How Antibiotics Have Changed Our World

four-pillsAntibiotics are by many considered to be one of man’s greatest creations. The people who hold this belief are typically the same ones who praise modern medicine and are of the opinion that the development of the arsenal of pharmaceutical drugs that today’s physicians have at their disposal represents the pinnacle of human achievement.

What many of these folks don’t know is that there’s a dark side to modern medicine; a side that’s ugly and devoid of light. Many of the drugs that we humans have created over the past centuries have indeed proven to be useful in certain medical contexts; however, many of them have also caused us a lot of harm. Some, such as antibiotics, have left destruction in their wake.

We’re outsmarted by bacteria

We humans like to think of ourselves as the superior being here on Earth. We like to think that we’re in control of the rest of the living world. We certainly don’t like to think that other organisms may be controlling us or are outracing us in the evolutionary arms race that we call life. We operate under the belief that we’re intelligent beings who understand how the world works and are able to plan ahead and make wise decisions.

History has shown that we’re overestimating our influence and abilities. We often fail to see what the future holds and make decisions that prove unwise over the long-run. A general pattern is that we make decisions that seem to bring benefits in the moment, but that are detrimental over the long-term.

This brings us over to antibiotics. There’s no doubt that antibiotics have helped us out a lot. Many lives would have been lost had it not been for antibiotics. What we failed to release though, when we first started bombarding our world with antibiotics some decades ago, is that their use comes with a cost. This cost is much greater than most people realise.

Antibiotics are not harmless drugs that physicians should be allowed to prescribe to whoever wants them; rather, they are powerful compounds that we now know have caused a major change in the human biology. Not only have the widespread use of drugs, creams, and sprays with antimicrobial properties over the most recent decades triggered the evolution and spread of antibiotic resistant ”superbugs”, but it has also altered the microbial communities that surround us (1, 2, 3, 4, 5).

These problems are not isolated to our own bodies; many other parts of our world, including the animals we’ve domesticated and the soil we use to grow our food, have also been affected by our use of antibiotics (3, 4, 5). What we humans seem to fail to understand is that nature is built up of systems. When we go in and change the workings of these systems, bad things usually happens. Often, changes in one microbial ecosystem have ripple effects into others. For example, the antibiotics we use to treat sick farm animals don’t just affect the microbiota of these animals, they may also end up in the soil we use to grow plants, the food we eat, and eventually our own guts. On their way through these systems, they may leave a trail of destruction.

Here’s what a 2013 review paper had to say about this matter:

The antibiotic revolution may be having effects across the entire microbial biosphere, changing the basal rate of bacterial evolution, altering the composition of the resistome and mobilome, and promoting lateral transfer of mobile genetic elements. Antibiotic contamination promotes the fixation and mobilization of resistance genes between environmental and clinical microbiota, and resistance genes are now widely spread through the biosphere. (5)

It’s virtually impossible to know exactly what the outcome will be when you go in and use a drug you don’t fully understand to change a complex system that you can’t see with the naked eye and don’t know that much about. Hence, I’d argue that we should be very careful about using antimicrobial drugs that are capable of majorly altering microbial ecosystems, regardless of whether it’s in the context of human medicine, agriculture, or any other venture. 

Evolutionary science to the rescue

Evolutionary science not only helps us understand how and why antibiotics resistance develops, but it also helps us predict what will happen when we use antibiotics and understand why antibiotics harm our health and what we can do to prevent and reverse the damage that we’ve caused via our massive use of drugs such as penicillin and doxycycline.

The first things that’s important to acknowledge it that antibiotic resistance, as well as the structural changes that occur in microbial ecosystems that are exposed to antibiotics, develops as a result of natural selection.

Let’s imagine that you take a broad-spectrum antibiotic drug. In the morning, you take three capsules, which travel down your esophagus, through your stomach, and into your intestine. Once in the intestine, the antibiotic comes into full effect; triggering a selection event by changing the environmental conditions of the gut.

Those microbes that are genetically resistant to the effects of the antibiotics either stand their ground or proliferate, expanding in numbers, whereas those that are susceptible to the antimicrobial substances that are now omnipresent in their environment dwindle in numbers and perhaps even die out completely.

Is this a problem? Yes. It is. Any ecosystem that rapidly loses diversity is bound to lose resilience and become “shaky”. When some members of the community are lost, others may get an opportunity to roam the world in which they find themselves, exploiting newly opened niches and greatly expand in numbers.

This is exactly what happens in the human gut in situations when organisms such as Clostridium difficile are allowed to take over. In a healthy gut, C. diff is kept in check by the rest of the microbial community that it is a part of. It’s unable to “take over the gut”, due to the fact that other microbes – some of which produce substances that are toxic to C. diff – hinders its growth. However, if these C. diff antagonists lose their ground, C. diff can cease the opportunity and proliferate in the gut.

Similar mechanisms apply to other cases of severe dysbiosis. For example, on normal, healthy skin, Propionibacterium acnes, a bacterium involved in the development of acne vulgaris, is kept in check by other members of the skin microbiota. However, if something – like chronic inflammation, hormonal imbalance, or a topical cream of some sort – were to change the environment of the skin, P. acnes may find itself in a situation in which it is free to grow at a faster rate than what was previously possible.

All of these evolutionary events are complicated and intensified by the fact that microbes are able to swap DNA between each other. They are not like us humans, who are incapable of taking out some of the DNA found inside the nuclei of our cells and turn it over to a neighbor. This fact, that microbes exchange genetic material, helps explain how bugs are able to develop resistance to antibiotics and why we have such a hard time keeping up with bacteria in the evolutionary arms race.

The dramatic consequences of our actions

Our current approach to treating infectious illness, which involves constantly “designing” new antibiotics (most antibiotics were not originally created by humans; rather, they are derivatives of chemicals produced by microbes) in order to keep up with the evolution of antibiotic resistance, has proven to be fallacious. We’re not able to keep pace with our enemies. Every time we develop a new antibiotic, mutations that confer resistance to that antibiotic starts spreading within the microbial populations we target. Sometimes, bacteria that are resistant to the antibiotic are already present in the population, and these microbes may expand, and perhaps share their resistance with other bugs. Consequently, antibiotic resistance is spread.

When these events occur in microbial ecosystems closely associated with the human body, the implications to human health are particularly profound. Not only have the widespread use of antimicrobial drugs (Note: Many drugs besides antibiotics have antimicrobial properties) triggered the evolution of antibiotic resistant superbugs, but it has also changed our microbiotas in novel ways, something that has contributed greatly to fueling the current epidemic of chronic disease; which includes autoimmune diseases, metabolic disorders, and many other types of conditions (1, 6, 7). The fact that the use of antibiotics has been shown to weaken our defense against many diseases shouldn’t come as a surprise, as antibiotics are capable of altering the co-evolutionary processes that take place between man and microbes.

Here’s what a recent review paper had to say about the impact antibiotics have had on the human microbiota:

In 2010, more than 70 billion individual doses of antibiotics were consumed world-wide. Broad-spectrum antibiotics can impact up to 30% of the bacteria among the human microbiota, resulting in severe loss of taxonomic and functional diversity. This dramatic shift in the microbiota can develop immediately following antibiotic administration, and can sometimes last for years after its cessation. The perturbation of the endogenous flora has been linked to many disease states including obesity and autoimmunity. (6)

It’s time for a strategic change

I think it’s long past time that we change our approach to treating diseases and health problems caused by viruses, parasites, and microbial pathogens. Many of the infectious conditions that affect us humans don’t develop because the pathogen(s) in question carry weapons that we are totally incapable of protecting ourselves against; rather, they develop because our defenses are weakened.

A microbial ecosystem that lacks diversity and stability is much more prone to invasion by foreign organisms than an ecosystem that is diverse and stable. This is true regardless of whether the ecosystem in question is found in the vagina of a human female, the gut of a farm animal, the Pacific Ocean, or any other place here on Earth.

There is no doubt in my mind that the global incidence of many diseases would have been dramatically lower if all humans alive today carried a robust, diverse microbiota. This notion is supported by studies showing that friendly bacteria can protect us against C. diff infection, influenza, yeast overgrowth, and many other pathogen-related conditions (8, 9, 10, 11). Even HIV has trouble setting up shop in the body of someone who carries a microbiota dominated by “friendly” bugs (8).

Instead of killing bad bugs, I’d argue that we should nurture good ones. We should divert some or much of the energy and resources we use on developing new antimicrobial drugs to developing products that can be used to restore the human microbiome. This effort will not only help lower the incidence of acute illness, but also the incidence of chronic illness.

Moreover, we should seek to change our environment in such a way that the microbial milieu becomes more compatible with our genetics. This intervention is perhaps even more urgently needed in developing countries than in developed ones. In some developing parts of the world, the pathogenic burden is high and the nutritional status of the inhabitants is poor; hence, infectious illness is a major problem. In these areas, you’re never going to be able to combat infectious disease unless you change the overall conditions of life. Unlike what some people believe, the decline in infectious disease incidence in industrialized societies over the most recent centuries wasn’t primarily brought about by antibiotics, but rather by public health measures related to nutrition, sanitation, and vaccination.

Perhaps needless to say, we shouldn’t completely stop using antimicrobial drugs. However, we should definitely be more careful about how and when we use them!


  1. Susan Short says:

    I have been an appreciative reader of this blog and realize the author and readers are not in the business of offering medical advice. This comment is more just a wail of despair. I try to follow an ancestral lifestyle and have, until recently, been very content with my microbial community. I am now recovering from a miserable bout of pneumonia. It was followed by a debilitating middle ear infection caused by resistant staf. The infection has affected my hearing and balance and has made it hard to fulfill my many responsibilities. I have just begun, very reluctantly, taking a week’s course of Clindamyacin. I was warned of the possibility of a C. diff takeover but decided to take it anyway. Am I doomed? Can my community recover? Any advice (or sympathy) welcomed.

    • HI Susan,

      You’re not doomed. My suggestion would be that you follow the microbiome restoration guidelines listed in this post. I highly recommend that you make and eat smaller quantities of fermented vegetables.

      Let me know if you have any additional questions.


  1. […] over time. However, if you’re sick and/or are constantly exposing yourself to new foods and antimicrobial drugs, your microbiome will most likely be in a constant state of […]

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