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How The Overuse of Antibiotics Can Compromise Overall Health

Updated: Mar 8, 2023

There is most likely a time throughout your life that you’ve taken an antibiotic prescribed by your physician for one reason or another. In fact, healthcare providers prescribe nearly 270 million antibiotics to patients every single year! This makes them the most commonly prescribed medication in the United States.


While antibiotics are sometimes unavoidable, nearly 50% are prescribed inappropriately, are unnecessary (doing more harm than good), and are contributing to widespread antibiotic resistance and an epidemic of insufficient gut bacteria health.


Antibiotics should ONLY be taken if absolutely necessary and restoring your gut health afterwards is critical to maintain and achieve optimal health and wellness.


Fortunately, by understanding how antibiotics work and their effects on our body, we can take steps to use them responsibly while also making sure to protect and nourish our delicate digestive tract and our essential probiotic friends who reside there.


How Do Antibiotics Work?


Just as their name implies, antibiotics are “against life,” or more specifically, against bacterial life. Antibiotics work by either preventing bacterial cells from multiplying (so our immune system can finish the job) or by killing the offending bacteria completely. To accomplish this, antibiotics interfere with important bacterial processes.


Antibiotics cannot tell the difference between good bacteria and bad bacteria. Their job is to simply go to your gut and kill bacteria. When antibiotics enter your system and kill off bacteria seemingly at random, your balance of good and bad bacteria can be thrown out of whack.


Antibiotics can be narrow spectrum, meaning they only work against a select few bacterial families, or broad-spectrum, which are effective against a wide range of bacteria. Unfortunately, the overuse of antibiotics (especially broad-spectrum types) has led to something called antibiotic resistance.


There will always be some bacteria in every population that are naturally resistant to antibiotics. So, when you take antibiotics, they indiscriminately wipe out all of the susceptible bad and good bacteria in your system. Without other bacteria to take up space, the resistant bacteria have free run of your body, where they can multiply and pass their resistance on to other bacteria that make your body their home.


The problem is that it’s a vicious cycle, every time we use antibiotics, resistant bacteria have the opportunity to grow and thrive, leading to even more resistance and possible “super bugs” that don’t respond to antibiotics at all.


The good news is that we can mitigate antibiotic resistance and the effects of antibiotics on our health by being mindful and taking great care of our microbiome.


What is the Microbiome:


Your gut microbiome is its own ecosystem, a biological community of interacting organisms that live in harmony with one another. It’s home to 100 trillion microorganisms, including at least 400-500 different species of bacteria. These microbes in your gut play crucial roles in digestion, immunity, metabolism, and mood. Each and every microscopic being in the gut plays an invaluable role in a variety of physiological processes. In their absence, the system just doesn’t run as smoothly.


Here are some of the most crucial tasks performed by gut bacteria:

  • Digesting food

  • Maintaining bacterial balance

  • Creating energy

  • Protecting skin health

  • Regulating mood (80% of serotonin is made in the gut and 50% of dopamine)

  • Repairing gut lining (crucial in protecting against ‘leaky gut’)

  • Assisting the immune system

  • Absorbing nutrients

  • Maintaining healthy weight and blood sugar

Humans have evolved to live with microbes for millions of years. During this time, microbes have learned to play very important roles in the human body. In fact, without the gut microbiome, it would be very difficult to survive. The gut microbiome begins to affect your body from the moment you’re born.


You’re first exposed to microbes when you pass through your mother’s birth canal. However, new evidence suggests that babies may come in contact with some microbes while still inside the womb.


As you grow, your gut microbiome begins to diversify, meaning it starts to contain many different types of microbial species. This happens through breastfeeding, our environment (when your little one begins touching everything and anything - and right into the mouth it goes) and our foods.


In fact, the higher your microbiome DIVERSITY is,

the better your overall health will be.


Ideally, all these microbes live in a balanced state. However, when the balance is thrown off, and the ‘bad’ or opportunistic bacteria begins to take over, it can keep all of your systems from working optimally.


Too few or too many microorganisms can cause an array of issues in your gut such as leaky gut, SIBO, or Candida overgrowth, which are precursors to autoimmune disease among other troubling issues and uncomfortable symptoms.


1) While a small amount of yeast/candida is normal and necessary, it is opportunistic. If given the chance, such as antibiotic usage killing off protective good bacteria, it will grow and multiply quickly — especially when it’s fed sugar, carbohydrates, or alcohol. When yeast starts to multiply, it can damage the lining of your intestinal wall. This then leads to increased intestinal permeability or what’s known as leaky gut.


2) Another symptom of an unbalanced gut is small intestinal bacterial overgrowth, or SIBO. When your gut flora is out of balance, the bacteria normally found in the large intestine and colon overgrow and colonize in your small intestine. This can lead to symptoms ranging from digestive imbalance to chronic illness and autoimmune conditions. This is why it is important to restore your gut health after you take antibiotics.


It’s important to remember that 80% of your immune system is located in your gut, along with 80-90% of the neurotransmitters that help regulate your mood.


Even just ONE cycle of antibiotics can throw off

the microbiome balance in your gut for a whole year.


Why Diversity is Important:


Every bacterial species has a purpose in our internal ecosystem. Even Escherichia coli (E.coli), the bacteria strain known for foodborne illnesses, helps your body produce Vitamin K and Vitamin B12. However, E. coli is an opportunistic bacterial strain. If it sees a chance, such as an empty gut post-antibiotics, it will rapidly start to overtake the gut microbiome.


So, as you see, our body relies on other gut bacteria to keep these overgrowths from happening. As bacteria levels for certain species taper off, different bacteria strains will step up to fill the void. In a healthy, diverse gut microbiome, the resident microbes help protect against invasion by pathogens that could cause infection or disease. They work together, using different methods to inhibit pathogens, such as:

  • producing antimicrobial compounds that fight bad bacteria off.

  • crowding pathogens out and preventing them from ‘setting up shop’ in the gut.

  • maintaining the mucus layer that lines the intestines so pathogens can’t reach intestinal cells.

  • training the immune system to respond to pathogens.

The gut microbiome must already compete with poor dietary choices, environmental toxins, and viral attacks. Over time, these health hurdles could deplete numbers of beneficial bacteria. For those who already have a compromised gut microbiome, a round of unneeded antibiotics can create an environment conducive to opportunistic overgrowth, and all the negative consequences that delivers.


How The Overuse of Antibiotics Can Compromise Gut Health


Yes, taking antibiotics can save a person’s life in certain situations. Unfortunately, the aftermath of prescription antibiotics can leave the gut microbiome void of probiotic bacteria.


This unwanted side effect can have lasting implications after your antibiotic treatment. Here are some ways that a lack of bacterial diversity post-antibiotics might cause issues for your overall health.


1. Degrades Gut Lining


Probiotic bacteria help us digest dietary fibers that our bodies can’t break down. These fibers are known as prebiotics. Prebiotics are found in a wide variety of plants, including chicory, onions, and artichokes.


Since probiotics are living beings, they must expel waste. Their waste comes in the form of metabolites. The most common metabolites produced by our stomach bacteria are short-chain fatty acids or SCFAs. A healthy gut lining or barrier heavily relies on short-chain fatty acids, especially butyrate and acetate.


2. Impacts Immune System


The gut barrier has microscopic holes. These allow nutrients from our food to permeate from the small intestine to our bloodstream. Unfortunately, these holes can become larger or more permeable due to chronic inflammation caused by a lifetime of factors, including poor diet choices and long-term use of medications.


Therefore, your immune system must always be on hand to stop these pathogens at the gate. Our immune system cells and probiotic bacteria remain in constant contact. In fact, they can influence each other’s functions. If your gut microbiome doesn’t have probiotic bacteria, your immune system cells must fight off pathogens from your intestine alone. Without proper support, your body can become more susceptible to illness and infection.


3. Antibiotic Resistance


The overuse of antibiotics doesn’t just impact the person prescribed. It can cause an antibiotic resistance that can impact humanity as a whole. Bacteria can adapt for survival. Over time, pathogenic stomach bacteria can learn how to overcome antibiotic prescriptions.


These concerns are even more valid when we consider the overuse of antibiotics in the food industry. Farmers use antibiotics to stop the spread of bacteria to other animals and stimulate growth. Those antibiotics stay in the muscle, fat and other tissue of the animal and are passed along to you when you eat them.


The only way to ensure the food you eat is free of genetically modified organisms (GMOs) and antibiotics, is to buy certified organic meats, fruits, and vegetables. I understand that it can be expensive to buy all organic food. At the very least, you should buy pasture-raised, organic meats.


Antibiotics are also prevalent in our water supply. Humans have gotten in the habit of flushing pills down the toilet. Research shows that antibiotics are one of the many medications found in 80% of water samples in 30 states.


Here’s the Issue:


Research shows that just one course of antibiotics can negatively impact your gut microbiome for up to an entire year. Just imagine what happens with continued antibiotic use beyond one course, and the depletion of more and more beneficial bacteria! After several cycles, you may even find that your health (beyond just your digestion) is impacted on multiple fronts.


Antibiotics and Autoimmunity


Since antibiotics wipe out anything in your gut microbiome on their quest to kill bacteria, this causes an imbalance in gut flora called dysbiosis. As the dysbiosis gets more out of control it can suppress your immune system – remember 80% of your immune system is in the gut – which then can lead to being susceptible to other infections that may require more antibiotics and the cycle just keeps going.


Over time, having this dysbiosis in your gut microbiome will eventually lead to a leaky gut. If your gut is leaky, food particles, toxins, and infections can get through your intestinal lining and into your bloodstream where your immune system detects them as foreign invaders and goes on high alert, attacking them and creating inflammation. Your body never ‘attacks itself’ – there is always a reason or ‘an invader’.


The Amount of Damage Depends on Many Different Factors:


1. The length and number of courses


Multiple courses of antibiotics appear to be the most damaging, and higher doses of antibiotics taken over a longer period of time have the biggest impact. Keep this in mind if you’ve been taking antibiotics for months on end in an attempt to treat acne – there are healthier ways.


2. The type of antibiotic


If you go to your doctor with an infection, you’re very likely to come away with a broad-spectrum antibiotic. That’s because unless your doctor takes a sample and sends it to a lab to be cultured, they don’t know what type of bacteria is causing your infection. Prescribing a broad-spectrum antibiotic makes it more likely to work on your infection, but your gut bacteria will take a harder hit.


3. At what stage of your life you take them


Our first years seem to be crucial for setting up a healthy microbiome FOR LIFE. Studies have found an association between antibiotics given in the first year of life and later neurocognitive difficulties, such as ADHD, depression and anxiety, and others have found that the more courses of antibiotics a person receives during childhood, the higher their risk of juvenile rheumatoid arthritis, inflammatory bowel disease and even diabetes.


Others have linked antibiotic exposure in the womb and early childhood (and the subsequent altered gut microbial composition) to the development of asthma and allergies later in life and obesity in children as well adults.


In this post we discussed the effects of antibiotics on our important microbiome and overall health. What’s important for you to know, is that all of this is in YOUR control! Read on to learn how you can restore your gut health during and after antibiotic use as well as what you can do to avoid them completely.



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