Functional Metagenomics to Study Antibiotic Resistance

Bejan Mahmud; Manish Boolchandani; Sanket Patel; Gautam Dantas

doi:10.1007/978-1-0716-2855-3_21

Functional Metagenomics to Study Antibiotic Resistance

Methods Mol Biol. 2023:2601:379-401. doi: 10.1007/978-1-0716-2855-3_21.

Authors

Bejan Mahmud¹, Manish Boolchandani¹, Sanket Patel^{1

2}, Gautam Dantas^{3

4

5

6

7}

Affiliations

¹ The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
² Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
³ The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA. dantas@wustl.edu.
⁴ Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA. dantas@wustl.edu.
⁵ Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA. dantas@wustl.edu.
⁶ Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA. dantas@wustl.edu.
⁷ Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA. dantas@wustl.edu.

PMID: 36445596
DOI: 10.1007/978-1-0716-2855-3_21

Abstract

The construction and screening of metagenomic expression libraries have a great potential to identify novel genes with desired functions. Here, we describe metagenomic library preparation from fecal DNA, screening of libraries for antibiotic resistance genes (ARGs), massively parallel DNA sequencing of the enriched DNA fragments, and a computational pipeline for high-throughput assembly and annotation of functionally selected DNA.

Keywords: Antibiotic resistance genes; Functional metagenomics; Functional selections; High-throughput assembly; Massively parallel DNA sequencing; PARFuMS; Profile HMM-based annotation; Resfams; Resistome.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Drug Resistance, Microbial / genetics
Gene Library
Metagenome*
Metagenomics*
Sequence Analysis, DNA

Abstract

Publication types

MeSH terms

Grants and funding