Antibiotics: Can They Really Mess Up Your Gut?

5 min read

This is one of the questions we get day in and day out, especially during our Reddit Ask Me Anything forums, so let’s settle this for everyone: what do antibiotics do to the gut microbiome? Before we get into the details of the current research on the field, let’s talk about all that goes into developing the human gut microbiome. No two people’s microbiomes are identical because of the array of factors that contribute to their makeup. It all starts in the womb: the interaction between the fetus and the outside world goes through the mother, whose diet and external environment can affect the development of the baby’s microbiome. From here, delivery method, feeding method, antibiotic usage, nutrient intake, and the environment after birth all contribute to the development of the microbiome. The first few weeks of a newborn’s life are incredibly consequential, and after infancy, an individual’s microbiome is basically set for life. (1,2)


But we’re getting ahead of ourselves. You’re most likely familiar with the term antibiotics and have a basic idea of what they do; probably because you’ve had to take one yourself. In 2014 in the US alone, the CDC reported that over 266 million antibiotic prescriptions were fulfilled in pharmacies (3). With so many people being prescribed antibiotics, and up to a third of antibiotic prescriptions estimated to be unnecessary altogether, there’s a host of consequences to look out for. The list of problems related to antibiotic use and misuse is long, including global issues such as antimicrobial resistance and negative environmental impact, but one effect that has garnered a lot of attention in the intestinal health community is how antibiotics affect the gut microbiome.


You may be wondering how this could actually happen. Antibiotics are infection fighters; they’re meant to indiscriminately fight bacteria, no matter if they’re beneficial or harmful to the gut and the human being who hosts these microorganisms. This can be problematic because intestinal health issues are largely tied to dysfunction of the gut microbiome due to imbalances in the microbe populations present (in terms of diversity microbes, types of microbes present, and relative amounts of these species). (4)

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With these impacts on gut health, antibiotics can trigger diarrhea and other gastrointestinal symptoms. In some cases, such as using antibiotics for a severe infection such as C. difficile infection, gut bacteria can actually become resistant to the drugs, instigating antibiotic-resistant recurrent C. difficile infection (5). There’s a lot to consider for a resistant intestinal infection, antibiotic resistance is a global health issue that demands attention in its own right, as the dangers of it go far beyond gut health.


Although antibiotics are often overprescribed by clinicians, contributing to the problem of antibiotic resistance, sometimes antibiotic use is necessary and unavoidable. You don’t have to be afraid to take a prescription, but make sure you’ve asked your pharmacist about how to take the antibiotics safely and why they’re important for your health at that time. While not everyone will feel the impacts of a course of antibiotics on their gut, it’s a common enough occurrence that people tend to ask what might happen to their microbiome, and what they can do to restore it.

So while adverse reactions are not a characteristic of antibiotic use in most cases, the immediate and long-term changes to microbiome health have been established. Research out there goes beyond just discussing the risks of resistance and changes in diversity of microbes and composition. Since antibiotics can affect all types of bacteria, including those that produce vitamins, aid in metabolism, and control proper immune response, all these features can be affected. So becoming deficient in some vitamins such as B12 and K2, having issues with digestion, and triggering inappropriate/unnecessary immune responses can all occur due to antibiotic use (6). On the disease level, research has linked taking antibiotics to the development of a whole host of issues that are currently on the rise in many parts of the world, such as obesity, weight gain, gastrointestinal infections, inflammatory bowel disease, and colorectal cancer, not to mention the risk of promoting antibiotic resistance (7). Being exposed to antibiotics early in life is common, but getting these treatments during childhood doesn’t exempt you from these potential impacts later in life. In fact, infants who received antibiotics between the ages of 6 and 12 months have shown significant delays in the development of their microbiota by the age of two (8). Since we know that early childhood is pivotal to one’s microbial profile for their entire lives, this delay in their development and associated changes in bacterial diversity is a significant issue.


Importantly, taking antibiotics at such a young age triggers imbalance in the microbiome that may lead to the development of inflammatory bowel disease. Although the environment, genetics, and other factors may contribute to inflammatory bowel disease occurrence, the fact that studies have found a link to early antibiotic use and repeated exposure to these treatments during childhood really puts the role of the microbiome in this disease under a bigger spotlight.


So we get that the microbiome, especially during development, is susceptible to the effects of antibiotic exposure. But that doesn’t really help anyone who has already taken these treatments.

With all this in mind, how do you really restore your gut microbiota if you feel affected by antibiotic use? Long story short, the science is still evolving on this subject and there’s no magic bullet solution to solve your gastrointestinal woes. However, there are a number of things that are known to help healthy bacteria grow, thrive, and populate the gut. This can help your microbiome work more in harmony with the rest of your body, avoiding further adverse effects of antibiotic use. (9)


So while there’s lots of discussion going around about using probiotics, fecal microbiota transplants, phage therapy, and other interventions, there’s not enough research or accessibility of these options for us to confidently support them at this time. Thankfully, there are things that can actively be done to help your microbiome rebuild and thrive. Here’s some tips for healing your microbiome and self (10):

  • Try the Mediterranean diet. The variety of foods rich in fibers, vitamins, minerals, omega 3 fatty acids, and more nutrients feed your gut bacteria, helping them survive and produce byproducts needed for healthy digestion.

  • Incorporate fermented foods and beverages, such as sauerkraut and kefir, into your diet. Fermented products contain beneficial bacterial species that can help restore the gut microbiota.

  • Make sure to keep stress to a minimum, because this negatively affects the gut microbiome and mental health, which are linked as well.

  • Exercise and sleep are good for all aspects of your health, including your gut microbiome, so make sure you’re staying active and resting enough!

  • Reduce your sugar and artificial sweetener consumption, as these products can increase inflammation or lead to further imbalance in the gut microbiome.


If these solutions don’t satisfy you, we have another recommendation for you. Phyla has a microbiome test kit designed specifically to help you understand your intestinal balance and health. It’s on promotion for a limited time, so if you want to learn about your gut bacteria levels and what you can do to improve them, order yours today!


Download the Phyla app on iOS or Android!


Sources

1 https://www.nature.com/articles/s41586-019-1560-1

2 https://pubmed.ncbi.nlm.nih.gov/28492938/

3 https://www.cdc.gov/antibiotic-use/data/outpatient-prescribing/index.html

4 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4315779/

5 https://www.frontiersin.org/articles/10.3389/fcimb.2020.572912/full

6 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831151/

7 https://pubmed.ncbi.nlm.nih.gov/27028893/

8 https://pubmed.ncbi.nlm.nih.gov/27306664/

9 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831151/

10 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6121872/