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Updated: Mar 1, 2023

Are antibiotics bad for you? As we enter yet another cold and flu season — and yet another Covid winter, with hand sanitizer once again ubiquitous — it’s time to return once more to this perennial question (as well as another, even more basic, question: what are antibiotics, exactly?). That’s why we created this comprehensive guide to all things antibiotics (including links to three short & super informative videos we made!). Read on to learn how antibiotics work, the harmful effects of antibiotics, how to prevent antibiotic resistance, and more.

What Are Antibiotics, and Are They Bad for You? Unfortunately, antibiotics are an increasingly common part of many people’s everyday lives. It’s too easy to ask for a prescription when you feel a sniffle coming on, instead of waiting to see if you can kick it on your own or undergoing a test to see if you really need the drug. After all, who doesn’t want a simple, get-better-quick solution (or at least the promise of one)? But most of us have never taken the time to ask, “What are antibiotics?” or given all that much thought to how they impact your health. As it turns out, these are very important questions to address. So, in the simplest terms possible, here’s the deal: antibiotics are chemical substances that can inhibit or destroy (that’s where the “anti” comes from) the growth of microorganisms (that’s where the “biotic” comes from. Biotic literally means “living things.”). They are produced either naturally by soil bacteria and fungi, or synthetically in a lab. Once antibiotics enter your system, they travel throughout the body killing bacteria. The thing is though, they don’t have the ability to differentiate between the bad, disease-causing bacteria and the good, nourishing bacteria, so while they were created with the idea of killing harmful microorganisms, it ends up being a massacre for all the bugs they encounter, good or bad. This is where the harmful effects of antibiotics come in. In many cases, antibiotics end up destroying the beneficial bacteria in your gut, organs, and tissues. This, in turn, affects your microbiome, the network of microbial species that have an outsize impact on both your physical and mental health. This effect is so profound that just one weeklong course of antibiotics can change your microbiome for up to a full year after you stop taking the medication! Want a visual? Check out our video, “What are antibiotics?” The Importance of Good Bacteria and Probiotics In a healthy, balanced microbiome, there’s a balance of about 85% good bacteria and 15% bad bacteria. One of the harmful effects of antibiotics is that when you take them, you upset this balance and knock down the amount of good bacteria. And when your good bacteria drops, it can lead to a whole host of health issues, such as:

  • increased inflammation

  • decreased cancer resistance

  • stress in the gut

  • weakened immune defenses

So what can you do to avoid upsetting this balance if you get sick? First, make sure that your doctor runs a test to confirm that the infection is bacterial and not viral. If it’s a virus (like Covid-19), an antibiotic won’t help anyway. If you have confirmation that your infection is bacterial — and have also confirmed there aren’t other less aggressive alternatives you could pursue to resolve it — make sure that you don’t leave until your doctor recommends a good probiotic for you, based on your medical history. This can be anything from fermented foods — such as sauerkraut, yogurt, or apple cider vinegar — to probiotic or prebiotic pills.

Probiotics are good bacteria that help keep your digestive system healthy, while prebiotics are food for probiotics, and both are key to maintaining a healthy microbiome. If you’re getting chronic bacterial infections (colds, flu, bronchitis, sinusitis, UTIs), there’s a good chance your bad bacteria are ruling the roost in your gut and your good bacteria have been taken prisoner. Send in reinforcements (aka probiotics) to take back control of your health! For a full list of prebiotic and probiotic foods and supplements, as well as other ways to support your gut health, download our free gut health guide.

The Harmful Effects of Antibiotics (and Where They’re Hiding)

One of the most concerning ways that antibiotics are being used began around 60 years ago, when scientists figured out that putting antibiotics in the feed or water of healthy cattle, hogs, and poultry helped them gain weight faster. This is because low doses of antibiotics alter the way animals break down food in their gut, enabling fat build-up. Today, 40% of all global antibiotics are used for this— even in fish farms.

Our first reaction to discovering this was: Good thing we aren’t getting antibiotics in our food or water! Oh wait, it turns out we are. Humans consume antibiotics not only through the meat we eat, but also via the water we drink. See, when you eat meat from an animal or fish that’s been fed antibiotics, your body absorbs that antibiotic. This has a few pretty bad consequences. First, studies suggest that this leads to the development of antibiotic-resistant bacteria in humans (and these so-called superbugs are such a problem that in 2015, the Obama administration issued a federal action plan to combat antibiotic-resistant bacteria). Second, there’s the concern that our ability to fight off disease could be diminished by overuse of antibiotics in farm animals. And third, exposure to antibiotics from food may alter the balance of your gut (see above!). This last one means that weight gain is among the many harmful effects of antibiotics: research has shown that obese people’s gut bacteria mix is different than that of lean people.

And if you’re thinking you’re okay because you only eat organic meat (or don’t eat meat at all) — there’s more. It’s estimated that 75% of antibiotics delivered to an animal aren’t even used. Instead, the drugs exit via feces or urine. This contaminated manure eventually ends up in groundwater and surface water via runoff. Given that more than 50% of the world’s population relies on groundwater for drinking water, this is a major concern. It’s also interesting to note that the widespread use of antibiotics in livestock— and their subsequent rapid weight gain — coincides with the human obesity epidemic of the last 20 years. Because gut health is so, so important to overall health, the harmful effects of antibiotics on your health are pretty widespread: A 2015 study showed an increase in cancer formation, inflammation, and oxidative stress as a result of people taking antibiotics. Long-term antibiotic use at any age has been linked to a host of antibiotic resistance issues later in life, such as overgrowth of Candida (yeast), which manifests itself as chronic pain, MS, depression, severe allergies, and cancer. A super recent study showed that antibiotic use is associated with colon cancer. It’s also worth noting that antibiotics can have the greatest negative effect when taken at a young age. That’s because they can change the development of kids’ “adult” microbiota by not allowing it to develop normally. Early frequent use of antibiotics has been linked to Crohn’s disease, diabetes, and obesity. Want a visual? Check out our video guide to the harmful effects of antibiotics.

How to Prevent Antibiotic Resistance

Antibiotic resistance, which we mentioned briefly above, is a major global health problem. Each year, almost 3 million people in the U.S. are infected with antibiotic-resistant bacteria and approximately 35,000 people die as a direct result, according to the Centers for Disease Control and Prevention (CDC). That’s pretty terrifying, and definitely qualifies as a public health crisis.

So how is antibiotic resistance created? How do superbugs relate to chronic disease? And what does it have to do with the meat you eat and your health? The U.S. leads the world in antibiotic consumption per capita. However, 30% of all antibiotics prescribed in our country are unnecessary. Even scarier — more than 70% of the bacteria that cause hospital infections are resistant to antibiotics. Antibiotic resistance occurs when a bacteria changes in some way that either protects it from the action of the drug or neutralizes the drug. Any bacteria that survive an antibiotic treatment (by changing itself) can then multiply and pass on its properties, making more bacteria that are immune to modern antibiotic medicines.

So why is this happening? In short, overuse of antibiotics. When you take an antibiotic that your body doesn’t need, the drug will still attack good bacteria. The good bacteria can then become antibiotic-resistant and spread that property to other, more harmful bacteria. Plus, antibiotic-resistant bacterial biofilms (thin slimy films of bacteria) are responsible for several chronic diseases that are difficult to treat, like cystic fibrosis. They can even coat the surfaces of implanted medical devices such as catheters or prosthetic cardiac valves. Biofilms have been connected to between 65% – 80% of bacterial infections in the U.S. In 2017, the WHO warned that a dozen antibiotic-resistant superbugs pose a threat equivalent to terrorism. Want a visual explanation? Check out our video guide to how to prevent antibiotic resistance.

How to Avoid Unnecessary Antibiotics

If you’re now wondering how to prevent antibiotic resistance, the simplest answer is by avoiding unnecessary antibiotics — and that doesn’t just mean prescriptions. Over 30 million pounds of antibiotics are sold for use in food animals — that’s 80% of the antibiotics sold in the United States. Globally, it’s estimated that antibiotic use will increase by 67% by 2030. Consuming these animal products promotes the spread of superbugs, which enter our homes via uncooked meat and poultry. If contamination occurs, you could be affected with a life-threatening antibiotic-resistant illness. Sure makes the meat aisle of the grocery store a little more ominous, no? It’s unknown how often people get sick from this, but we do know that there are 48 million cases of foodborne illness in the U.S. each year. To make sure you’re not one of those cases:

  • Avoid consuming meat, poultry, and other food products raised with antibiotics and instead buy those that are certified organic.

  • If you feel an infection coming on, don’t go for an antibiotic first. Allow your body the chance to fight it off. Only about 2-6% of common colds become bacterial sinus infections that could benefit from antibiotics — the other 94-98% of sinus infections are caused by viruses that can’t be treated with antibiotics.

  • Avoid antibacterial soaps and hand sanitizer and instead use plain soap and water for effective hand-washing. In the same vein, skip antibacterial wipes for surface cleaning, and instead use non-antibacterial cleaners. For a full list of vetted personal care and home cleaning products that don’t contain antibiotics, check out our Non-Toxic Product Database.

The WellBe Takeaway: Are Antibiotics Bad for You?

So, are antibiotics bad for you? As we explained above, the answer is complicated, but the potential harmful effects of antibiotics mean it’s important to understand. Here’s a quick summary of the important things to remember about antibiotics and your health:

  • First, it’s important to know, what are antibiotics? Antibiotics can be natural, but are generally synthetic chemical substances that inhibit the growth of harmful microorganisms. However, they also kill beneficial microorganisms, which can have far-ranging impacts on your health.

  • Taking too many or unnecessary antibiotics can lead to tons of issues, including obesity, weakened immune system, many chronic illnesses, and antibiotic resistance.

  • If you are prescribed an antibiotic, you can offset some of the negative effects on your gut health by taking prebiotics or probiotics (either in food or supplement form).

  • Overprescription of antibiotics has led to antibiotic-resistant bacteria, aka superbugs, that pose a major threat to our health. The best way to prevent antibiotic resistance is to avoid unnecessary antibiotics.

  • Even if you’re not taking any antibiotics, you could still be consuming them, as they’re fed to many animals destined for human consumption. That means antibiotics end up in meat, poultry, and fish, as well as soil and groundwater.

  • Reduce your risk of feeling the harmful effects of antibiotics by avoiding unnecessary antibiotics, not using antibacterial soaps or cleaning products, eating certified organic, and consuming prebiotics and probiotics.


  1. Balaban, N.Q., Helaine, S., Lewis, K. et al. Definitions and guidelines for research on antibiotic persistence. Nat Rev Microbiol 17, 441–448 (2019).

  2. Zaura, E. et al. Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces. mBio, Volume 6 • Number 6 • 31 December 2015

  3. Jamal M, et al. Bacterial biofilm and associated infections. J Chin Med Assoc. 2018 Jan;81(1):7-11.

  4. Langdon, Amy et al. “The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation.” Genome medicine vol. 8,1 39. 13 Apr. 2016.

  5. Miranda, Claudio D et al. “Current Status of the Use of Antibiotics and the Antimicrobial Resistance in the Chilean Salmon Farms.” Frontiers in microbiology vol. 9 1284. 18 Jun. 2018.

  6. Riley LW, Raphael E, Faerstein E. Obesity in the United States – dysbiosis from exposure to low-dose antibiotics? Front Public Health. 2013 Dec 19;1:69.


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