title: Antibiotic use and microbiome function.
abstract: 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.
authors.affiliation: Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain. Electronic address: mferrer@icp.csic.es.
authors.forename: Manuel
authors.initials: M
authors.lastname: Ferrer
authors.affiliation: Carl R. Woese Institute for Genomic Biology, Urbana, USA.
authors.forename: Celia
authors.initials: C
authors.lastname: Méndez-García
authors.affiliation: Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain.
authors.forename: David
authors.initials: D
authors.lastname: Rojo
authors.affiliation: Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain.
authors.forename: Coral
authors.initials: C
authors.lastname: Barbas
authors.affiliation: Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain. Electronic address: andres.Moya@uv.es.
authors.forename: Andrés
authors.initials: A
authors.lastname: Moya
mesh_terms: D000818:Animals; D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D006801:Humans; D064307:Microbiota / Q000187:drug effects* / Q000502:physiology*
chemical_list: D000900:Anti-Bacterial Agents
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)