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Related Experiment Video

Updated: Mar 9, 2026

Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes
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FARME DB: a functional antibiotic resistance element database.

James C Wallace1, Jesse A Port1, Marissa N Smith1

  • 1Department of Environmental and Occupational Health Sciences, Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, USA.

Database : the Journal of Biological Databases and Curation
|January 13, 2017
PubMed
Summary

A new database, FARME, catalogs antibiotic resistance (AR) genes from environmental DNA. This resource aids understanding of AR in uncultured bacteria and its link to clinical antibiotic resistance genes.

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Area of Science:

  • Microbiology
  • Environmental Science
  • Bioinformatics

Background:

  • Antibiotic resistance (AR) poses a significant global health threat.
  • Existing AR gene databases primarily use clinical isolates, neglecting environmental sources.
  • Environmental AR sequences often lack similarity to clinical ones and lack flanking genetic information.

Purpose of the Study:

  • To create a comprehensive database of AR genes from environmental metagenomic sequences.
  • To include flanking regulatory and mobile genetic elements associated with environmental AR genes.
  • To provide a resource for studying AR in uncultured bacteria and its environmental origins.

Main Methods:

  • Compiled DNA and protein sequences from environmental metagenomic studies demonstrating AR.
  • Annotated sequences for AR genes, flanking regulatory elements, and mobile genetic elements.
  • Developed the Functional Antibiotic Resistant Metagenomic Element (FARME) database.

Main Results:

  • The FARME database exclusively contains AR elements from environmental sources.
  • It includes DNA, protein, regulatory, and mobile genetic elements.
  • FARME is the first database focused on functional metagenomic AR gene elements.

Conclusions:

  • FARME addresses the gap in cataloging environmental AR genes.
  • It enhances understanding of AR in the vast uncultured bacterial populations.
  • The database facilitates research into the environmental reservoirs and spread of antibiotic resistance.