) treatment to restore health. As an FMT contract manufacturer, we leverage our years of experience in FMT to manufacture high-quality FMT products utilizing our highly-screened donors and stringent manufacturing standards. If you are interested in learning more about our FMT products and manufacturing capabilities, please contact us HERE or to register as a clinical partner to order FMT products, click HERE.

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