Use Antibiotics Wisely

Commensal (friendly) organisms have an important role regulating the physiology of their hosts.

From metabolism, nutrition, physiology, and immune function, one of the major functions of the gut microbiota is to protect the intestine against colonization by outside microorganisms and overgrowth of pathogenic bacteria.

Because of its role, there are consequences when the microbiota is thrown off balance – also called “dysbiosis”. Recent research reviews have shown that the condition of the gut microbiome is related to disorders such as metabolic syndrome, inflammatory bowel disease, liver disease, and colorectal cancer.



Clostridium difficile (C. diff.) is perhaps the best known example of overgrowth of a pathogen after disruption of the normal microbiome in the gut. Treatment with broad-spectrum antibiotics eliminates the competition that would otherwise keep C. diff. at bay. Proliferation of C. diff. spores and toxin-mediated disruption of the intestinal barrier leads to a severe condition known as pseudomembranous colitis and potentially sepsis.

In this setting, it is important to stop the use of broad-spectrum antibiotics – although metronidazole and vancomycin are used in severe cases because it also creates the possibility of a second pathogenic infection by vancomycin-resistant Enterococcus.

The commensal microbiome can be manipulated to treat Enterococcus and C. diff. infection and fecal transplantation is a fairly new therapy which has been shown to have a promising role in the treatment of C. diff. infection.



The impact of antibiotic use extends far beyond the time you are actually receiving the medication. A group from the Swedish Institute for Infectious Disease Control found that some members of the gut microbiota are affected for up to FOUR years post-treatment. This is important because colonization by some beneficial microbiomes, like Bacteroids fragilis, enhances mucosal tolerance and can suppress pathogen-mediated colitis.


A relationship between antibiotic use and clinical behavior in IBD has been reported. It is unclear whether dysbiosis is a cause or a consequence of IBD. Antibiotics appear to have a beneficial role in Crohn’s disease (a type of IBD), but the evidence is not strong enough at this time to warrant any recommendations.

A recent prospective longitudinal study showed that the majority of IBD patients receive antibiotic treatment and those individuals also have more severe diseases. Studies have reported higher carriage rate of C. diff. in patients with IBD which can range in clinical presentation ranging from asymptomatic carriage to mild diarrhea to life-threatening colitis.


Over the last 15 years, there has been an increase in the incidence of C. diff. infection, which predominantly affects elderly patients on antibiotics. Organ transplant patients are also at higher risk due to extensive use of antibiotics, their immunosuppressed states and other factors.

Dysbiosis and inflammation can not only lead to IBD, but also colitis-associated cancer as well.


Consequences of antibiotic therapy in the intestinal microbiome goes beyond C. diff. antibiotic-associated infections and an increased risk for developing IBD. Research on the recovery of microbial communities and how probiotic treatment can positively or negatively affect it is needed. Stimulation and regulation of the immune system are an important avenue that must be considered, especially in the cases of dysbiosis present in immunocompromised patients.


Cervantes J. “Use your antibiotics wisely. Consequences to the intestinal microbiome.” FEMS Microbiology Letters, 363, 2016 fnw081.

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