Antibiotics Are Good – Right?

By: John Roberts

There is no doubt that antibiotics have saved millions of lives, but is it all good news? I suspect you have been seeing more news stories related to problems with overprescribing antibiotics that can result in antibiotic-resistant bacteria. Alexander Fleming, who discovered penicillin, warned of this inevitability in his Nobel Prize acceptance speech in 1945. Dr. Sally Davies, the former Chief Medical Officer of the United Kingdom, has equated the critical health threat of antibiotic resistance to the risk of terrorism.

Each year in the United States, two million people are infected with antibiotic-resistant bacteria and 23,000 die. An excellent CDC report on the topic was published in 2019 and can be downloaded at The primary cause of resistant bacteria is the overuse of antibiotics, both in medicine and agribusiness. This is also complicated by the fact that very few new antibiotics are being developed since there is little profit in drugs that will quickly become ineffective as bacteria continue to develop antibiotic resistance.

In addition to the growth of resistant bacteria and the infections associated with them, the overuse of antibiotics has also been identified as a probable cause of a number of other medical conditions involving the immune system. This is an absolutely fascinating and rapidly expanding area of medical research. It may hold the key to putting the brakes on many of the disease trends that have been on the rise in the decades since antibiotic use has become commonplace. Researchers have hypothesized that altering the bacteria that reside in the gastrointestinal tract and elsewhere in and on our bodies can lead to a number of medical conditions.

Shortly after we are born our bodies are colonized, both inside and out, by trillions of bacteria. The entire collection is referred to as our “microbiome.” In fact, some estimate that there are over ten times as many organisms in a person’s microbiome than there are cells in the body, yet a person’s microbiome is estimated to weigh only about seven ounces. Humans and the organisms in their microbiomes have evolved together over the millennia to form a fine-tuned symbiotic relationship – we gain certain things from the microorganisms and they, in turn, gain things from us. It is a truly fascinating relationship and one we are just beginning to understand.

One of the main interactions we have with our microbiomes occurs in our gastrointestinal tracts. The organisms colonizing our GI tracts have a very close association with the cells that line it. This close association is critically important for the training and regulation of our immune systems. The interaction of our microbiome with organisms outside of it (i.e. infectious microorganisms) is also very important in helping to develop our immunity.

So, what does all this have to do with antibiotic use? Depending on what antibiotic is taken and for how long, it can lead to varying levels of damage to a person’s microbiome. More often than not, the person does not notice much difference – perhaps a little diarrhea or bloating that eventually resolves. However, the insidious effects can be very significant.

When a part of the microbiome is killed off, it may or may not be able to regenerate. If not, there are other organisms that are more than willing to inhabit the open turf. When this occurs, a couple of things can happen. First, the open space can be taken over by pathogenic organisms that cause disease. You may have read or heard about Clostridium difficile or “C. diff” infections. These are bacteria that normally live a peaceful life in the gut, but can become invasive and infect the wall of the intestine if a person’s normal bacterial ecosystem is altered.

Second, the interaction between the microbiome and the cells in the gut can be altered causing changes in immune system function. Since a properly functioning immune system is critical to maintaining health, altering it can lead to many diseases, particularly autoimmune diseases. These diseases result when the immune system does not recognize the normal body tissues as friendly and attacks them.

Inflammatory bowel disease (Crohn’s disease and ulcerative colitis), diabetes, multiple sclerosis and rheumatoid arthritis are a few examples of autoimmune diseases. Other diseases such as allergies and asthma can be caused or worsened by an overactive immune system. It’s hypothesized the microbiome is important in regulating and training the immune system to not over-react to an infection or allergen.

Another fascinating branch of this research examines the interaction of the microbiome and obesity. The microbiome is very important in aiding digestion and metabolism. Has altering people’s microbiomes, perhaps through antibiotic use, led to or worsened the rates of obesity?

It is very likely many more diseases will be tied to altered microbiomes and that novel treatments such as replacing or altering our microbiomes may become commonplace. We are already witnessing the incredible success rates of fecal transplants (putting someone else’s feces inside a patient) to treat conditions such as ulcerative colitis and resistant C. diff infections. In the meantime, you should avoid taking antibiotics unless they are definitely indicated. Remember that 90 percent of coughs and 80 percent of sinus infections are caused by viruses and will improve with time. And parents, be particularly cautious about asking for antibiotics for your kids – it’s possible that early alteration of their microbiomes could lead to diseases later in life.

– Dr. John Roberts is a retired member of the Franciscan Physician Network specializing in Family Medicine.