A Case for Antibiotic Perturbation of the Microbiota Leading to Allergy Development

Lisa A Reynolds; B Brett Finlay


Expert Rev Clin Immunol. 2013;9(11):1019-1030. 

In This Article

Effects of Antibiotic Use on the Microbiota

Antibiotic treatment generally results in a greater widespread species disturbance than simply the loss of bacterial populations directly targeted by the antibiotic administered, since many microbes are dependent on the presence of other bacterial species for their persistence in the mammalian host. Thus, antibiotic treatment results in loss of primary bacterial populations, as well as those secondary populations which are dependent on metabolites or waste-removal processes initiated by primary species.[32] Additionally, the sites affected by antibiotic treatment are dependent on the route of administration, and the absorptive properties of the antibiotic.

The persistence of antibiotic-induced perturbations of the microbiota depends on the class of antibiotic being administered. Mice treated with a combination of amoxicillin, metronidazole and bismuth, or with the single antibiotic vancomycin, harbored significant changes in intestinal microbiota composition, although their bacterial communities returned to baseline following withdrawal of antibiotics.[33] By contrast, the diversity of microbes in cefoperazone-treated mice was still quite disrupted even 6 weeks following the end of antibiotic treatment.[33]

Human studies have also examined the persistence of antibiotic-mediated disruptions. Following clindamycin treatment in adults there was a reduction in diversity among fecal Bacteroides species, accompanied by an elevation in clindamycin-resistance associated genes, which persisted for up to 2 years following antibiotic exposure.[34] A separate study on the long-term effects of ciprofloxacin treatment in adults suggests that the intestinal composition returns to a similar state as before treatment within 4 weeks, yet there is a long-term loss of some individual taxa up to 6 months post-treatment.[35] Taken together, these reports suggest that after antibiotic treatment in adults the microbial communities broadly return to baseline, yet there are long-term effects of antibiotic treatment. In the majority of cases, functional redundancy between individual species, and resiliency of the complex community likely prevents any detrimental effects of antibiotic treatment.[35]

Exposure to antibiotic treatment during childhood, however, may have more severe long-term effects on microbial community structure due to the less stable nature of the immature microbiota.[36] The microbiota of human infants receiving cefalexin during the first 4 days of life was less diverse than that of antibiotic-free infants until at least 2 months of age.[37] Longitudinal studies are underway to determine to what extent these early-life perturbations extend to dictate the composition and diversity of the microbiota in adult humans.