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Nat Biotechnol. 2017 Sep 12;35(9):833-844. doi: 10.1038/nbt.3935.

Shotgun metagenomics, from sampling to analysis.

Author information

1
Warwick Medical School, University of Warwick, Warwick, UK.
2
Microbiology Group, The Rowett Institute, University of Aberdeen, Aberdeen, UK.
3
Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
4
Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
5
Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK.
6
Centre for Integrative Biology, University of Trento, Trento, Italy.

Abstract

Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging of members and understanding of how communities function. High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome the 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 offers biotechnological promise in therapeutic discovery and innovative ways to synthesize products using microbial factories and can pinpoint the contributions of microorganisms to planetary, animal and human health.

PMID:
28898207
DOI:
10.1038/nbt.3935
[Indexed for MEDLINE]

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