Antibiotic use and microbiome function

Biochem Pharmacol. 2017 Jun 15:134:114-126. doi: 10.1016/j.bcp.2016.09.007. Epub 2016 Sep 15.


Our microbiome should be understood as one of the most complex components of the human body. The use of β-lactam antibiotics is one of the microbiome covariates that influence its composition. The extent to which our microbiota changes after an antibiotic intervention depends not only on the chemical nature of the antibiotic or cocktail of antibiotics used to treat specific infections, but also on the type of administration, duration and dose, as well as the level of resistance that each microbiota develops. We have begun to appreciate that not all bacteria within our microbiota are vulnerable or reactive to different antibiotic interventions, and that their influence on both microbial composition and metabolism may differ. Antibiotics are being used worldwide on a huge scale and the prescription of antibiotics is continuing to rise; however, their effects on our microbiota have been reported for only a limited number of them. This article presents a critical review of the antibiotics or antibiotic cocktails whose use in humans has been linked to changes in the composition of our microbial communities, with a particular focus on the gut, oral, respiratory, skin and vaginal microbiota, and on their molecular agents (genes, proteins and metabolites). We review the state of the art as of June 2016, and cover a total of circa 68 different antibiotics. The data herein are the first to compile information about the bacteria, fungi, archaea and viruses most influenced by the main antibiotic treatments prescribed nowadays.

Keywords: Ampicillin (PubChem CID: 6249); Antibiotics; Cephalosporin (PubChem CID: 25058126); Ciprofloxacin (PubChem CID: 2764); Clindamycin (PubChem CID: 29029); Erythromycin (PubChem CID: 12560); Gentamicin (PubChem CID: 3467); Metronidazole (PubChem CID: 4173); Microbiome; Microbiota; OMICS; Streptomycin (PubChem CID: 19649); Tetracycline (PubChem CID: 54675776); Vancomycin (PubChem CID: 14969).

Publication types

  • Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Anti-Bacterial Agents / pharmacology*
  • Humans
  • Microbiota / drug effects*
  • Microbiota / physiology*


  • Anti-Bacterial Agents