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Functional Metagenomics to Study Antibiotic Resistance.

Manish Boolchandani1, Sanket Patel1,2, Gautam Dantas3,4,5,6

  • 1Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.

Methods in Molecular Biology (Clifton, N.J.)
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PubMed
Summary

Metagenomic libraries from fecal DNA help discover novel antibiotic resistance genes (ARGs). This study details library construction, screening, sequencing, and computational analysis for identifying ARGs.

Keywords:
Antibiotic resistance genesFunctional metagenomicsFunctional selectionsHigh-throughput assemblyMassively parallel DNA sequencingPARFuMSProfile HMM-based annotationResfamsResistome

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Metagenomic expression libraries offer a powerful approach for discovering novel genes and functions.
  • Fecal DNA is a rich source for exploring microbial genetic diversity.

Purpose of the Study:

  • To describe the methodology for constructing and screening metagenomic libraries from fecal DNA.
  • To identify novel antibiotic resistance genes (ARGs) using functional screening.
  • To present a computational pipeline for analyzing sequencing data.

Main Methods:

  • Preparation of metagenomic libraries from human fecal DNA.
  • Screening of libraries for clones exhibiting antibiotic resistance.
  • Massively parallel DNA sequencing of enriched DNA fragments.
  • High-throughput computational assembly and annotation of selected DNA sequences.

Main Results:

  • Successful construction and screening of metagenomic libraries.
  • Identification of DNA fragments conferring antibiotic resistance.
  • Generation of sequence data amenable to computational analysis.

Conclusions:

  • Metagenomic library screening is effective for discovering ARGs.
  • The described computational pipeline facilitates high-throughput analysis of functional genomic data.
  • This approach advances the identification of novel microbial genes and functions.