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Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities

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Next Generation Sequencing

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1712))

Abstract

The emergence of high-throughput sequencing technologies has deepened our understanding of complex microbial communities and greatly facilitated the study of as-yet uncultured microbes and viruses. Studies of complex microbial communities require high-quality data to generate valid results. Here, we detail current methods of microbial and viral community sample acquisition, DNA extraction, sample preparation, and sequencing on Illumina high-throughput platforms. While using appropriate analytical tools is important, it must not overshadow the need for establishing a proper experimental design and obtaining sufficient numbers of samples for statistical purposes. Researchers must also take care to sample biologically relevant sites and control for potential confounding factors (e.g., contamination).

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Author information

Authors and Affiliations

  1. Department of Biology, San Diego State University, San Diego, CA, USA

    Pedro J. Torres & Scott T. Kelley Ph.D.

Authors
  1. Pedro J. Torres
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  2. Scott T. Kelley Ph.D.
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Corresponding author

Correspondence to Scott T. Kelley Ph.D. .

Editor information

Editors and Affiliations

  1. Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, California, USA

    Steven R. Head

  2. Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, California, USA

    Phillip Ordoukhanian

  3. Department of Molecular Medicine, The Scripps Research Institute Center for Organ and Cell Transplantation, La Jolla, California, USA

    Daniel R. Salomon

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Torres, P.J., Kelley, S.T. (2018). Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities. In: Head, S., Ordoukhanian, P., Salomon, D. (eds) Next Generation Sequencing. Methods in Molecular Biology, vol 1712. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7514-3_11

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  • DOI: https://doi.org/10.1007/978-1-4939-7514-3_11

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7512-9

  • Online ISBN: 978-1-4939-7514-3

  • eBook Packages: Springer Protocols

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