Functional metagenomics for the investigation of antibiotic resistance

Virulence. 2014 Apr 1;5(3):443-7. doi: 10.4161/viru.28196. Epub 2014 Feb 20.


Antibiotic resistance is a major threat to human health and well-being. To effectively combat this problem we need to understand the range of different resistance genes that allow bacteria to resist antibiotics. To do this the whole microbiota needs to be investigated. As most bacteria cannot be cultivated in the laboratory, the reservoir of antibiotic resistance genes in the non-cultivatable majority remains relatively unexplored. Currently the only way to study antibiotic resistance in these organisms is to use metagenomic approaches. Furthermore, the only method that does not require any prior knowledge about the resistance genes is functional metagenomics, which involves expressing genes from metagenomic clones in surrogate hosts. In this review the methods and limitations of functional metagenomics to isolate new antibiotic resistance genes and the mobile genetic elements that mediate their spread are explored.

Keywords: antibiotic resistance; functional metagenomics; gene libraries; mobile genetic elements; vector systems.

Publication types

  • Review

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Bacteria / drug effects*
  • Bacteria / genetics*
  • Drug Resistance, Bacterial*
  • Ecosystem
  • Gene Expression
  • Genetics, Microbial / methods*
  • Humans
  • Interspersed Repetitive Sequences
  • Metagenomics / methods*


  • Anti-Bacterial Agents