Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments

• Published in: Microbial Ecology Vol. 73; no. 2; pp. 479 - 491
• Main Authors: dos Santos, Débora Farage Knupp, Istvan, Paula, Quirino, Betania Ferraz, Kruger, Ricardo Henrique
• Format: Journal Article Book Review
• Language: English
• Published: New York Springer Science + Business Media 01.02.2017; Springer US; Springer Nature B.V
• Subjects: Animals; Anti-Bacterial Agents - classification; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Bacterial Infections - drug therapy; Bacterial Infections - microbiology; Base Sequence; Biomedical and Life Sciences; Culture Techniques; DNA, Bacterial; Drug Resistance, Bacterial - genetics; Drug Resistance, Bacterial - physiology; Drug Resistance, Microbial - genetics; Ecology; Environment; Genes, Bacterial - genetics; Geoecology/Natural Processes; Humans; Life Sciences; Metagenome - genetics; Metagenomics - methods; Microbial Ecology; Microbiology; Microorganisms; MINIREVIEWS; Natural environment; Nature Conservation; Water Quality/Water Pollution; Environment; Functional metagenomics; Resistome; Antibiotic resistance genes
• ISSN: 0095-3628; 1432-184X
• DOI: 10.1007/s00248-016-0866-x

Antibiotic resistance has become a major concern for human and animal health, as therapeutic alternatives to treat multidrug-resistant microorganisms are rapidly dwindling. The problem is compounded by low investment in antibiotic research and lack of new effective antimicrobial drugs on the market. Exploring environmental antibiotic resistance genes (ARGs) will help us to better understand bacterial resistance mechanisms, which may be the key to identifying new drug targets. Because most environment-associated microorganisms are not yet cultivable, culture-independent techniques are essential to determine which organisms are present in a given environmental sample and allow the assessment and utilization of the genetic wealth they represent. Metagenomics represents a powerful tool to achieve these goals using sequence-based and functional-based approaches. Functional metagenomic approaches are particularly well suited to the identification new ARGs from natural environments because, unlike sequence-based approaches, they do not require previous knowledge of these genes. This review discusses functional metagenomics-based ARG research and describes new possibilities for surveying the resistome in environmental samples.