There is no doubt that antibiotics have saved millions of lives. But, is it all good news? I hope our readers have been noting the increasing number of news stories related to problems with the overuse of antibiotics and the development of resistant microorganisms. We have known this was coming for decades, but it has now reached a tipping point. Sally Davies, the Chief Medical Officer of the United Kingdom, has equated the critical health threat of antibiotic resistance to an act of terrorism.

Each year in the United States two million people are infected with antibiotic-resistant microorganisms and 23,000 die. The CDC published an excellent report in 2013 on the threat that can be downloaded here: 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 - there's no money in drugs that will become quickly ineffective as bacteria become resistant.

In addition to the development of resistant bacteria and the infections associated with them, the overuse of antibiotics is also being identified as a likely cause of a number of other medical conditions involving the immune system. This is an absolutely fascinating area of medical research and 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 (primarily in the gastrointestinal or "GI" tract) and on our bodies can lead to the development of many diseases that I will point out toward the end of the article.

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 there are over ten times as many organisms in a person's microbiome than there are cells in the body, yet it 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 that is just beginning to be understood.

One of the main interactions between our microbiomes and us occurs in our gastrointestinal tracts. The organisms colonize our GI tracts and have a very close association with the cells lining our guts. It has been found that this close association is critically important for the development and regulation of our immune systems. It has also been shown that the interaction of our microbiome with organisms that are not part of our microbiome (i.e. infectious microorganisms) is also critically important to help 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 the death of some of a person's microbiome. More often than not, the person does not notice much difference - he or she may have a little diarrhea or bloating that eventually resolves. However, the microscopic effects can be very significant.

When a portion 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 take over dead organism's 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 in the gut peacefully, but can become invasive and infect the wall of the intestine if the normal microbiome defenses are altered.

Secondly, 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 are caused 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 examples of autoimmune diseases. Other diseases such as allergies and asthma can be caused by an immune system that is in overdrive. It's hypothesized the microbiome is important in teaching the immune system to "chill out."

Another fascinating branch of this research is looking at obesity. The microbiome is very important in aiding digestion. Has alteration of 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 this problem and that novel treatments such as replacing/altering the microbiome may become commonplace. We are already seeing the incredible success of fecal transplants (putting someone else's feces inside the patient) to treat conditions such as ulcerative colitis. In the meantime, avoid taking antibiotics unless they are definitely indicated. Remember that 90 percent of coughs and 80 percent of sinus infections are viral and will improve on their own. And parents, be particularly cautious about asking for antibiotics for your kids - it's possible that early alteration of their microbiomes could lead to disease later in life.

Dr. John Roberts is a Crawfordsville physician and one of the owners of The Paper. In addition to his weekly column, he writes a daily health tip that can be found on page A1.