Antibiotics, while highly effective at treating and preventing infections, may also increase the risk of susceptibility to infections, allergy, and metabolic syndrome and might even decrease efficacy outcomes of pharmacologic therapies by altering the composition and functions of the commensal microbiota.


In a perspective paper published in Science, Dr. Martin Blaser, from the New York University Langone Medical Centre (NYULMC), discussed the consequences of antibiotic use for the healthy microbiota. Young children are the most sensitive to gut microbiota disturbance and indeed they are the most likely to be treated with antibiotics. Blaser’s mouse studies suggest antibiotic use during early childhood poses the greatest risk to long-term health, contributing to the rise of what Blaser calls our modern plagues: obesity, asthma, allergies, diabetes, and certain forms of cancer. Alarmingly, American children, for instance, receive on average seventeen courses of antibiotics before they are twenty years old. According to Dr. Blaser, “rather than carpet-bombing germs into submission with broad-spectrum antibiotics, we will need more laserlike approaches to develop drugs against specific pathogens, minimize damage to essential symbiotic microbial species, and preserve community structure and function in the healthy and developing microbiome”.


A recent review, led by Dr. Eric G. Pamer from the Memorial Sloan Kettering Cancer Centre in New York (USA), focused on potential strategies to prevent the adverse effects of antibiotics on the healthy gut microbiota. These strategies are currently lying at various stages of clinical development and include:

  • To avoid unnecessary antibiotic use through antibiotic supervision. Improving sanitation, expanding the use of vaccines, strengthening hospital infection control and reducing the use of antibiotics for livestock may help diminish the need for antibiotic use.
  • To develop and use more targeted, narrow-spectrum antibiotics. A rational use of highly-specific antibiotics would selectively deplete detrimental bacterial strains; for instance, those involved in inflammatory responses and drug inactivation.
  • To replace depleted microbes through the use of faecal microbiota transplantation (FMT) or probiotics. This strategy implies that antibiotic-induced microbiota defects and the resulting loss of colonization resistance may be corrected by administration of commensal bacterial species. As antibiotic treatment also decreases mucus layer thickness and the expression of antimicrobial peptides, it has also been proposed that the restoration of appropriate immune responses through controlled administration of bacterial ligands, such fragments of bacteria, may provide a selective pathogen targeting without perturbing the commensal microbiota in subjects undergoing antibiotic treatment.

In conclusion, the current inappropriate use of antibiotics has likely led various negative health consequences in Western populations. Avoiding unnecessary antibiotic use through antibiotic supervision, developing and using narrow-spectrum antibiotics, and replacing depleted microbes through the use of faecal microbiota transplantation or probiotics emerge as useful strategies to selectively target pathogens without perturbing the beneficial commensal bacterial communities in the gut.




Becattini S, Taur Y, Pamer EG. Antibiotic-induced changes in the intestinal microbiota and disease. Trends Mol Med. 2016. doi:10.1016/j.molmed.2016.04.003.

Blaser MJ. Antibiotic use and its consequences for the normal microbiome. Science. 2016; 352(6285):544-5. doi:10.1126/science.aad9358.