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Functional Metagenomics to Study Antibiotic Resistance

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Antibiotics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1520))

Abstract

The construction and screening of metagenomic expression libraries has great potential to identify novel genes and their 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.

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Acknowledgments

The original implementation of functional metagenomics selections for interrogating resistance genes was described by J. Handelsman and colleagues in 1998. We thank A. Moore and B. Wang for protocol optimization of high-throughput versions of this method presented in this manuscript, A. Reyes and K. Forsberg for computational implementation of PARFuMS , M. Gibson for development of the Resfams database, and members of the Dantas lab for helpful general discussions and for comments on the manuscript.

This work was supported in part by the NIH Director’s New Innovator Award (http://commonfund.nih.gov/newinnovator/), the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK:http://www.niddk.nih.gov/), and the National Institute of General Medical Sciences (NIGMS: http://www.nigms.nih.gov/), of the National Institutes of Health (NIH) under award numbers DP2DK098089 and R01GM099538 to G.D. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies.

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    Authors and Affiliations

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

      Manish Boolchandani, Sanket Patel & Gautam Dantas

    2. Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA

      Sanket Patel & Gautam Dantas

    3. Department of Biomedical Engineering, Washington University, St. Louis, MO, USA

      Gautam Dantas

    4. Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA

      Gautam Dantas

    Authors
    1. Manish Boolchandani
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    2. Sanket Patel
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    3. Gautam Dantas
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    Correspondence to Gautam Dantas .

    Editor information

    Editors and Affiliations

    1. Interfaculty Institute for Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany

      Peter Sass

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    Boolchandani, M., Patel, S., Dantas, G. (2017). Functional Metagenomics to Study Antibiotic Resistance. In: Sass, P. (eds) Antibiotics. Methods in Molecular Biology, vol 1520. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6634-9_19

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    • DOI: https://doi.org/10.1007/978-1-4939-6634-9_19

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    • Publisher Name: Humana Press, New York, NY

    • Print ISBN: 978-1-4939-6632-5

    • Online ISBN: 978-1-4939-6634-9

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