The Dark Side Of Antibiotics

January 8, 2019



It’s without question that the advantages of antibiotics are clear. Since their discovery in the 1940s they have saved countless lives from bacterial infection. Antibiotics have not only saved patient’s lives, they have played a pivotal role in achieving major advances in medicine and surgery. However their success came at a price.


In this article I will outline the negative effects that antibiotics have on our body, lives and even the environment around us. I will explain why proper post antibiotic management is so important and discuss when and why antibiotics are appropriate to take. 


As a Nutritional Medicine Practitioner, I have found that most of my clients have had 10+ antibiotic cycles in their lives and less than 5% of my clients have managed the course of antibiotics with appropriate aftercare. Therefore, with this article I hope to increase awareness of antibiotic use and provide some useful tips, which you can easily integrate into any post antibiotic treatment protocol.


Firstly, lets discuss what are antibiotics?


 “Antibiotics are a class of natural or chemical substances that kill or inhibit the growth of microorganisms”.


Most antibiotics are an extract from a natural substance, which either affect a select few species of bacteria or act in a broader spectrum affecting many different species of bacteria.


In the roughly 70 years since antibiotics became available on the market, we have produced millions of metric tons and employed them for a wide variety of purposes. Antibiotic use hasn’t just been limited to humans; veterinary animals and livestock are also regular recipients of this medication. 



Antibiotic resistance – antibiotic overuse, misuse & inappropriate prescribing


Since as early as the 1960s, only a few years after antibiotics became available, scientists found that bacteria had the extraordinary capacity to genetically mutate so they are resistant to antibiotics. Termed antibiotic resistance, this mutation means that an antibiotic has lost its ability to effectively control or kill bacterial growth. The resistant bacteria will continue to multiply/reproduce, even in the presence of therapeutic levels of an antibiotic. Because bacteria can collect multiple resistance traits over

time, they can become resistant to many different types of antibiotics. In some cases antibiotic resistance has lead to the rise of super bugs, which are no longer susceptible to any antibiotics. The rise of these super bugs is a severe risk to the human population.




So what causes antibiotic resistance?


There are 3 primary reasons why antibiotic resistance has become an issue: incomplete courses of antibiotics, the misuse and overuse.


When antibiotics are prescribed a dose is given for the duration of time that ‘should’ eradicate the intended bacteria completely. When the intended duration or treatment is not followed or ignored (primarily because the patient’s symptoms have improved) ruminants of the offending bacteria survive and learn how to resist the antibiotic in the future. Therefore, always completing the antibiotic treatment for the full duration recommended, reduces the risk of creating antibiotic resistant strains of bacterium.



The overuse of antibiotics clearly drives the evolution of resistance. The more we use antibiotics the more chances the bacterium have of learning or mutating to be resistant.


The misuse of antibiotics is the biggest driver of antibiotic resistance. When an antibiotic is prescribed unnecessarily or inappropriately, the risk of creating bacterial resistant super bugs is at its highest. One of the most common forms of misuse is in the treatment of viral caused disease. Antibiotics treat bacterial infections but not viral infections. For example, an antibiotic is an appropriate treatment for strep throat, which is caused by the bacterium Streptococcus pyogenes. But it's not the right treatment for most sore throats, which are caused by viruses. Similarly; colds, Influenza, Bronchitis, coughs, ear infections, sinus infections and the stomach flu are commonly (not always) caused by viruses and cannot or should not be treated with antibiotics.


According to the Centers for Disease Control and Prevention, between one-third to one-half of antibiotic use in humans is unnecessary or inappropriate.


Antibiotics as stated previously, are being prescribed for conditions that aren’t even associated with bacterial infections. Often these simple conditions can easily be prevented or treated by dietary, lifestyle and supplements; essentially by having a strong healthy immune system.

Don’t get me wrong; I believe antibiotics are imperative if someone is suffering from a highly contagious bacterial infection such as strep throat, scarlet fever, meningitis, septic wound infection etc. 

Unfortunately, even when antibiotics become necessary they cause damage to our gut.



Our micro-biome, is an ecosystem! 


Our body is quite literally crawling with microorganisms. We have approximately 37 trillion cells in our body and we have approximately 38 trillion microorganisms living within or on us. These collectively are called the microbiome and they live in a mini ecosystem, just as complex as any jungle. Although the microbiome is made up of all sorts of microorganisms (bacteria, archaea, fungi, protozoa and viruses), it is primarily populated with bacteria which are located mostly in our gut.


So what’s the big deal? It turns out that we have a symbiotic relationship with our microbiome, which means they depend on us and we depend on them. These microbes play crucial roles in our digestion, immunity, metabolism and mental health. This was illustrated in a study where researchers created sterile mice (no microbiome) and then put these mice through a number of tests. They discovered that, not only is the microbiome necessary for digestion, it is also required for normal stress responses, the ability to interact with others and everyday brain function. Furthermore, they found that a balanced microbiome is linked to a healthy; immune system, nervous system, endocrine system, hepatic system, cardiovascular system and almost every other system we have in the body!

The gut’s microbiome has such a profound effect on our mood and mental state that is often nicknamed the second brain. Maintaining the proper balance of bacteria and other microorganisms in your gut is crucial, not just to your digestion, but to your overall health and wellbeing.



Antibiotic effect


When we take an antibiotic we are inevitably killing or harming a portion of our bacteria or microbiome. Unfortunately, antibiotics cannot differentiate between the “bad” bacteria that may be causing a bacterial infection and the “good” bacteria that belong in our gut. Instead, antibiotics destroy all bacteria of a similar strain.


A single dose of antibiotics can reduce the diversity of the gut’s microbiome by one third.


When antibiotics kill the bacteria that belong in your gut, it disrupts the delicate ecosystem, creating a state of dysbiosis. In this state foreign or opportunistic microbes (e.g. Helicobacter pylori) outgrow beneficial gut bacteria.  



From the beginning it was known that antibiotics could cause diarrhea, constipation, cramps, bloating and other digestive complaints. However the more far reaching negative effects and why this occurs has only been discovered in the last decade.


As such if you have or present with:

  • Frequent gas, bloating, belching

  • Loose stools, diarrhea or constipation

  • Acid reflux

  • Unexplained weight gain and/or difficult weight loss

  • Irritable bowel syndrome (IBS) or Irritable bowel disease (IBD)

  • Depression and/or frequent low mood

  • ADHD or similar condition.

  • Halitosis (bad breath)

  • Brain fog

  • Joint pain

  • Skin conditions (acne, eczema, psoriasis)

  • Low energy and chronic fatigue

  • Diagnosis of an autoimmune condition (such as Hashimoto’s thyroiditis or rheumatoid arthritis)

  • Allergies and food sensitivities

  • Yeast or fungal infections

You most likely have a disturbance in your micro biome, which is named dsybiosis.


As seen above, even small disruptions to the fragile ecosystem that is our microbiome can have disastrous effects on our health. Antibiotics are known to cause long-term and profound changes to our gut microbiota, which in turn leads to secondary changes in your immune, nervous and endocrine systems. 



What to do about it and selecting the right antibiotic


Although herbicides and pesticides, environmental toxins, poor diet and even stress can affect our microbiome, the biggest and simplest culprits are antibiotics.


Antibiotics may at times be necessary. However selecting the right antibiotic, completing the entire course and recolonizing the gut appropriately after treatment are required for ongoing health.


There are many different types of antibiotics on the market today. Therefore when prescribed an antibiotic please ask your doctor details about the side effect profile, whether this antibiotic is specific to the infection you have or a broad spectrum that kills a variety of species of bacteria. If you are in a position to postpone treatment until a laboratory culture has been completed and a more specific antibiotic can be prescribed, do so.

Broad-spectrum antibiotics generally contribute the strongest to antibiotic resistance and have a greater damaging effect on the micro biome.


Recolonizing the Gut after antibiotic treatment


The specific treatment following antibiotics can change depending on pre-existing conditions, the condition the antibiotic was treating, the type of antibiotic and the duration of time following the antibiotic treatment. Therefore I will not discuss specific probiotic supplementation and rather focus on the re-enforcing the environment in the gut that promotes healthy microbiome growth.


Avoiding Conventionally grown foods


Inorganic vegetables contain pesticides and herbicides, which can work very similarly to antibiotics damaging the bacterial ecosystem within. When the microbiome is already damaged due to antibiotic use, consuming foods laden with pesticides has an even stronger effect; as normally the bacterial army in the gut are in fact able to break down and neutralize many toxins we consume. Inorganic meat is commonly treated with antibiotics through the animal’s lifespan. This means that remnants of antibiotic metabolites can still be in the meat and expose you to more antibiotics.


Fiber (complex carbohydrates)


Your microbiome loves fiber, as it is their major food source. Providing adequate fiber in your diet gives the bacteria the food they need to flourish and grow. The recommended daily fiber intake is 30grams, which is easy to achieve when eating a diet that is rich in whole foods. Whole grains are the highest, followed by fruits and vegetables, then nuts and seeds.

Eating a diet high in fiber also reduces your consumption of refined carbohydrates (sugar) that can feed the bad bacteria in your gut.




As mentioned above, the specific probiotics that should be prescribed following an antibiotic cycle depend on a range factors. However, a species of yeast named Saccharomyces Boulardii (SB) grows very quickly in the gut and creates the perfect environment for healthy bacterial growth. Therefore the supplementation of SB can generally be undertaken regardless of other factors.


Fermented food


 Naturally Fermented food contains Bacteria, Prebiotics and Acids that are essential of healthy Gut function and the Microbiome. Every civilization has some form of fermented food in their diet, unfortunately since westernization this practice has largely stopped and is one of the contributors to the global declining gut health. There are many forms of fermented food, however the most common are: 

  • Sauerkraut

  • Kimchi 

  • Kombucha 

  • Pickled vegetables 

If you are purchasing any of these ensure that they are not pasteurized (heat treated) as this will kill all the beneficial bacteria that we are trying to gain by eating these foods. However, they are also quite easy to make and last well in the fridge once they have fermented. Sauerkraut, kimchi and pickled vegetables are very high in Lactobacillus strains. Lactobacillus and some of the other strains found in fermented food stimulate Serotonin (happy neurotransmitter) production and can produce GABA (chill out neurotransmitter). Fermented foods also provide the gut with essential acids for the bacterial survival and communication; some of these acids even support liver function. 





Antibiotics have revolutionized medicine in many respects and saved countless lives, however their overuse and misuse has lead to the rise of antibiotic resistance. In doing so, the risk of death due to a once thought of treatable bacterial infection is becoming a reality. Reducing overuse and misuse isn’t just the doctor’s responsibility. You too can make a difference by taking stewardship of your own health journey.


Regardless of the rise of antibiotics resistance, the profound effect antibiotics have on our entire system by disrupting our microbiome is a major contributor to chronic health conditions. Almost all diseases have a contributing causative factor in the gut. Therefore reducing antibiotic use, using the tips in this article along with specific probiotic treatment following any current or past treatment with antibiotics, is vital for your ongoing health and well being.


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