
Think back to a time when you were sick. You went to the doctor, and he prescribed you a medication – some sort of antibiotic that could get you up and running in a couple of days. Did you every ask yourself: do antibiotics weaken your immune system? As you were swallowing that medication, did you ever wonder how it could target just the bad bacteria? How it would know to destroy only the bad guys while leaving the good ones alone? Well, antibiotics aren’t that smart. Don’t get me wrong, antibiotics have made a huge contribution to medicine, but overuse can lead to more harm than good for your immune system.
How Antibiotics Work
First off, antibiotics work against bacteria, not viruses. Both bacteria and viruses are pathogens that can make us sick; however, their components are vastly different. Viruses basically just hijack our body’s cells to replicate and survive while bacteria have their own organelles and are more self-sufficient. This is why we can make drugs to target bacteria.
The main goal of antibiotics is to inhibit bacteria from surviving inside humans. How this is done varies among antibiotic classes. For instance, the penicillin group of antibiotics that many of us are familiar with, work to inhibit the formation of peptidoglycan – the main ingredient for creating a bacterial cell wall (something that human cells do not have).1 Other antibiotics block bacterial protein formation or DNA synthesis – all things that bacteria need for survival.
All of this sounds great so far. Antibiotics inhibit the survival of bacteria in our bodies, and then a day or two after starting the medication – Bam! We feel better. Why then do people question the use of antibiotics?
The Gut and Immunity

Did you know one of the most important contributors to the development of our immune systems is in the gut? The gastrointestinal (GI) tract houses microbiota – a collection of diverse ‘good’ bacteria that support the immune system. These little guys comprise approximately ten times more cells than human cells in our bodies.2 With this information some would say we are more bacteria than human.
The plentiful microbiota has quite the job to do. It makes essential vitamins, creates a mucous layer to protect our GI tract, and most importantly, helps develop the immune system and secretes antimicrobial substances.2 In other words, gut microbiota is largely responsible for keeping us healthy. When microbiota is not thriving or bountiful, a condition called dysbiosis occurs.2 This is when disease processes make their ugly appearances. No two microbiotas are the same, and many different factors contribute to a happy functioning microbiota including genetics, environment, and diet.
What You Aren’t Told About Antibiotics
You know the small print warning labels that we all ‘acknowledge’ but don’t really read? Yeah, that’s where antibiotic use and immune suppression come into play. It turns out, antibiotics do weaken your immune system.
Antibiotics negatively impact microbiota in the gut. These medications are prescribed to treat bacterial infections and kill the ‘bad’ bacteria in our bodies; however, antibiotics aren’t specific enough and end up killing some of the ‘good’ bacteria at the same time. One study showed that a seven-day course of the antibiotic clindamycin resulted in decreased diversity of microbiota for 2 years following administration. Other antibiotics have shown similar adverse effects with metronidazole even thinning out the protective mucous layer in the GI tract, leading to inflammation.4 These studies illustrate the harmful impact antibodies can have on our microbiota which ultimately end up dampening our immune system.
We said the microbiota are responsible for making a robust immune system, and when that microbiota is diminished, so is our immunity. The immune system gets compromised by a decline in lymphocytes (white blood cells) and innate antibodies. This makes the body more susceptible to subsequent pathogens and may not have the necessary defenses to combat them.
In addition to a weakened immune system, possibly more unsettling is the fact that some bacteria have become resistant to antibiotics. We’re talking about the ‘bad’ bacteria here that in response to overuse of antibiotics, adapt and change their genetics so the antibiotic is no longer able to destroy it. This leaves us with superbugs – pathogens that are resistant to antibiotics. And when our antibiotics are inadequate, there is often not much else that can be done for a patient other than supportive care and hope that they recover on their own.
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There’s Still Hope for your Immune System
Now that I have painted a dire landscape surrounding antibiotics, immune suppression, and superbugs, I want to reassure you that just because you have been exposed to antibiotics (as almost all of us have), there are ways to bolster your microbiota and thereby immunity. Remember when I mentioned that everyone’s microbiota is different, and its diversity and strength are determined by a number of factors? Well, diet is one of those factors that is easily modifiable. When I say diet, I am not talking about restricting calories to fit into a summer bikini, but rather, the food on your plate. A diet rich in plants confers great benefits to the GI microbiota.
Plants are full of fiber and pro- and pre-biotics that nourish your gut bacteria. A study showed individuals who ate a wide variety of plants every week (>30 types) had greater microbiota diversity than those who consumed <10 types each week.6 The fiber in plants is fermented by the microbiota and used as food.
Prebiotics and probiotics are also beneficial to the ‘good’ bacteria. Prebiotics are actually a special type of fiber; therefore, they also feed the microbiota. Probiotics, on the other hand, are live bacteria that can be consumed and add to the diversity and strength of the microbiota. Fermented foods are common sources of probiotics – yogurt, kimchi, and kombucha are all packed with ‘good’ bacteria.
Final Thoughts on Antibiotics and Immunity

Antibiotics are beneficial to fight severe infections. Long-term use or overuse of antibiotics, however, is detrimental to the flourishing microbiota in your gut. When the microbiota is diminished, the immune system gets injured and cannot perform to its full potential. No one wants a sidelined immune system because that makes it easier for pathogens to sneak in and do their damage. Antibiotics are not always avoidable, so it is imperative to take steps to create a diverse microbiota that can keep immunity strong. This can be done by feeding the ‘good’ bacteria in your gut with a variety of plants every week.
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