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An Introduction to Whole-Metagenome Shotgun Sequencing Studies

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Deep Sequencing Data Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2243))

Abstract

Microbial communities are found across diverse environments, including within and across the human body. As many microbes are unculturable in the lab, much of what is known about a microbiome—a collection of bacteria, fungi, archaea, and viruses inhabiting an environment—-is from the sequencing of DNA from within the constituent community. Here, we provide an introduction to whole-metagenome shotgun sequencing studies, a ubiquitous approach for characterizing microbial communities, by reviewing three major research areas in metagenomics: assembly, community profiling, and functional profiling. Though not exhaustive, these areas encompass a large component of the metagenomics literature. We discuss each area in depth, the challenges posed by whole-metagenome shotgun sequencing, and approaches fundamental to the solutions of each. We conclude by discussing promising areas for future research. Though our emphasis is on the human microbiome, the methods discussed are broadly applicable across study systems.

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Authors and Affiliations

  1. Department of Computer Science, Fu Foundation School of Engineering & Applied Science, Columbia University, New York, NY, USA

    Tyler A. Joseph & Itsik Pe’er

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  1. Tyler A. Joseph
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  2. Itsik Pe’er
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Correspondence to Itsik Pe’er .

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  1. Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel

    Noam Shomron

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Joseph, T.A., Pe’er, I. (2021). An Introduction to Whole-Metagenome Shotgun Sequencing Studies. In: Shomron, N. (eds) Deep Sequencing Data Analysis. Methods in Molecular Biology, vol 2243. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1103-6_6

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  • DOI: https://doi.org/10.1007/978-1-0716-1103-6_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1102-9

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