Shotgun metagenomics, from sampling to analysis

Christopher Quince, Alan W Walker, Jared T. Simpson, Nicholas J Loman, Nicola Segata (Corresponding Author)

Research output: Contribution to journalArticle

102 Citations (Scopus)
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Abstract

Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging members and understanding how communities function.
Cheap, high-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methodsthat have transformed microbiology. Still, computational approaches to overcome challenges that affect both assembly-based and mapping-based metagenomic
profiling, particularly of high-complexity samples, or environments containing organisms with limited similarity to sequenced genomes, are needed. Understanding the functions and characterizing specific strains of these communities offer biotechnological promise in therapeutic discovery, or innovative ways to synthesize products using microbial factories, but can also pinpoint the contributions of microorganisms to planetary, animal and human health.
Original languageEnglish
Pages (from-to)833-844
Number of pages12
JournalNature Biotechnology
Volume35
Issue number9
DOIs
Publication statusPublished - 12 Sep 2017

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Metagenomics
Firearms
Cataloging
Health
Sampling
Microbiology
Archaea
Eukaryota
Viruses
Microorganisms
Industrial plants
Bacteria
Animals
Pipelines
Genes
Throughput
Genome
Technology
Therapeutics

Cite this

Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017). Shotgun metagenomics, from sampling to analysis. Nature Biotechnology, 35(9), 833-844. https://doi.org/10.1038/nbt.3935

Shotgun metagenomics, from sampling to analysis. / Quince, Christopher; Walker, Alan W; Simpson, Jared T. ; Loman, Nicholas J; Segata, Nicola (Corresponding Author).

In: Nature Biotechnology, Vol. 35, No. 9, 12.09.2017, p. 833-844.

Research output: Contribution to journalArticle

Quince, C, Walker, AW, Simpson, JT, Loman, NJ & Segata, N 2017, 'Shotgun metagenomics, from sampling to analysis' Nature Biotechnology, vol. 35, no. 9, pp. 833-844. https://doi.org/10.1038/nbt.3935
Quince, Christopher ; Walker, Alan W ; Simpson, Jared T. ; Loman, Nicholas J ; Segata, Nicola. / Shotgun metagenomics, from sampling to analysis. In: Nature Biotechnology. 2017 ; Vol. 35, No. 9. pp. 833-844.
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