Shotgun metagenomics, from sampling to analysis

Research output: Contribution to journalReview article

Authors

  • Christopher Quince
  • Alan W Walker
  • Jared T Simpson
  • Nicholas J Loman
  • Nicola Segata

Colleges, School and Institutes

External organisations

  • Warwick Medical School, University of Warwick
  • University of Aberdeen
  • Institute for Microbiology and Infection, University of Birmingham , Edgbaston, Birmingham B15 2TT, U.K.
  • 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.

Details

Original languageEnglish
Pages (from-to)833-844
Number of pages12
JournalNature Biotechnology
Volume35
Issue number9
Publication statusPublished - 12 Sep 2017

Keywords

  • Animals, Biomedical Research, High-Throughput Nucleotide Sequencing, Humans, Metagenomics, Microbiota/genetics